Iron in PDB 3gm6: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
Protein crystallography data
The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate, PDB code: 3gm6
was solved by
A.A.Trofimov,
K.M.Polyakov,
K.M.Boyko,
A.A.Filimonenkov,
P.V.Dorovatovsky,
T.V.Tikhonova,
V.O.Popov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.90 /
1.80
|
|
Space group
|
P 21 3
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
196.560,
196.560,
196.560,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
15.9 /
17.2
|
Other elements in 3gm6:
The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Iron atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
(pdb code 3gm6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the
Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate, PDB code: 3gm6:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 1 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1004
b:13.9
occ:1.00
|
FE
|
A:HEC1004
|
0.0
|
13.9
|
1.0
|
|
O2
|
A:PO4526
|
1.9
|
15.4
|
1.0
|
|
NZ
|
A:LYS188
|
1.9
|
16.5
|
1.0
|
|
NB
|
A:HEC1004
|
2.1
|
13.0
|
1.0
|
|
NA
|
A:HEC1004
|
2.1
|
14.2
|
1.0
|
|
NC
|
A:HEC1004
|
2.1
|
12.9
|
1.0
|
|
ND
|
A:HEC1004
|
2.1
|
13.5
|
1.0
|
|
CE
|
A:LYS188
|
3.1
|
18.1
|
1.0
|
|
C1C
|
A:HEC1004
|
3.1
|
14.3
|
1.0
|
|
C4B
|
A:HEC1004
|
3.1
|
15.6
|
1.0
|
|
C1A
|
A:HEC1004
|
3.1
|
13.2
|
1.0
|
|
C4D
|
A:HEC1004
|
3.1
|
15.4
|
1.0
|
|
C4A
|
A:HEC1004
|
3.1
|
12.7
|
1.0
|
|
C1D
|
A:HEC1004
|
3.1
|
13.6
|
1.0
|
|
C1B
|
A:HEC1004
|
3.1
|
13.7
|
1.0
|
|
C4C
|
A:HEC1004
|
3.1
|
13.3
|
1.0
|
|
HE2
|
A:LYS188
|
3.2
|
16.8
|
1.0
|
|
HE3
|
A:LYS188
|
3.2
|
16.8
|
1.0
|
|
P
|
A:PO4526
|
3.3
|
17.4
|
1.0
|
|
CHC
|
A:HEC1004
|
3.4
|
15.3
|
1.0
|
|
CHA
|
A:HEC1004
|
3.4
|
15.3
|
1.0
|
|
CHD
|
A:HEC1004
|
3.5
|
13.0
|
1.0
|
|
CHB
|
A:HEC1004
|
3.5
|
14.2
|
1.0
|
|
O1
|
A:PO4526
|
3.5
|
16.3
|
1.0
|
|
NE2
|
A:HIS361
|
4.1
|
16.1
|
1.0
|
|
O3
|
A:PO4526
|
4.3
|
16.2
|
1.0
|
|
O4
|
A:PO4526
|
4.3
|
14.5
|
1.0
|
|
C3A
|
A:HEC1004
|
4.3
|
14.1
|
1.0
|
|
C2C
|
A:HEC1004
|
4.3
|
14.5
|
1.0
|
|
C2A
|
A:HEC1004
|
4.3
|
12.9
|
1.0
|
|
C2D
|
A:HEC1004
|
4.4
|
15.4
|
1.0
|
|
C3D
|
A:HEC1004
|
4.4
|
12.9
|
1.0
|
|
C2B
|
A:HEC1004
|
4.4
|
14.0
|
1.0
|
|
C3B
|
A:HEC1004
|
4.4
|
14.9
|
1.0
|
|
HHC
|
A:HEC1004
|
4.4
|
15.1
|
1.0
|
|
C3C
|
A:HEC1004
|
4.4
|
12.3
|
1.0
|
|
HHA
|
A:HEC1004
|
4.4
|
14.9
|
1.0
|
|
HHB
|
A:HEC1004
|
4.5
|
13.7
|
1.0
|
|
HHD
|
A:HEC1004
|
4.5
|
13.2
|
1.0
|
|
CD
|
A:LYS188
|
4.6
|
14.4
|
1.0
|
|
HH21
|
A:ARG131
|
4.6
|
14.4
|
1.0
|
|
HD3
|
A:LYS188
|
4.7
|
15.5
|
1.0
|
|
O
|
A:HOH733
|
4.7
|
20.8
|
1.0
|
|
HD2
|
A:HIS361
|
4.8
|
14.7
|
1.0
|
|
CD2
|
A:HIS361
|
4.9
|
14.9
|
1.0
|
|
O
|
A:HOH720
|
4.9
|
14.4
|
1.0
|
|
HD2
|
A:LYS188
|
5.0
|
15.5
|
1.0
|
|
HB2
|
A:CYS187
|
5.0
|
13.6
|
1.0
|
|
Iron binding site 2 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 2 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1005
b:13.0
occ:1.00
|
FE
|
A:HEC1005
|
0.0
|
13.0
|
1.0
|
|
NE2
|
A:HIS231
|
2.0
|
13.2
|
1.0
|
|
NE2
|
A:HIS398
|
2.0
|
14.6
|
1.0
|
|
NA
|
A:HEC1005
|
2.0
|
12.6
|
1.0
|
|
NC
|
A:HEC1005
|
2.0
|
14.2
|
1.0
|
|
ND
|
A:HEC1005
|
2.0
|
12.1
|
1.0
|
|
NB
|
A:HEC1005
|
2.1
|
11.8
|
1.0
|
|
CE1
|
A:HIS231
|
2.9
|
13.1
|
1.0
|
|
CE1
|
A:HIS398
|
3.0
|
12.7
|
1.0
|
|
CD2
|
A:HIS398
|
3.0
|
14.2
|
1.0
|
|
CD2
|
A:HIS231
|
3.0
|
13.4
|
1.0
|
|
C1D
|
A:HEC1005
|
3.0
|
12.9
|
1.0
|
|
C4A
|
A:HEC1005
|
3.0
|
11.9
|
1.0
|
|
C1C
|
A:HEC1005
|
3.1
|
11.6
|
1.0
|
|
C4C
|
A:HEC1005
|
3.1
|
13.4
|
1.0
|
|
C4D
|
A:HEC1005
|
3.1
|
12.7
|
1.0
|
|
C1A
|
A:HEC1005
|
3.1
|
12.2
|
1.0
|
|
C4B
|
A:HEC1005
|
3.1
|
12.3
|
1.0
|
|
C1B
|
A:HEC1005
|
3.1
|
13.2
|
1.0
|
|
HE1
|
A:HIS231
|
3.1
|
12.8
|
1.0
|
|
HE1
|
A:HIS398
|
3.2
|
13.8
|
1.0
|
|
HD2
|
A:HIS398
|
3.2
|
14.3
|
1.0
|
|
HD2
|
A:HIS231
|
3.2
|
13.3
|
1.0
|
|
CHD
|
A:HEC1005
|
3.4
|
13.0
|
1.0
|
|
CHC
|
A:HEC1005
|
3.4
|
12.9
|
1.0
|
|
CHB
|
A:HEC1005
|
3.4
|
12.6
|
1.0
|
|
CHA
|
A:HEC1005
|
3.4
|
13.4
|
1.0
|
|
ND1
|
A:HIS231
|
4.1
|
11.8
|
1.0
|
|
ND1
|
A:HIS398
|
4.1
|
13.0
|
1.0
|
|
CG
|
A:HIS398
|
4.1
|
15.1
|
1.0
|
|
CG
|
A:HIS231
|
4.1
|
14.5
|
1.0
|
|
C3A
|
A:HEC1005
|
4.3
|
12.9
|
1.0
|
|
C2D
|
A:HEC1005
|
4.3
|
13.1
|
1.0
|
|
C2C
|
A:HEC1005
|
4.3
|
14.0
|
1.0
|
|
C2A
|
A:HEC1005
|
4.3
|
11.9
|
1.0
|
|
C3C
|
A:HEC1005
|
4.3
|
12.0
|
1.0
|
|
C3D
|
A:HEC1005
|
4.3
|
13.7
|
1.0
|
|
C2B
|
A:HEC1005
|
4.3
|
12.8
|
1.0
|
|
HHD
|
A:HEC1005
|
4.3
|
13.0
|
1.0
|
|
HHC
|
A:HEC1005
|
4.4
|
12.4
|
1.0
|
|
C3B
|
A:HEC1005
|
4.4
|
12.2
|
1.0
|
|
HHB
|
A:HEC1005
|
4.4
|
12.6
|
1.0
|
|
HHA
|
A:HEC1005
|
4.4
|
12.9
|
1.0
|
|
HG2
|
A:GLN73
|
4.6
|
13.5
|
1.0
|
|
HB3
|
A:GLN73
|
4.7
|
14.8
|
1.0
|
|
HD1
|
A:HIS231
|
4.8
|
12.8
|
1.0
|
|
HB2
|
A:CYS230
|
4.8
|
12.5
|
1.0
|
|
HD1
|
A:HIS398
|
4.9
|
13.4
|
1.0
|
|
Iron binding site 3 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 3 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1006
b:12.3
occ:1.00
|
FE
|
A:HEC1006
|
0.0
|
12.3
|
1.0
|
|
NE2
|
A:HIS300
|
2.0
|
12.1
|
1.0
|
|
NE2
|
A:HIS119
|
2.0
|
11.9
|
1.0
|
|
NB
|
A:HEC1006
|
2.0
|
10.8
|
1.0
|
|
ND
|
A:HEC1006
|
2.0
|
12.0
|
1.0
|
|
NA
|
A:HEC1006
|
2.1
|
12.4
|
1.0
|
|
NC
|
A:HEC1006
|
2.1
|
10.3
|
1.0
|
|
CE1
|
A:HIS119
|
2.9
|
14.2
|
1.0
|
|
CE1
|
A:HIS300
|
2.9
|
10.1
|
1.0
|
|
CD2
|
A:HIS300
|
3.0
|
14.4
|
1.0
|
|
C1B
|
A:HEC1006
|
3.0
|
9.5
|
1.0
|
|
C4A
|
A:HEC1006
|
3.1
|
12.0
|
1.0
|
|
C1D
|
A:HEC1006
|
3.1
|
11.7
|
1.0
|
|
HE1
|
A:HIS119
|
3.1
|
13.1
|
1.0
|
|
C4B
|
A:HEC1006
|
3.1
|
9.1
|
1.0
|
|
CD2
|
A:HIS119
|
3.1
|
12.3
|
1.0
|
|
C1C
|
A:HEC1006
|
3.1
|
11.9
|
1.0
|
|
C4D
|
A:HEC1006
|
3.1
|
12.0
|
1.0
|
|
C1A
|
A:HEC1006
|
3.1
|
10.4
|
1.0
|
|
HE1
|
A:HIS300
|
3.1
|
11.9
|
1.0
|
|
C4C
|
A:HEC1006
|
3.1
|
11.4
|
1.0
|
|
HD2
|
A:HIS300
|
3.2
|
13.0
|
1.0
|
|
HD2
|
A:HIS119
|
3.3
|
12.6
|
1.0
|
|
CHC
|
A:HEC1006
|
3.4
|
11.2
|
1.0
|
|
CHB
|
A:HEC1006
|
3.4
|
10.7
|
1.0
|
|
CHD
|
A:HEC1006
|
3.4
|
12.3
|
1.0
|
|
CHA
|
A:HEC1006
|
3.4
|
11.7
|
1.0
|
|
ND1
|
A:HIS119
|
4.1
|
12.0
|
1.0
|
|
ND1
|
A:HIS300
|
4.1
|
12.6
|
1.0
|
|
CG
|
A:HIS300
|
4.1
|
13.1
|
1.0
|
|
CG
|
A:HIS119
|
4.2
|
12.8
|
1.0
|
|
C3A
|
A:HEC1006
|
4.3
|
8.7
|
1.0
|
|
C2B
|
A:HEC1006
|
4.3
|
12.1
|
1.0
|
|
C3B
|
A:HEC1006
|
4.3
|
10.3
|
1.0
|
|
C2A
|
A:HEC1006
|
4.3
|
10.0
|
1.0
|
|
C2D
|
A:HEC1006
|
4.3
|
14.8
|
1.0
|
|
C2C
|
A:HEC1006
|
4.3
|
10.4
|
1.0
|
|
HHB
|
A:HEC1006
|
4.3
|
10.7
|
1.0
|
|
C3D
|
A:HEC1006
|
4.4
|
10.4
|
1.0
|
|
HHC
|
A:HEC1006
|
4.4
|
10.9
|
1.0
|
|
HHD
|
A:HEC1006
|
4.4
|
11.9
|
1.0
|
|
C3C
|
A:HEC1006
|
4.4
|
10.4
|
1.0
|
|
HHA
|
A:HEC1006
|
4.4
|
11.4
|
1.0
|
|
HAD1
|
A:HEC1004
|
4.7
|
13.1
|
1.0
|
|
HD1
|
A:HIS119
|
4.8
|
12.7
|
1.0
|
|
HD1
|
A:HIS300
|
4.8
|
12.1
|
1.0
|
|
Iron binding site 4 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 4 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1007
b:14.2
occ:1.00
|
FE
|
A:HEC1007
|
0.0
|
14.2
|
1.0
|
|
NE2
|
A:HIS383
|
1.9
|
12.3
|
1.0
|
|
NE2
|
A:HIS491
|
2.0
|
13.4
|
1.0
|
|
NC
|
A:HEC1007
|
2.0
|
13.5
|
1.0
|
|
NA
|
A:HEC1007
|
2.0
|
13.5
|
1.0
|
|
NB
|
A:HEC1007
|
2.0
|
11.8
|
1.0
|
|
ND
|
A:HEC1007
|
2.1
|
11.7
|
1.0
|
|
CE1
|
A:HIS491
|
2.9
|
14.8
|
1.0
|
|
CE1
|
A:HIS383
|
2.9
|
14.0
|
1.0
|
|
CD2
|
A:HIS383
|
2.9
|
11.8
|
1.0
|
|
HE1
|
A:HIS491
|
3.0
|
13.7
|
1.0
|
|
C4D
|
A:HEC1007
|
3.0
|
12.5
|
1.0
|
|
C1C
|
A:HEC1007
|
3.0
|
12.7
|
1.0
|
|
C1A
|
A:HEC1007
|
3.0
|
10.1
|
1.0
|
|
C1B
|
A:HEC1007
|
3.0
|
11.4
|
1.0
|
|
C4A
|
A:HEC1007
|
3.1
|
12.1
|
1.0
|
|
C4B
|
A:HEC1007
|
3.1
|
12.9
|
1.0
|
|
CD2
|
A:HIS491
|
3.1
|
13.2
|
1.0
|
|
C1D
|
A:HEC1007
|
3.1
|
13.1
|
1.0
|
|
C4C
|
A:HEC1007
|
3.1
|
12.3
|
1.0
|
|
HE1
|
A:HIS383
|
3.1
|
13.4
|
1.0
|
|
HD2
|
A:HIS383
|
3.2
|
12.9
|
1.0
|
|
CHA
|
A:HEC1007
|
3.3
|
12.3
|
1.0
|
|
HD2
|
A:HIS491
|
3.3
|
13.2
|
1.0
|
|
CHC
|
A:HEC1007
|
3.3
|
14.1
|
1.0
|
|
CHB
|
A:HEC1007
|
3.4
|
11.9
|
1.0
|
|
CHD
|
A:HEC1007
|
3.4
|
12.7
|
1.0
|
|
ND1
|
A:HIS491
|
4.0
|
14.0
|
1.0
|
|
ND1
|
A:HIS383
|
4.0
|
14.1
|
1.0
|
|
CG
|
A:HIS383
|
4.1
|
14.4
|
1.0
|
|
CG
|
A:HIS491
|
4.2
|
12.1
|
1.0
|
|
C2B
|
A:HEC1007
|
4.3
|
12.6
|
1.0
|
|
C2A
|
A:HEC1007
|
4.3
|
10.9
|
1.0
|
|
C3A
|
A:HEC1007
|
4.3
|
11.1
|
1.0
|
|
C2C
|
A:HEC1007
|
4.3
|
13.9
|
1.0
|
|
C3D
|
A:HEC1007
|
4.3
|
13.3
|
1.0
|
|
HHA
|
A:HEC1007
|
4.3
|
11.8
|
1.0
|
|
HHC
|
A:HEC1007
|
4.3
|
13.5
|
1.0
|
|
C3B
|
A:HEC1007
|
4.3
|
12.6
|
1.0
|
|
C2D
|
A:HEC1007
|
4.3
|
11.8
|
1.0
|
|
C3C
|
A:HEC1007
|
4.3
|
12.7
|
1.0
|
|
HHB
|
A:HEC1007
|
4.4
|
11.8
|
1.0
|
|
HB3
|
A:SER487
|
4.4
|
12.6
|
1.0
|
|
HHD
|
A:HEC1007
|
4.4
|
12.7
|
1.0
|
|
HD1
|
A:HIS491
|
4.8
|
13.7
|
1.0
|
|
HD1
|
A:HIS383
|
4.8
|
14.1
|
1.0
|
|
HB2
|
A:CYS382
|
4.9
|
13.6
|
1.0
|
|
HB2
|
A:SER487
|
5.0
|
12.6
|
1.0
|
|
Iron binding site 5 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 5 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1008
b:16.4
occ:1.00
|
FE
|
A:HEC1008
|
0.0
|
16.4
|
1.0
|
|
NE2
|
A:HIS415
|
1.9
|
18.8
|
1.0
|
|
ND
|
A:HEC1008
|
2.0
|
17.6
|
1.0
|
|
NE2
|
A:HIS372
|
2.0
|
14.5
|
1.0
|
|
NB
|
A:HEC1008
|
2.0
|
15.6
|
1.0
|
|
NA
|
A:HEC1008
|
2.1
|
17.4
|
1.0
|
|
NC
|
A:HEC1008
|
2.1
|
18.9
|
1.0
|
|
CE1
|
A:HIS415
|
2.9
|
20.9
|
1.0
|
|
CE1
|
A:HIS372
|
3.0
|
18.6
|
1.0
|
|
CD2
|
A:HIS372
|
3.0
|
18.2
|
1.0
|
|
C4D
|
A:HEC1008
|
3.0
|
19.4
|
1.0
|
|
C1B
|
A:HEC1008
|
3.0
|
14.5
|
1.0
|
|
C1D
|
A:HEC1008
|
3.0
|
19.1
|
1.0
|
|
HE1
|
A:HIS415
|
3.0
|
19.9
|
1.0
|
|
CD2
|
A:HIS415
|
3.0
|
19.5
|
1.0
|
|
C4B
|
A:HEC1008
|
3.1
|
16.3
|
1.0
|
|
C4A
|
A:HEC1008
|
3.1
|
17.3
|
1.0
|
|
C1A
|
A:HEC1008
|
3.1
|
18.9
|
1.0
|
|
C1C
|
A:HEC1008
|
3.1
|
18.0
|
1.0
|
|
HD2
|
A:HIS372
|
3.2
|
17.1
|
1.0
|
|
C4C
|
A:HEC1008
|
3.2
|
19.7
|
1.0
|
|
HE1
|
A:HIS372
|
3.2
|
17.5
|
1.0
|
|
HD2
|
A:HIS415
|
3.3
|
19.4
|
1.0
|
|
CHB
|
A:HEC1008
|
3.4
|
18.2
|
1.0
|
|
CHA
|
A:HEC1008
|
3.4
|
19.9
|
1.0
|
|
CHC
|
A:HEC1008
|
3.4
|
19.1
|
1.0
|
|
CHD
|
A:HEC1008
|
3.4
|
19.9
|
1.0
|
|
ND1
|
A:HIS415
|
4.0
|
20.9
|
1.0
|
|
ND1
|
A:HIS372
|
4.1
|
20.1
|
1.0
|
|
CG
|
A:HIS372
|
4.1
|
16.4
|
1.0
|
|
CG
|
A:HIS415
|
4.1
|
18.7
|
1.0
|
|
C3D
|
A:HEC1008
|
4.2
|
22.7
|
1.0
|
|
C2D
|
A:HEC1008
|
4.2
|
22.1
|
1.0
|
|
C2B
|
A:HEC1008
|
4.2
|
17.5
|
1.0
|
|
C3B
|
A:HEC1008
|
4.3
|
16.2
|
1.0
|
|
C3A
|
A:HEC1008
|
4.3
|
17.3
|
1.0
|
|
C2A
|
A:HEC1008
|
4.3
|
19.5
|
1.0
|
|
C2C
|
A:HEC1008
|
4.3
|
21.0
|
1.0
|
|
HHB
|
A:HEC1008
|
4.3
|
17.1
|
1.0
|
|
HHA
|
A:HEC1008
|
4.4
|
19.5
|
1.0
|
|
HHC
|
A:HEC1008
|
4.4
|
18.2
|
1.0
|
|
HHD
|
A:HEC1008
|
4.4
|
19.6
|
1.0
|
|
C3C
|
A:HEC1008
|
4.4
|
18.8
|
1.0
|
|
HD1
|
A:HIS415
|
4.8
|
20.4
|
1.0
|
|
HZ3
|
A:TRP418
|
4.8
|
17.4
|
1.0
|
|
HD1
|
A:HIS372
|
4.9
|
18.8
|
1.0
|
|
Iron binding site 6 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 6 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1002
b:14.6
occ:1.00
|
FE
|
A:HEC1002
|
0.0
|
14.6
|
1.0
|
|
NE2
|
A:HIS234
|
1.9
|
15.0
|
1.0
|
|
NE2
|
A:HIS39
|
1.9
|
15.9
|
1.0
|
|
ND
|
A:HEC1002
|
2.0
|
13.7
|
1.0
|
|
NA
|
A:HEC1002
|
2.1
|
13.0
|
1.0
|
|
NB
|
A:HEC1002
|
2.1
|
13.5
|
1.0
|
|
NC
|
A:HEC1002
|
2.1
|
13.8
|
1.0
|
|
CE1
|
A:HIS234
|
2.9
|
13.2
|
1.0
|
|
CE1
|
A:HIS39
|
2.9
|
14.1
|
1.0
|
|
CD2
|
A:HIS234
|
2.9
|
13.8
|
1.0
|
|
CD2
|
A:HIS39
|
3.0
|
14.8
|
1.0
|
|
C1D
|
A:HEC1002
|
3.0
|
15.4
|
1.0
|
|
C4A
|
A:HEC1002
|
3.0
|
17.2
|
1.0
|
|
C1B
|
A:HEC1002
|
3.1
|
14.6
|
1.0
|
|
C4C
|
A:HEC1002
|
3.1
|
15.3
|
1.0
|
|
C4D
|
A:HEC1002
|
3.1
|
13.3
|
1.0
|
|
C1A
|
A:HEC1002
|
3.1
|
13.4
|
1.0
|
|
C1C
|
A:HEC1002
|
3.1
|
13.1
|
1.0
|
|
HE1
|
A:HIS234
|
3.1
|
13.9
|
1.0
|
|
HE1
|
A:HIS39
|
3.1
|
15.2
|
1.0
|
|
C4B
|
A:HEC1002
|
3.1
|
13.9
|
1.0
|
|
HD2
|
A:HIS234
|
3.2
|
13.8
|
1.0
|
|
HD2
|
A:HIS39
|
3.2
|
15.2
|
1.0
|
|
CHB
|
A:HEC1002
|
3.4
|
15.5
|
1.0
|
|
CHD
|
A:HEC1002
|
3.4
|
14.8
|
1.0
|
|
CHA
|
A:HEC1002
|
3.5
|
15.7
|
1.0
|
|
CHC
|
A:HEC1002
|
3.5
|
14.1
|
1.0
|
|
ND1
|
A:HIS234
|
4.0
|
15.2
|
1.0
|
|
ND1
|
A:HIS39
|
4.1
|
16.1
|
1.0
|
|
CG
|
A:HIS234
|
4.1
|
12.8
|
1.0
|
|
CG
|
A:HIS39
|
4.1
|
15.1
|
1.0
|
|
C3A
|
A:HEC1002
|
4.3
|
15.2
|
1.0
|
|
C2D
|
A:HEC1002
|
4.3
|
15.1
|
1.0
|
|
C2A
|
A:HEC1002
|
4.3
|
14.8
|
1.0
|
|
C2B
|
A:HEC1002
|
4.3
|
14.8
|
1.0
|
|
C3D
|
A:HEC1002
|
4.3
|
13.5
|
1.0
|
|
HHB
|
A:HEC1002
|
4.3
|
15.7
|
1.0
|
|
C2C
|
A:HEC1002
|
4.3
|
11.9
|
1.0
|
|
C3C
|
A:HEC1002
|
4.4
|
14.3
|
1.0
|
|
HHD
|
A:HEC1002
|
4.4
|
15.1
|
1.0
|
|
C3B
|
A:HEC1002
|
4.4
|
15.0
|
1.0
|
|
HHA
|
A:HEC1002
|
4.4
|
14.6
|
1.0
|
|
HHC
|
A:HEC1002
|
4.5
|
13.8
|
1.0
|
|
HG2
|
A:PRO233
|
4.5
|
12.9
|
1.0
|
|
HB2
|
A:CYS38
|
4.7
|
13.1
|
1.0
|
|
HB2
|
A:PRO233
|
4.8
|
12.0
|
1.0
|
|
HD1
|
A:HIS234
|
4.8
|
14.2
|
1.0
|
|
HD1
|
A:HIS39
|
4.8
|
15.4
|
1.0
|
|
Iron binding site 7 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 7 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1003
b:13.9
occ:1.00
|
FE
|
A:HEC1003
|
0.0
|
13.9
|
1.0
|
|
NE2
|
A:HIS70
|
2.0
|
15.7
|
1.0
|
|
NE2
|
A:HIS30
|
2.0
|
14.8
|
1.0
|
|
NA
|
A:HEC1003
|
2.0
|
12.6
|
1.0
|
|
NB
|
A:HEC1003
|
2.0
|
12.6
|
1.0
|
|
NC
|
A:HEC1003
|
2.1
|
12.0
|
1.0
|
|
ND
|
A:HEC1003
|
2.1
|
13.3
|
1.0
|
|
CE1
|
A:HIS30
|
2.9
|
15.7
|
1.0
|
|
CD2
|
A:HIS70
|
3.0
|
15.9
|
1.0
|
|
CE1
|
A:HIS70
|
3.0
|
15.4
|
1.0
|
|
C1B
|
A:HEC1003
|
3.0
|
10.8
|
1.0
|
|
C4A
|
A:HEC1003
|
3.0
|
12.8
|
1.0
|
|
C1A
|
A:HEC1003
|
3.1
|
9.6
|
1.0
|
|
CD2
|
A:HIS30
|
3.1
|
15.0
|
1.0
|
|
C1D
|
A:HEC1003
|
3.1
|
12.9
|
1.0
|
|
C4C
|
A:HEC1003
|
3.1
|
13.6
|
1.0
|
|
C4D
|
A:HEC1003
|
3.1
|
11.8
|
1.0
|
|
C1C
|
A:HEC1003
|
3.1
|
11.6
|
1.0
|
|
HE1
|
A:HIS30
|
3.1
|
15.3
|
1.0
|
|
C4B
|
A:HEC1003
|
3.1
|
9.5
|
1.0
|
|
HD2
|
A:HIS70
|
3.1
|
15.4
|
1.0
|
|
HE1
|
A:HIS70
|
3.2
|
14.9
|
1.0
|
|
HD2
|
A:HIS30
|
3.3
|
15.1
|
1.0
|
|
CHB
|
A:HEC1003
|
3.4
|
11.4
|
1.0
|
|
CHD
|
A:HEC1003
|
3.4
|
13.5
|
1.0
|
|
CHA
|
A:HEC1003
|
3.4
|
11.6
|
1.0
|
|
CHC
|
A:HEC1003
|
3.4
|
10.6
|
1.0
|
|
ND1
|
A:HIS30
|
4.1
|
15.0
|
1.0
|
|
ND1
|
A:HIS70
|
4.1
|
13.4
|
1.0
|
|
CG
|
A:HIS70
|
4.1
|
14.8
|
1.0
|
|
CG
|
A:HIS30
|
4.2
|
15.1
|
1.0
|
|
C2B
|
A:HEC1003
|
4.3
|
13.2
|
1.0
|
|
C3A
|
A:HEC1003
|
4.3
|
13.2
|
1.0
|
|
C2A
|
A:HEC1003
|
4.3
|
12.0
|
1.0
|
|
C3B
|
A:HEC1003
|
4.3
|
12.6
|
1.0
|
|
C2C
|
A:HEC1003
|
4.3
|
12.4
|
1.0
|
|
C2D
|
A:HEC1003
|
4.3
|
13.1
|
1.0
|
|
C3D
|
A:HEC1003
|
4.3
|
15.4
|
1.0
|
|
C3C
|
A:HEC1003
|
4.3
|
11.9
|
1.0
|
|
HHB
|
A:HEC1003
|
4.3
|
11.6
|
1.0
|
|
HHD
|
A:HEC1003
|
4.4
|
13.4
|
1.0
|
|
HHA
|
A:HEC1003
|
4.4
|
11.2
|
1.0
|
|
HHC
|
A:HEC1003
|
4.4
|
10.6
|
1.0
|
|
HB2
|
A:CYS69
|
4.8
|
15.7
|
1.0
|
|
HD1
|
A:HIS30
|
4.8
|
15.2
|
1.0
|
|
HD1
|
A:HIS70
|
4.9
|
14.2
|
1.0
|
|
Iron binding site 8 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 8 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:16.1
occ:1.00
|
FE
|
A:HEC1001
|
0.0
|
16.1
|
1.0
|
|
NE2
|
A:HIS18
|
1.9
|
15.5
|
1.0
|
|
NE2
|
A:HIS44
|
1.9
|
16.1
|
1.0
|
|
NA
|
A:HEC1001
|
2.0
|
15.3
|
1.0
|
|
ND
|
A:HEC1001
|
2.1
|
18.1
|
1.0
|
|
NB
|
A:HEC1001
|
2.1
|
15.8
|
1.0
|
|
NC
|
A:HEC1001
|
2.1
|
15.2
|
1.0
|
|
CE1
|
A:HIS18
|
2.8
|
16.3
|
1.0
|
|
CE1
|
A:HIS44
|
2.9
|
16.3
|
1.0
|
|
CD2
|
A:HIS44
|
3.0
|
16.6
|
1.0
|
|
HE1
|
A:HIS18
|
3.0
|
16.3
|
1.0
|
|
CD2
|
A:HIS18
|
3.0
|
16.0
|
1.0
|
|
C1A
|
A:HEC1001
|
3.0
|
15.7
|
1.0
|
|
C4D
|
A:HEC1001
|
3.1
|
17.4
|
1.0
|
|
C4A
|
A:HEC1001
|
3.1
|
15.8
|
1.0
|
|
C1C
|
A:HEC1001
|
3.1
|
16.5
|
1.0
|
|
C1D
|
A:HEC1001
|
3.1
|
17.1
|
1.0
|
|
C1B
|
A:HEC1001
|
3.1
|
15.9
|
1.0
|
|
C4B
|
A:HEC1001
|
3.1
|
15.9
|
1.0
|
|
HE1
|
A:HIS44
|
3.1
|
17.0
|
1.0
|
|
C4C
|
A:HEC1001
|
3.1
|
17.2
|
1.0
|
|
HD2
|
A:HIS44
|
3.2
|
16.8
|
1.0
|
|
HD2
|
A:HIS18
|
3.3
|
16.0
|
1.0
|
|
CHA
|
A:HEC1001
|
3.4
|
17.0
|
1.0
|
|
CHB
|
A:HEC1001
|
3.4
|
16.6
|
1.0
|
|
CHC
|
A:HEC1001
|
3.4
|
17.1
|
1.0
|
|
CHD
|
A:HEC1001
|
3.5
|
17.9
|
1.0
|
|
ND1
|
A:HIS18
|
4.0
|
15.6
|
1.0
|
|
ND1
|
A:HIS44
|
4.0
|
16.8
|
1.0
|
|
CG
|
A:HIS44
|
4.1
|
17.3
|
1.0
|
|
CG
|
A:HIS18
|
4.1
|
16.1
|
1.0
|
|
HG3
|
A:PRO57
|
4.2
|
16.4
|
1.0
|
|
C3A
|
A:HEC1001
|
4.3
|
14.0
|
1.0
|
|
C2A
|
A:HEC1001
|
4.3
|
16.2
|
1.0
|
|
C3D
|
A:HEC1001
|
4.3
|
18.6
|
1.0
|
|
C2D
|
A:HEC1001
|
4.3
|
18.5
|
1.0
|
|
C2B
|
A:HEC1001
|
4.3
|
16.0
|
1.0
|
|
C2C
|
A:HEC1001
|
4.3
|
16.0
|
1.0
|
|
HHA
|
A:HEC1001
|
4.4
|
16.8
|
1.0
|
|
C3B
|
A:HEC1001
|
4.4
|
16.4
|
1.0
|
|
C3C
|
A:HEC1001
|
4.4
|
15.8
|
1.0
|
|
HHB
|
A:HEC1001
|
4.4
|
16.2
|
1.0
|
|
HHC
|
A:HEC1001
|
4.4
|
16.7
|
1.0
|
|
HHD
|
A:HEC1001
|
4.4
|
17.6
|
1.0
|
|
HD1
|
A:HIS18
|
4.8
|
15.9
|
1.0
|
|
HD1
|
A:HIS44
|
4.8
|
16.8
|
1.0
|
|
HB2
|
A:CYS17
|
4.9
|
18.5
|
1.0
|
|
CMA
|
A:HEC1002
|
5.0
|
16.3
|
1.0
|
|
Iron binding site 9 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 9 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1004
b:12.9
occ:1.00
|
FE
|
B:HEC1004
|
0.0
|
12.9
|
1.0
|
|
NZ
|
B:LYS188
|
1.9
|
17.5
|
1.0
|
|
O2
|
B:PO4526
|
2.0
|
13.6
|
1.0
|
|
NB
|
B:HEC1004
|
2.1
|
12.8
|
1.0
|
|
NA
|
B:HEC1004
|
2.1
|
14.5
|
1.0
|
|
NC
|
B:HEC1004
|
2.1
|
13.3
|
1.0
|
|
ND
|
B:HEC1004
|
2.1
|
12.8
|
1.0
|
|
C1C
|
B:HEC1004
|
3.0
|
13.4
|
1.0
|
|
C4B
|
B:HEC1004
|
3.1
|
14.7
|
1.0
|
|
CE
|
B:LYS188
|
3.1
|
19.2
|
1.0
|
|
C4A
|
B:HEC1004
|
3.1
|
11.8
|
1.0
|
|
C1A
|
B:HEC1004
|
3.1
|
13.1
|
1.0
|
|
C1B
|
B:HEC1004
|
3.1
|
13.8
|
1.0
|
|
C1D
|
B:HEC1004
|
3.1
|
12.0
|
1.0
|
|
C4D
|
B:HEC1004
|
3.1
|
13.2
|
1.0
|
|
C4C
|
B:HEC1004
|
3.2
|
12.3
|
1.0
|
|
HE2
|
B:LYS188
|
3.2
|
17.9
|
1.0
|
|
HE3
|
B:LYS188
|
3.2
|
17.9
|
1.0
|
|
P
|
B:PO4526
|
3.3
|
15.1
|
1.0
|
|
CHC
|
B:HEC1004
|
3.4
|
13.7
|
1.0
|
|
CHA
|
B:HEC1004
|
3.4
|
14.1
|
1.0
|
|
CHB
|
B:HEC1004
|
3.5
|
13.7
|
1.0
|
|
CHD
|
B:HEC1004
|
3.5
|
12.1
|
1.0
|
|
O1
|
B:PO4526
|
3.6
|
15.2
|
1.0
|
|
NE2
|
B:HIS361
|
4.1
|
13.4
|
1.0
|
|
O3
|
B:PO4526
|
4.3
|
17.0
|
1.0
|
|
C2C
|
B:HEC1004
|
4.3
|
13.0
|
1.0
|
|
C3A
|
B:HEC1004
|
4.3
|
13.6
|
1.0
|
|
O4
|
B:PO4526
|
4.3
|
10.3
|
1.0
|
|
HHC
|
B:HEC1004
|
4.3
|
13.9
|
1.0
|
|
C3B
|
B:HEC1004
|
4.3
|
12.7
|
1.0
|
|
C2A
|
B:HEC1004
|
4.3
|
13.0
|
1.0
|
|
C2B
|
B:HEC1004
|
4.4
|
12.7
|
1.0
|
|
C2D
|
B:HEC1004
|
4.4
|
14.1
|
1.0
|
|
C3D
|
B:HEC1004
|
4.4
|
12.3
|
1.0
|
|
C3C
|
B:HEC1004
|
4.4
|
11.9
|
1.0
|
|
HHA
|
B:HEC1004
|
4.4
|
13.6
|
1.0
|
|
HHB
|
B:HEC1004
|
4.4
|
13.3
|
1.0
|
|
HHD
|
B:HEC1004
|
4.5
|
12.1
|
1.0
|
|
CD
|
B:LYS188
|
4.6
|
15.6
|
1.0
|
|
HH21
|
B:ARG131
|
4.6
|
14.6
|
1.0
|
|
HD3
|
B:LYS188
|
4.7
|
16.4
|
1.0
|
|
HD2
|
B:HIS361
|
4.8
|
12.3
|
1.0
|
|
CD2
|
B:HIS361
|
4.9
|
12.6
|
1.0
|
|
O
|
B:HOH773
|
4.9
|
13.1
|
1.0
|
|
HB2
|
B:CYS187
|
5.0
|
13.0
|
1.0
|
|
Iron binding site 10 out
of 16 in 3gm6
Go back to
Iron Binding Sites List in 3gm6
Iron binding site 10 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Phosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1005
b:12.6
occ:1.00
|
FE
|
B:HEC1005
|
0.0
|
12.6
|
1.0
|
|
NE2
|
B:HIS398
|
2.0
|
13.4
|
1.0
|
|
NE2
|
B:HIS231
|
2.0
|
14.0
|
1.0
|
|
NA
|
B:HEC1005
|
2.0
|
12.2
|
1.0
|
|
NC
|
B:HEC1005
|
2.0
|
12.2
|
1.0
|
|
ND
|
B:HEC1005
|
2.0
|
12.7
|
1.0
|
|
NB
|
B:HEC1005
|
2.1
|
12.7
|
1.0
|
|
CE1
|
B:HIS398
|
2.9
|
14.0
|
1.0
|
|
CE1
|
B:HIS231
|
3.0
|
14.6
|
1.0
|
|
CD2
|
B:HIS398
|
3.0
|
13.9
|
1.0
|
|
CD2
|
B:HIS231
|
3.0
|
12.9
|
1.0
|
|
C1D
|
B:HEC1005
|
3.0
|
11.8
|
1.0
|
|
C4A
|
B:HEC1005
|
3.0
|
11.6
|
1.0
|
|
C1A
|
B:HEC1005
|
3.0
|
10.7
|
1.0
|
|
C1C
|
B:HEC1005
|
3.1
|
12.4
|
1.0
|
|
C4C
|
B:HEC1005
|
3.1
|
12.0
|
1.0
|
|
C4B
|
B:HEC1005
|
3.1
|
13.4
|
1.0
|
|
C4D
|
B:HEC1005
|
3.1
|
13.4
|
1.0
|
|
C1B
|
B:HEC1005
|
3.1
|
13.4
|
1.0
|
|
HE1
|
B:HIS398
|
3.1
|
14.5
|
1.0
|
|
HE1
|
B:HIS231
|
3.2
|
13.3
|
1.0
|
|
HD2
|
B:HIS398
|
3.2
|
14.2
|
1.0
|
|
HD2
|
B:HIS231
|
3.2
|
13.2
|
1.0
|
|
CHD
|
B:HEC1005
|
3.4
|
12.3
|
1.0
|
|
CHC
|
B:HEC1005
|
3.4
|
11.2
|
1.0
|
|
CHB
|
B:HEC1005
|
3.4
|
11.9
|
1.0
|
|
CHA
|
B:HEC1005
|
3.4
|
13.1
|
1.0
|
|
ND1
|
B:HIS398
|
4.1
|
15.1
|
1.0
|
|
ND1
|
B:HIS231
|
4.1
|
12.0
|
1.0
|
|
CG
|
B:HIS398
|
4.1
|
14.9
|
1.0
|
|
CG
|
B:HIS231
|
4.2
|
12.3
|
1.0
|
|
C2A
|
B:HEC1005
|
4.3
|
12.5
|
1.0
|
|
C2D
|
B:HEC1005
|
4.3
|
13.2
|
1.0
|
|
C3A
|
B:HEC1005
|
4.3
|
14.8
|
1.0
|
|
C3C
|
B:HEC1005
|
4.3
|
11.8
|
1.0
|
|
C2C
|
B:HEC1005
|
4.3
|
12.8
|
1.0
|
|
C2B
|
B:HEC1005
|
4.3
|
12.2
|
1.0
|
|
C3D
|
B:HEC1005
|
4.3
|
14.0
|
1.0
|
|
C3B
|
B:HEC1005
|
4.3
|
12.3
|
1.0
|
|
HHD
|
B:HEC1005
|
4.3
|
12.1
|
1.0
|
|
HHC
|
B:HEC1005
|
4.3
|
12.0
|
1.0
|
|
HHB
|
B:HEC1005
|
4.4
|
12.2
|
1.0
|
|
HHA
|
B:HEC1005
|
4.4
|
12.6
|
1.0
|
|
HG2
|
B:GLN73
|
4.6
|
12.6
|
1.0
|
|
HB3
|
B:GLN73
|
4.7
|
13.2
|
1.0
|
|
HD1
|
B:HIS398
|
4.8
|
14.8
|
1.0
|
|
HB2
|
B:CYS230
|
4.8
|
12.2
|
1.0
|
|
HD1
|
B:HIS231
|
4.9
|
12.7
|
1.0
|
|
Reference:
A.A.Trofimov,
K.M.Polyakov,
K.M.Boiko,
A.A.Filimonenkov,
P.V.Dorovatovskii,
T.V.Tikhonova,
V.O.Popov,
M.V.Koval'chuk.
Structure of Octaheme Cytochrome C Nitrite Reductase From Thioalkalivibrio Nitratireducens in A Complex with Phosphate Crystallography Reports V. 55 58 2010.
ISSN: ISSN 1063-7745
DOI: 10.1134/S1063774510010104
Page generated: Sun Aug 4 10:46:26 2024
|
