Iron in PDB 3mmo: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
Protein crystallography data
The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide, PDB code: 3mmo
was solved by
A.A.Trofimov,
K.M.Polyakov,
K.M.Boyko,
T.V.Tikhonova,
V.S.Lamzin,
G.P.Bourenkov,
V.O.Popov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
11.98 /
1.55
|
|
Space group
|
P 21 3
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
194.560,
194.560,
194.560,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.8 /
16.2
|
Other elements in 3mmo:
The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide 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 Cyanide
(pdb code 3mmo). 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 Cyanide, PDB code: 3mmo:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 1 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1004
b:13.6
occ:1.00
|
FE
|
A:HEC1004
|
0.0
|
13.6
|
1.0
|
|
C
|
A:CYN526
|
1.9
|
13.2
|
1.0
|
|
NZ
|
A:LYS188
|
2.0
|
13.8
|
1.0
|
|
ND
|
A:HEC1004
|
2.0
|
13.3
|
1.0
|
|
NC
|
A:HEC1004
|
2.0
|
13.8
|
1.0
|
|
NA
|
A:HEC1004
|
2.0
|
14.3
|
1.0
|
|
NB
|
A:HEC1004
|
2.0
|
14.2
|
1.0
|
|
C1D
|
A:HEC1004
|
3.0
|
12.5
|
1.0
|
|
C4C
|
A:HEC1004
|
3.0
|
12.2
|
1.0
|
|
C1A
|
A:HEC1004
|
3.0
|
13.2
|
1.0
|
|
N
|
A:CYN526
|
3.0
|
16.4
|
1.0
|
|
C1C
|
A:HEC1004
|
3.0
|
14.2
|
1.0
|
|
C1B
|
A:HEC1004
|
3.1
|
15.3
|
1.0
|
|
C4D
|
A:HEC1004
|
3.1
|
11.8
|
1.0
|
|
C4B
|
A:HEC1004
|
3.1
|
15.0
|
1.0
|
|
C4A
|
A:HEC1004
|
3.1
|
14.9
|
1.0
|
|
CE
|
A:LYS188
|
3.1
|
15.1
|
1.0
|
|
HE2
|
A:LYS188
|
3.2
|
14.8
|
1.0
|
|
HE3
|
A:LYS188
|
3.2
|
14.8
|
1.0
|
|
CHD
|
A:HEC1004
|
3.4
|
13.6
|
1.0
|
|
CHA
|
A:HEC1004
|
3.4
|
13.7
|
1.0
|
|
CHB
|
A:HEC1004
|
3.4
|
14.8
|
1.0
|
|
CHC
|
A:HEC1004
|
3.4
|
13.7
|
1.0
|
|
C2C
|
A:HEC1004
|
4.3
|
13.0
|
1.0
|
|
C2A
|
A:HEC1004
|
4.3
|
13.2
|
1.0
|
|
C3D
|
A:HEC1004
|
4.3
|
12.4
|
1.0
|
|
C2D
|
A:HEC1004
|
4.3
|
13.5
|
1.0
|
|
C3C
|
A:HEC1004
|
4.3
|
13.7
|
1.0
|
|
C3B
|
A:HEC1004
|
4.3
|
16.9
|
1.0
|
|
C3A
|
A:HEC1004
|
4.3
|
13.1
|
1.0
|
|
C2B
|
A:HEC1004
|
4.3
|
17.2
|
1.0
|
|
HHD
|
A:HEC1004
|
4.4
|
13.0
|
1.0
|
|
HHA
|
A:HEC1004
|
4.4
|
13.1
|
1.0
|
|
HHB
|
A:HEC1004
|
4.4
|
14.9
|
1.0
|
|
HHC
|
A:HEC1004
|
4.4
|
14.1
|
1.0
|
|
NE2
|
A:HIS361
|
4.4
|
14.6
|
1.0
|
|
CD
|
A:LYS188
|
4.5
|
15.2
|
1.0
|
|
HH21
|
A:ARG131
|
4.5
|
16.1
|
1.0
|
|
HD3
|
A:LYS188
|
4.6
|
15.3
|
1.0
|
|
O
|
A:HOH743
|
4.6
|
18.6
|
1.0
|
|
OH
|
A:TYR303
|
4.6
|
17.2
|
1.0
|
|
O
|
A:HOH972
|
4.7
|
22.2
|
1.0
|
|
HD2
|
A:LYS188
|
4.7
|
15.3
|
1.0
|
|
HH22
|
A:ARG131
|
4.8
|
16.1
|
1.0
|
|
HB2
|
A:CYS187
|
4.9
|
13.8
|
1.0
|
|
CMD
|
A:HEC1006
|
4.9
|
12.3
|
1.0
|
|
Iron binding site 2 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 2 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1005
b:13.2
occ:1.00
|
FE
|
A:HEC1005
|
0.0
|
13.2
|
1.0
|
|
NE2
|
A:HIS231
|
2.0
|
12.7
|
1.0
|
|
NE2
|
A:HIS398
|
2.0
|
12.4
|
1.0
|
|
NA
|
A:HEC1005
|
2.0
|
12.3
|
1.0
|
|
ND
|
A:HEC1005
|
2.0
|
13.1
|
1.0
|
|
NB
|
A:HEC1005
|
2.0
|
12.3
|
1.0
|
|
NC
|
A:HEC1005
|
2.0
|
11.8
|
1.0
|
|
CE1
|
A:HIS231
|
3.0
|
13.2
|
1.0
|
|
CD2
|
A:HIS398
|
3.0
|
13.3
|
1.0
|
|
CE1
|
A:HIS398
|
3.0
|
13.5
|
1.0
|
|
C1C
|
A:HEC1005
|
3.0
|
12.4
|
1.0
|
|
CD2
|
A:HIS231
|
3.0
|
13.9
|
1.0
|
|
C4D
|
A:HEC1005
|
3.0
|
12.2
|
1.0
|
|
C4A
|
A:HEC1005
|
3.0
|
11.7
|
1.0
|
|
C1D
|
A:HEC1005
|
3.0
|
12.4
|
1.0
|
|
C1A
|
A:HEC1005
|
3.1
|
12.5
|
1.0
|
|
C4C
|
A:HEC1005
|
3.1
|
12.1
|
1.0
|
|
C4B
|
A:HEC1005
|
3.1
|
11.1
|
1.0
|
|
C1B
|
A:HEC1005
|
3.1
|
12.4
|
1.0
|
|
HE1
|
A:HIS231
|
3.2
|
13.2
|
1.0
|
|
HD2
|
A:HIS398
|
3.2
|
13.3
|
1.0
|
|
HE1
|
A:HIS398
|
3.2
|
13.2
|
1.0
|
|
HD2
|
A:HIS231
|
3.2
|
13.5
|
1.0
|
|
CHC
|
A:HEC1005
|
3.4
|
11.0
|
1.0
|
|
CHA
|
A:HEC1005
|
3.4
|
13.8
|
1.0
|
|
CHD
|
A:HEC1005
|
3.4
|
13.5
|
1.0
|
|
CHB
|
A:HEC1005
|
3.4
|
12.0
|
1.0
|
|
ND1
|
A:HIS231
|
4.1
|
13.7
|
1.0
|
|
ND1
|
A:HIS398
|
4.1
|
13.3
|
1.0
|
|
CG
|
A:HIS398
|
4.1
|
14.2
|
1.0
|
|
CG
|
A:HIS231
|
4.2
|
13.5
|
1.0
|
|
C2C
|
A:HEC1005
|
4.2
|
12.9
|
1.0
|
|
C2A
|
A:HEC1005
|
4.2
|
13.2
|
1.0
|
|
C3C
|
A:HEC1005
|
4.3
|
11.3
|
1.0
|
|
C2D
|
A:HEC1005
|
4.3
|
13.6
|
1.0
|
|
C3D
|
A:HEC1005
|
4.3
|
13.4
|
1.0
|
|
C2B
|
A:HEC1005
|
4.3
|
13.1
|
1.0
|
|
C3A
|
A:HEC1005
|
4.3
|
13.8
|
1.0
|
|
C3B
|
A:HEC1005
|
4.3
|
11.9
|
1.0
|
|
HHC
|
A:HEC1005
|
4.3
|
11.4
|
1.0
|
|
HHA
|
A:HEC1005
|
4.4
|
13.2
|
1.0
|
|
HHD
|
A:HEC1005
|
4.4
|
12.9
|
1.0
|
|
HHB
|
A:HEC1005
|
4.4
|
12.0
|
1.0
|
|
HG2
|
A:GLN73
|
4.5
|
13.5
|
1.0
|
|
HB3
|
A:GLN73
|
4.6
|
13.6
|
1.0
|
|
HB2
|
A:CYS230
|
4.8
|
12.9
|
1.0
|
|
Iron binding site 3 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 3 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1006
b:12.1
occ:1.00
|
FE
|
A:HEC1006
|
0.0
|
12.1
|
1.0
|
|
NE2
|
A:HIS119
|
2.0
|
11.0
|
1.0
|
|
NA
|
A:HEC1006
|
2.0
|
11.9
|
1.0
|
|
NE2
|
A:HIS300
|
2.0
|
11.1
|
1.0
|
|
ND
|
A:HEC1006
|
2.0
|
12.3
|
1.0
|
|
NB
|
A:HEC1006
|
2.0
|
12.0
|
1.0
|
|
NC
|
A:HEC1006
|
2.0
|
11.2
|
1.0
|
|
CE1
|
A:HIS119
|
2.9
|
11.4
|
1.0
|
|
CE1
|
A:HIS300
|
3.0
|
11.0
|
1.0
|
|
C1B
|
A:HEC1006
|
3.0
|
11.5
|
1.0
|
|
C1A
|
A:HEC1006
|
3.0
|
11.6
|
1.0
|
|
C1D
|
A:HEC1006
|
3.0
|
11.3
|
1.0
|
|
C4A
|
A:HEC1006
|
3.0
|
12.4
|
1.0
|
|
CD2
|
A:HIS300
|
3.0
|
12.2
|
1.0
|
|
C1C
|
A:HEC1006
|
3.0
|
12.3
|
1.0
|
|
C4D
|
A:HEC1006
|
3.1
|
12.0
|
1.0
|
|
CD2
|
A:HIS119
|
3.1
|
11.3
|
1.0
|
|
C4C
|
A:HEC1006
|
3.1
|
10.5
|
1.0
|
|
C4B
|
A:HEC1006
|
3.1
|
11.3
|
1.0
|
|
HE1
|
A:HIS119
|
3.1
|
11.4
|
1.0
|
|
HE1
|
A:HIS300
|
3.2
|
11.1
|
1.0
|
|
HD2
|
A:HIS300
|
3.2
|
11.8
|
1.0
|
|
HD2
|
A:HIS119
|
3.3
|
11.1
|
1.0
|
|
CHB
|
A:HEC1006
|
3.4
|
12.0
|
1.0
|
|
CHC
|
A:HEC1006
|
3.4
|
11.8
|
1.0
|
|
CHA
|
A:HEC1006
|
3.4
|
11.2
|
1.0
|
|
CHD
|
A:HEC1006
|
3.4
|
12.9
|
1.0
|
|
ND1
|
A:HIS119
|
4.1
|
11.9
|
1.0
|
|
ND1
|
A:HIS300
|
4.1
|
11.4
|
1.0
|
|
CG
|
A:HIS300
|
4.2
|
11.4
|
1.0
|
|
CG
|
A:HIS119
|
4.2
|
10.7
|
1.0
|
|
C3A
|
A:HEC1006
|
4.3
|
11.3
|
1.0
|
|
C2B
|
A:HEC1006
|
4.3
|
11.7
|
1.0
|
|
C2A
|
A:HEC1006
|
4.3
|
11.8
|
1.0
|
|
C2D
|
A:HEC1006
|
4.3
|
11.2
|
1.0
|
|
C2C
|
A:HEC1006
|
4.3
|
12.2
|
1.0
|
|
C3D
|
A:HEC1006
|
4.3
|
11.5
|
1.0
|
|
C3B
|
A:HEC1006
|
4.3
|
12.1
|
1.0
|
|
C3C
|
A:HEC1006
|
4.3
|
11.7
|
1.0
|
|
HHB
|
A:HEC1006
|
4.4
|
12.0
|
1.0
|
|
HHD
|
A:HEC1006
|
4.4
|
12.0
|
1.0
|
|
HHC
|
A:HEC1006
|
4.4
|
11.8
|
1.0
|
|
HHA
|
A:HEC1006
|
4.4
|
11.5
|
1.0
|
|
HAD1
|
A:HEC1004
|
4.6
|
12.0
|
1.0
|
|
CMD
|
A:HEC1004
|
5.0
|
12.5
|
1.0
|
|
HB2
|
A:CYS299
|
5.0
|
12.6
|
1.0
|
|
Iron binding site 4 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 4 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1007
b:12.7
occ:1.00
|
FE
|
A:HEC1007
|
0.0
|
12.7
|
1.0
|
|
NE2
|
A:HIS383
|
2.0
|
12.3
|
1.0
|
|
NC
|
A:HEC1007
|
2.0
|
12.1
|
1.0
|
|
NE2
|
A:HIS491
|
2.0
|
12.5
|
1.0
|
|
NB
|
A:HEC1007
|
2.0
|
11.9
|
1.0
|
|
NA
|
A:HEC1007
|
2.0
|
12.6
|
1.0
|
|
ND
|
A:HEC1007
|
2.0
|
11.8
|
1.0
|
|
CE1
|
A:HIS491
|
2.9
|
12.9
|
1.0
|
|
CE1
|
A:HIS383
|
3.0
|
12.9
|
1.0
|
|
CD2
|
A:HIS383
|
3.0
|
12.1
|
1.0
|
|
C1C
|
A:HEC1007
|
3.0
|
12.3
|
1.0
|
|
C4D
|
A:HEC1007
|
3.0
|
11.2
|
1.0
|
|
C1B
|
A:HEC1007
|
3.0
|
12.9
|
1.0
|
|
C4B
|
A:HEC1007
|
3.0
|
11.7
|
1.0
|
|
C4A
|
A:HEC1007
|
3.0
|
12.8
|
1.0
|
|
C1D
|
A:HEC1007
|
3.1
|
12.3
|
1.0
|
|
C4C
|
A:HEC1007
|
3.1
|
12.6
|
1.0
|
|
C1A
|
A:HEC1007
|
3.1
|
12.2
|
1.0
|
|
HE1
|
A:HIS491
|
3.1
|
12.7
|
1.0
|
|
CD2
|
A:HIS491
|
3.1
|
12.1
|
1.0
|
|
HE1
|
A:HIS383
|
3.2
|
12.7
|
1.0
|
|
HD2
|
A:HIS383
|
3.2
|
12.1
|
1.0
|
|
HD2
|
A:HIS491
|
3.3
|
12.4
|
1.0
|
|
CHC
|
A:HEC1007
|
3.4
|
10.9
|
1.0
|
|
CHB
|
A:HEC1007
|
3.4
|
12.7
|
1.0
|
|
CHA
|
A:HEC1007
|
3.4
|
12.2
|
1.0
|
|
CHD
|
A:HEC1007
|
3.4
|
12.5
|
1.0
|
|
ND1
|
A:HIS491
|
4.1
|
12.3
|
1.0
|
|
ND1
|
A:HIS383
|
4.1
|
12.8
|
1.0
|
|
CG
|
A:HIS383
|
4.1
|
11.8
|
1.0
|
|
CG
|
A:HIS491
|
4.2
|
13.2
|
1.0
|
|
C2B
|
A:HEC1007
|
4.2
|
13.3
|
1.0
|
|
C2C
|
A:HEC1007
|
4.2
|
12.4
|
1.0
|
|
C3C
|
A:HEC1007
|
4.3
|
12.0
|
1.0
|
|
C3A
|
A:HEC1007
|
4.3
|
12.6
|
1.0
|
|
C3B
|
A:HEC1007
|
4.3
|
13.0
|
1.0
|
|
C3D
|
A:HEC1007
|
4.3
|
12.4
|
1.0
|
|
C2A
|
A:HEC1007
|
4.3
|
12.8
|
1.0
|
|
C2D
|
A:HEC1007
|
4.3
|
13.2
|
1.0
|
|
HHC
|
A:HEC1007
|
4.3
|
11.4
|
1.0
|
|
HB3
|
A:SER487
|
4.4
|
12.5
|
1.0
|
|
HHA
|
A:HEC1007
|
4.4
|
12.0
|
1.0
|
|
HHB
|
A:HEC1007
|
4.4
|
12.8
|
1.0
|
|
HHD
|
A:HEC1007
|
4.4
|
12.5
|
1.0
|
|
HB2
|
A:CYS382
|
4.8
|
13.1
|
1.0
|
|
HB2
|
A:SER487
|
4.9
|
12.5
|
1.0
|
|
Iron binding site 5 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 5 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1008
b:15.0
occ:1.00
|
FE
|
A:HEC1008
|
0.0
|
15.0
|
1.0
|
|
NE2
|
A:HIS415
|
1.9
|
14.9
|
1.0
|
|
NE2
|
A:HIS372
|
2.0
|
14.8
|
1.0
|
|
ND
|
A:HEC1008
|
2.0
|
16.4
|
1.0
|
|
NB
|
A:HEC1008
|
2.0
|
14.6
|
1.0
|
|
NC
|
A:HEC1008
|
2.0
|
15.1
|
1.0
|
|
NA
|
A:HEC1008
|
2.0
|
16.5
|
1.0
|
|
CE1
|
A:HIS415
|
2.9
|
19.1
|
1.0
|
|
CE1
|
A:HIS372
|
3.0
|
15.9
|
1.0
|
|
CD2
|
A:HIS372
|
3.0
|
14.4
|
1.0
|
|
C1D
|
A:HEC1008
|
3.0
|
19.1
|
1.0
|
|
C1B
|
A:HEC1008
|
3.0
|
14.8
|
1.0
|
|
CD2
|
A:HIS415
|
3.0
|
13.7
|
1.0
|
|
C4D
|
A:HEC1008
|
3.0
|
16.9
|
1.0
|
|
C4B
|
A:HEC1008
|
3.0
|
13.8
|
1.0
|
|
C1C
|
A:HEC1008
|
3.1
|
15.4
|
1.0
|
|
HE1
|
A:HIS415
|
3.1
|
18.0
|
1.0
|
|
C4A
|
A:HEC1008
|
3.1
|
15.1
|
1.0
|
|
C1A
|
A:HEC1008
|
3.1
|
15.9
|
1.0
|
|
C4C
|
A:HEC1008
|
3.1
|
18.3
|
1.0
|
|
HE1
|
A:HIS372
|
3.2
|
15.8
|
1.0
|
|
HD2
|
A:HIS372
|
3.2
|
14.4
|
1.0
|
|
HD2
|
A:HIS415
|
3.3
|
14.4
|
1.0
|
|
CHD
|
A:HEC1008
|
3.4
|
20.0
|
1.0
|
|
CHB
|
A:HEC1008
|
3.4
|
14.5
|
1.0
|
|
CHA
|
A:HEC1008
|
3.4
|
17.4
|
1.0
|
|
CHC
|
A:HEC1008
|
3.4
|
14.3
|
1.0
|
|
ND1
|
A:HIS415
|
4.0
|
18.8
|
1.0
|
|
ND1
|
A:HIS372
|
4.1
|
16.3
|
1.0
|
|
CG
|
A:HIS372
|
4.1
|
14.0
|
1.0
|
|
CG
|
A:HIS415
|
4.1
|
15.3
|
1.0
|
|
C2B
|
A:HEC1008
|
4.2
|
15.9
|
1.0
|
|
C2D
|
A:HEC1008
|
4.2
|
22.1
|
1.0
|
|
C3B
|
A:HEC1008
|
4.2
|
14.9
|
1.0
|
|
C3D
|
A:HEC1008
|
4.2
|
21.9
|
1.0
|
|
C2C
|
A:HEC1008
|
4.3
|
16.7
|
1.0
|
|
C2A
|
A:HEC1008
|
4.3
|
16.7
|
1.0
|
|
C3A
|
A:HEC1008
|
4.3
|
17.1
|
1.0
|
|
C3C
|
A:HEC1008
|
4.3
|
21.3
|
1.0
|
|
HHD
|
A:HEC1008
|
4.4
|
19.4
|
1.0
|
|
HHB
|
A:HEC1008
|
4.4
|
14.7
|
1.0
|
|
HHA
|
A:HEC1008
|
4.4
|
16.9
|
1.0
|
|
HHC
|
A:HEC1008
|
4.4
|
14.4
|
1.0
|
|
HZ3
|
A:TRP418
|
4.8
|
14.5
|
1.0
|
|
HZ
|
A:PHE490
|
5.0
|
14.7
|
1.0
|
|
Iron binding site 6 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 6 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1002
b:14.1
occ:1.00
|
FE
|
A:HEC1002
|
0.0
|
14.1
|
1.0
|
|
NE2
|
A:HIS39
|
2.0
|
12.8
|
1.0
|
|
ND
|
A:HEC1002
|
2.0
|
13.4
|
1.0
|
|
NE2
|
A:HIS234
|
2.0
|
13.2
|
1.0
|
|
NB
|
A:HEC1002
|
2.0
|
13.3
|
1.0
|
|
NC
|
A:HEC1002
|
2.0
|
14.1
|
1.0
|
|
NA
|
A:HEC1002
|
2.0
|
14.1
|
1.0
|
|
CE1
|
A:HIS39
|
2.9
|
14.2
|
1.0
|
|
CD2
|
A:HIS234
|
3.0
|
13.0
|
1.0
|
|
CE1
|
A:HIS234
|
3.0
|
13.2
|
1.0
|
|
CD2
|
A:HIS39
|
3.0
|
13.2
|
1.0
|
|
C1C
|
A:HEC1002
|
3.0
|
14.1
|
1.0
|
|
C4B
|
A:HEC1002
|
3.0
|
13.4
|
1.0
|
|
C1D
|
A:HEC1002
|
3.0
|
13.6
|
1.0
|
|
C4D
|
A:HEC1002
|
3.0
|
13.3
|
1.0
|
|
C1A
|
A:HEC1002
|
3.0
|
12.8
|
1.0
|
|
C1B
|
A:HEC1002
|
3.0
|
14.4
|
1.0
|
|
C4C
|
A:HEC1002
|
3.1
|
13.6
|
1.0
|
|
C4A
|
A:HEC1002
|
3.1
|
14.7
|
1.0
|
|
HE1
|
A:HIS39
|
3.1
|
13.7
|
1.0
|
|
HD2
|
A:HIS234
|
3.2
|
13.2
|
1.0
|
|
HE1
|
A:HIS234
|
3.2
|
13.2
|
1.0
|
|
HD2
|
A:HIS39
|
3.2
|
13.2
|
1.0
|
|
CHB
|
A:HEC1002
|
3.4
|
13.6
|
1.0
|
|
CHD
|
A:HEC1002
|
3.4
|
13.1
|
1.0
|
|
CHC
|
A:HEC1002
|
3.4
|
15.2
|
1.0
|
|
CHA
|
A:HEC1002
|
3.4
|
15.0
|
1.0
|
|
ND1
|
A:HIS39
|
4.1
|
13.5
|
1.0
|
|
ND1
|
A:HIS234
|
4.1
|
13.3
|
1.0
|
|
CG
|
A:HIS39
|
4.1
|
13.3
|
1.0
|
|
CG
|
A:HIS234
|
4.1
|
13.4
|
1.0
|
|
C3A
|
A:HEC1002
|
4.2
|
14.0
|
1.0
|
|
C2B
|
A:HEC1002
|
4.2
|
15.2
|
1.0
|
|
C2D
|
A:HEC1002
|
4.3
|
13.0
|
1.0
|
|
C2A
|
A:HEC1002
|
4.3
|
14.2
|
1.0
|
|
C3C
|
A:HEC1002
|
4.3
|
13.6
|
1.0
|
|
C2C
|
A:HEC1002
|
4.3
|
15.5
|
1.0
|
|
C3B
|
A:HEC1002
|
4.3
|
15.9
|
1.0
|
|
C3D
|
A:HEC1002
|
4.3
|
14.4
|
1.0
|
|
HHD
|
A:HEC1002
|
4.4
|
13.3
|
1.0
|
|
HHB
|
A:HEC1002
|
4.4
|
14.1
|
1.0
|
|
HHC
|
A:HEC1002
|
4.4
|
14.5
|
1.0
|
|
HHA
|
A:HEC1002
|
4.4
|
14.1
|
1.0
|
|
HG2
|
A:PRO233
|
4.5
|
14.9
|
1.0
|
|
HB2
|
A:CYS38
|
4.6
|
14.1
|
1.0
|
|
HB2
|
A:PRO233
|
4.8
|
13.9
|
1.0
|
|
Iron binding site 7 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 7 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1003
b:13.7
occ:1.00
|
FE
|
A:HEC1003
|
0.0
|
13.7
|
1.0
|
|
NE2
|
A:HIS70
|
2.0
|
13.8
|
1.0
|
|
NC
|
A:HEC1003
|
2.0
|
12.4
|
1.0
|
|
NA
|
A:HEC1003
|
2.0
|
11.8
|
1.0
|
|
NE2
|
A:HIS30
|
2.0
|
13.6
|
1.0
|
|
NB
|
A:HEC1003
|
2.0
|
12.4
|
1.0
|
|
ND
|
A:HEC1003
|
2.0
|
12.4
|
1.0
|
|
CE1
|
A:HIS30
|
3.0
|
15.0
|
1.0
|
|
CE1
|
A:HIS70
|
3.0
|
14.7
|
1.0
|
|
CD2
|
A:HIS70
|
3.0
|
14.3
|
1.0
|
|
C1C
|
A:HEC1003
|
3.0
|
12.7
|
1.0
|
|
C4A
|
A:HEC1003
|
3.0
|
12.7
|
1.0
|
|
C4C
|
A:HEC1003
|
3.0
|
12.7
|
1.0
|
|
C1B
|
A:HEC1003
|
3.1
|
13.1
|
1.0
|
|
C4B
|
A:HEC1003
|
3.1
|
11.6
|
1.0
|
|
CD2
|
A:HIS30
|
3.1
|
13.8
|
1.0
|
|
C1D
|
A:HEC1003
|
3.1
|
11.9
|
1.0
|
|
C1A
|
A:HEC1003
|
3.1
|
13.3
|
1.0
|
|
C4D
|
A:HEC1003
|
3.1
|
12.6
|
1.0
|
|
HE1
|
A:HIS30
|
3.2
|
14.6
|
1.0
|
|
HE1
|
A:HIS70
|
3.2
|
14.3
|
1.0
|
|
HD2
|
A:HIS70
|
3.2
|
13.9
|
1.0
|
|
HD2
|
A:HIS30
|
3.3
|
13.8
|
1.0
|
|
CHC
|
A:HEC1003
|
3.4
|
12.4
|
1.0
|
|
CHB
|
A:HEC1003
|
3.4
|
12.6
|
1.0
|
|
CHD
|
A:HEC1003
|
3.4
|
12.3
|
1.0
|
|
CHA
|
A:HEC1003
|
3.4
|
13.5
|
1.0
|
|
ND1
|
A:HIS30
|
4.1
|
14.9
|
1.0
|
|
ND1
|
A:HIS70
|
4.1
|
13.9
|
1.0
|
|
CG
|
A:HIS70
|
4.2
|
13.2
|
1.0
|
|
CG
|
A:HIS30
|
4.2
|
13.9
|
1.0
|
|
C2B
|
A:HEC1003
|
4.2
|
14.5
|
1.0
|
|
C2C
|
A:HEC1003
|
4.2
|
13.9
|
1.0
|
|
C3C
|
A:HEC1003
|
4.3
|
12.5
|
1.0
|
|
C3A
|
A:HEC1003
|
4.3
|
13.1
|
1.0
|
|
C2D
|
A:HEC1003
|
4.3
|
15.0
|
1.0
|
|
C3B
|
A:HEC1003
|
4.3
|
13.2
|
1.0
|
|
C2A
|
A:HEC1003
|
4.3
|
12.4
|
1.0
|
|
C3D
|
A:HEC1003
|
4.3
|
14.4
|
1.0
|
|
HHB
|
A:HEC1003
|
4.4
|
12.8
|
1.0
|
|
HHC
|
A:HEC1003
|
4.4
|
12.3
|
1.0
|
|
HHD
|
A:HEC1003
|
4.4
|
12.3
|
1.0
|
|
HHA
|
A:HEC1003
|
4.4
|
13.3
|
1.0
|
|
HB2
|
A:CYS69
|
4.7
|
15.1
|
1.0
|
|
Iron binding site 8 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 8 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:15.4
occ:1.00
|
FE
|
A:HEC1001
|
0.0
|
15.4
|
1.0
|
|
NE2
|
A:HIS18
|
2.0
|
14.0
|
1.0
|
|
NE2
|
A:HIS44
|
2.0
|
14.4
|
1.0
|
|
NA
|
A:HEC1001
|
2.0
|
14.4
|
1.0
|
|
NC
|
A:HEC1001
|
2.0
|
14.8
|
1.0
|
|
NB
|
A:HEC1001
|
2.0
|
15.6
|
1.0
|
|
ND
|
A:HEC1001
|
2.0
|
15.4
|
1.0
|
|
CE1
|
A:HIS18
|
3.0
|
15.1
|
1.0
|
|
CE1
|
A:HIS44
|
3.0
|
16.2
|
1.0
|
|
CD2
|
A:HIS44
|
3.0
|
16.0
|
1.0
|
|
CD2
|
A:HIS18
|
3.0
|
14.5
|
1.0
|
|
C1C
|
A:HEC1001
|
3.0
|
17.6
|
1.0
|
|
C4D
|
A:HEC1001
|
3.0
|
16.2
|
1.0
|
|
C1A
|
A:HEC1001
|
3.1
|
14.2
|
1.0
|
|
C4A
|
A:HEC1001
|
3.1
|
14.1
|
1.0
|
|
C4B
|
A:HEC1001
|
3.1
|
16.6
|
1.0
|
|
C1D
|
A:HEC1001
|
3.1
|
16.5
|
1.0
|
|
C1B
|
A:HEC1001
|
3.1
|
14.5
|
1.0
|
|
C4C
|
A:HEC1001
|
3.1
|
16.5
|
1.0
|
|
HE1
|
A:HIS18
|
3.1
|
14.5
|
1.0
|
|
HE1
|
A:HIS44
|
3.2
|
15.8
|
1.0
|
|
HD2
|
A:HIS44
|
3.2
|
15.3
|
1.0
|
|
HD2
|
A:HIS18
|
3.2
|
14.4
|
1.0
|
|
CHA
|
A:HEC1001
|
3.4
|
16.1
|
1.0
|
|
CHC
|
A:HEC1001
|
3.4
|
17.1
|
1.0
|
|
CHB
|
A:HEC1001
|
3.4
|
15.0
|
1.0
|
|
CHD
|
A:HEC1001
|
3.4
|
17.0
|
1.0
|
|
ND1
|
A:HIS18
|
4.1
|
13.7
|
1.0
|
|
ND1
|
A:HIS44
|
4.1
|
16.4
|
1.0
|
|
HG3
|
A:PRO57
|
4.1
|
16.8
|
1.0
|
|
CG
|
A:HIS44
|
4.1
|
14.8
|
1.0
|
|
CG
|
A:HIS18
|
4.2
|
14.7
|
1.0
|
|
C3A
|
A:HEC1001
|
4.3
|
14.3
|
1.0
|
|
C2B
|
A:HEC1001
|
4.3
|
14.3
|
1.0
|
|
C2A
|
A:HEC1001
|
4.3
|
14.8
|
1.0
|
|
C2D
|
A:HEC1001
|
4.3
|
18.5
|
1.0
|
|
C2C
|
A:HEC1001
|
4.3
|
16.9
|
1.0
|
|
C3D
|
A:HEC1001
|
4.3
|
18.9
|
1.0
|
|
C3C
|
A:HEC1001
|
4.3
|
16.3
|
1.0
|
|
C3B
|
A:HEC1001
|
4.3
|
15.7
|
1.0
|
|
HHA
|
A:HEC1001
|
4.4
|
15.7
|
1.0
|
|
HHC
|
A:HEC1001
|
4.4
|
17.1
|
1.0
|
|
HHB
|
A:HEC1001
|
4.4
|
14.7
|
1.0
|
|
HHD
|
A:HEC1001
|
4.4
|
16.8
|
1.0
|
|
HB2
|
A:CYS17
|
4.9
|
19.6
|
1.0
|
|
Iron binding site 9 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 9 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1004
b:12.0
occ:1.00
|
FE
|
B:HEC1004
|
0.0
|
12.0
|
1.0
|
|
C
|
B:CYN526
|
1.9
|
12.4
|
1.0
|
|
NZ
|
B:LYS188
|
2.0
|
15.2
|
1.0
|
|
NA
|
B:HEC1004
|
2.0
|
12.2
|
1.0
|
|
ND
|
B:HEC1004
|
2.0
|
11.1
|
1.0
|
|
NB
|
B:HEC1004
|
2.0
|
12.2
|
1.0
|
|
NC
|
B:HEC1004
|
2.0
|
12.0
|
1.0
|
|
C1A
|
B:HEC1004
|
3.0
|
11.6
|
1.0
|
|
C1D
|
B:HEC1004
|
3.0
|
10.7
|
1.0
|
|
N
|
B:CYN526
|
3.0
|
16.7
|
1.0
|
|
C4C
|
B:HEC1004
|
3.0
|
11.7
|
1.0
|
|
C4D
|
B:HEC1004
|
3.0
|
11.3
|
1.0
|
|
C4A
|
B:HEC1004
|
3.0
|
11.5
|
1.0
|
|
C1C
|
B:HEC1004
|
3.1
|
11.5
|
1.0
|
|
C1B
|
B:HEC1004
|
3.1
|
13.1
|
1.0
|
|
CE
|
B:LYS188
|
3.1
|
16.7
|
1.0
|
|
C4B
|
B:HEC1004
|
3.1
|
11.6
|
1.0
|
|
HE3
|
B:LYS188
|
3.2
|
15.3
|
1.0
|
|
HE2
|
B:LYS188
|
3.2
|
15.3
|
1.0
|
|
CHA
|
B:HEC1004
|
3.4
|
10.6
|
1.0
|
|
CHC
|
B:HEC1004
|
3.4
|
11.9
|
1.0
|
|
CHB
|
B:HEC1004
|
3.4
|
12.6
|
1.0
|
|
CHD
|
B:HEC1004
|
3.4
|
12.3
|
1.0
|
|
C2C
|
B:HEC1004
|
4.3
|
11.5
|
1.0
|
|
C2A
|
B:HEC1004
|
4.3
|
11.8
|
1.0
|
|
C3D
|
B:HEC1004
|
4.3
|
11.3
|
1.0
|
|
C3A
|
B:HEC1004
|
4.3
|
11.6
|
1.0
|
|
C3C
|
B:HEC1004
|
4.3
|
12.3
|
1.0
|
|
C2B
|
B:HEC1004
|
4.3
|
15.7
|
1.0
|
|
C2D
|
B:HEC1004
|
4.3
|
11.9
|
1.0
|
|
C3B
|
B:HEC1004
|
4.3
|
14.7
|
1.0
|
|
HHA
|
B:HEC1004
|
4.4
|
11.0
|
1.0
|
|
HHC
|
B:HEC1004
|
4.4
|
11.7
|
1.0
|
|
NE2
|
B:HIS361
|
4.4
|
12.9
|
1.0
|
|
HHB
|
B:HEC1004
|
4.4
|
12.5
|
1.0
|
|
HHD
|
B:HEC1004
|
4.4
|
11.8
|
1.0
|
|
CD
|
B:LYS188
|
4.5
|
12.3
|
1.0
|
|
HH21
|
B:ARG131
|
4.5
|
14.2
|
1.0
|
|
OH
|
B:TYR303
|
4.6
|
15.4
|
1.0
|
|
HD3
|
B:LYS188
|
4.6
|
13.6
|
1.0
|
|
O
|
B:HOH822
|
4.7
|
17.4
|
1.0
|
|
O
|
B:HOH1057
|
4.7
|
20.8
|
1.0
|
|
HD2
|
B:LYS188
|
4.8
|
13.6
|
1.0
|
|
HH22
|
B:ARG131
|
4.8
|
14.2
|
1.0
|
|
HB2
|
B:CYS187
|
4.9
|
12.2
|
1.0
|
|
CMD
|
B:HEC1006
|
4.9
|
11.8
|
1.0
|
|
Iron binding site 10 out
of 16 in 3mmo
Go back to
Iron Binding Sites List in 3mmo
Iron binding site 10 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in Complex with Cyanide
 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 Cyanide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1005
b:12.7
occ:1.00
|
FE
|
B:HEC1005
|
0.0
|
12.7
|
1.0
|
|
NE2
|
B:HIS398
|
2.0
|
12.5
|
1.0
|
|
NC
|
B:HEC1005
|
2.0
|
10.8
|
1.0
|
|
NE2
|
B:HIS231
|
2.0
|
12.4
|
1.0
|
|
ND
|
B:HEC1005
|
2.0
|
12.0
|
1.0
|
|
NB
|
B:HEC1005
|
2.0
|
11.6
|
1.0
|
|
NA
|
B:HEC1005
|
2.0
|
11.7
|
1.0
|
|
CE1
|
B:HIS231
|
3.0
|
13.3
|
1.0
|
|
CE1
|
B:HIS398
|
3.0
|
13.3
|
1.0
|
|
CD2
|
B:HIS398
|
3.0
|
11.9
|
1.0
|
|
C1C
|
B:HEC1005
|
3.0
|
10.9
|
1.0
|
|
C1D
|
B:HEC1005
|
3.0
|
11.4
|
1.0
|
|
C4C
|
B:HEC1005
|
3.0
|
10.6
|
1.0
|
|
C4D
|
B:HEC1005
|
3.0
|
11.7
|
1.0
|
|
C4B
|
B:HEC1005
|
3.0
|
9.8
|
1.0
|
|
C4A
|
B:HEC1005
|
3.0
|
11.2
|
1.0
|
|
CD2
|
B:HIS231
|
3.0
|
13.1
|
1.0
|
|
C1A
|
B:HEC1005
|
3.1
|
13.2
|
1.0
|
|
C1B
|
B:HEC1005
|
3.1
|
12.1
|
1.0
|
|
HE1
|
B:HIS231
|
3.1
|
12.9
|
1.0
|
|
HE1
|
B:HIS398
|
3.2
|
13.3
|
1.0
|
|
HD2
|
B:HIS398
|
3.2
|
12.2
|
1.0
|
|
HD2
|
B:HIS231
|
3.3
|
12.8
|
1.0
|
|
CHD
|
B:HEC1005
|
3.4
|
10.5
|
1.0
|
|
CHC
|
B:HEC1005
|
3.4
|
9.7
|
1.0
|
|
CHA
|
B:HEC1005
|
3.4
|
13.0
|
1.0
|
|
CHB
|
B:HEC1005
|
3.4
|
11.7
|
1.0
|
|
ND1
|
B:HIS398
|
4.1
|
14.0
|
1.0
|
|
ND1
|
B:HIS231
|
4.1
|
12.7
|
1.0
|
|
CG
|
B:HIS398
|
4.1
|
12.8
|
1.0
|
|
CG
|
B:HIS231
|
4.2
|
12.6
|
1.0
|
|
C2C
|
B:HEC1005
|
4.2
|
13.1
|
1.0
|
|
C2D
|
B:HEC1005
|
4.2
|
12.9
|
1.0
|
|
C2B
|
B:HEC1005
|
4.2
|
12.1
|
1.0
|
|
C3C
|
B:HEC1005
|
4.3
|
11.4
|
1.0
|
|
C3A
|
B:HEC1005
|
4.3
|
13.4
|
1.0
|
|
C2A
|
B:HEC1005
|
4.3
|
13.5
|
1.0
|
|
C3D
|
B:HEC1005
|
4.3
|
13.6
|
1.0
|
|
C3B
|
B:HEC1005
|
4.3
|
11.3
|
1.0
|
|
HHD
|
B:HEC1005
|
4.4
|
10.7
|
1.0
|
|
HHC
|
B:HEC1005
|
4.4
|
10.0
|
1.0
|
|
HHA
|
B:HEC1005
|
4.4
|
12.7
|
1.0
|
|
HHB
|
B:HEC1005
|
4.4
|
11.7
|
1.0
|
|
HG2
|
B:GLN73
|
4.5
|
13.6
|
1.0
|
|
HB3
|
B:GLN73
|
4.7
|
13.2
|
1.0
|
|
HB2
|
B:CYS230
|
4.8
|
12.0
|
1.0
|
|
Reference:
A.A.Trofimov,
K.M.Polyakov,
K.M.Boyko,
T.V.Tikhonova,
T.N.Safonova,
A.V.Tikhonov,
A.N.Popov,
V.O.Popov.
Structures of Complexes of Octahaem Cytochrome C Nitrite Reductase From Thioalkalivibrio Nitratireducens with Sulfite and Cyanide. Acta Crystallogr.,Sect.D V. 66 1043 2010.
ISSN: ISSN 0907-4449
PubMed: 20944237
DOI: 10.1107/S0907444910031665
Page generated: Sun Dec 13 15:12:45 2020
|
