Iron in PDB 3rkh: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
Protein crystallography data
The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy), PDB code: 3rkh
was solved by
A.A.Trofimov,
K.M.Polyakov,
T.V.Tikhonova,
A.V.Tikhonov,
P.V.Dorovatovskii,
V.O.Popov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
100.00 /
1.83
|
|
Space group
|
P 21 3
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
192.800,
192.800,
192.800,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.1 /
16.2
|
Other elements in 3rkh:
The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy) 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 A Complex with Nitrite (Full Occupancy)
(pdb code 3rkh). 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 A Complex with Nitrite (Full Occupancy), PDB code: 3rkh:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 1 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1004
b:15.7
occ:1.00
|
FE
|
A:HEC1004
|
0.0
|
15.7
|
1.0
|
|
N
|
A:NO21
|
1.8
|
15.8
|
1.0
|
|
NZ
|
A:LYS188
|
1.9
|
16.5
|
1.0
|
|
NA
|
A:HEC1004
|
2.0
|
14.9
|
1.0
|
|
NC
|
A:HEC1004
|
2.0
|
15.9
|
1.0
|
|
ND
|
A:HEC1004
|
2.0
|
13.6
|
1.0
|
|
NB
|
A:HEC1004
|
2.0
|
16.7
|
1.0
|
|
O2
|
A:NO21
|
2.9
|
18.0
|
1.0
|
|
O1
|
A:NO21
|
2.9
|
16.1
|
1.0
|
|
C1A
|
A:HEC1004
|
3.0
|
16.7
|
1.0
|
|
C1C
|
A:HEC1004
|
3.0
|
15.5
|
1.0
|
|
C4A
|
A:HEC1004
|
3.0
|
15.2
|
1.0
|
|
C4C
|
A:HEC1004
|
3.0
|
16.3
|
1.0
|
|
C4B
|
A:HEC1004
|
3.0
|
17.0
|
1.0
|
|
C4D
|
A:HEC1004
|
3.0
|
15.5
|
1.0
|
|
C1D
|
A:HEC1004
|
3.0
|
16.8
|
1.0
|
|
C1B
|
A:HEC1004
|
3.1
|
16.0
|
1.0
|
|
CE
|
A:LYS188
|
3.1
|
17.0
|
1.0
|
|
CHA
|
A:HEC1004
|
3.4
|
15.1
|
1.0
|
|
CHC
|
A:HEC1004
|
3.4
|
15.5
|
1.0
|
|
CHD
|
A:HEC1004
|
3.4
|
14.4
|
1.0
|
|
CHB
|
A:HEC1004
|
3.4
|
16.0
|
1.0
|
|
C3A
|
A:HEC1004
|
4.2
|
15.2
|
1.0
|
|
C2A
|
A:HEC1004
|
4.2
|
14.6
|
1.0
|
|
C2C
|
A:HEC1004
|
4.3
|
15.2
|
1.0
|
|
C2B
|
A:HEC1004
|
4.3
|
16.7
|
1.0
|
|
C3C
|
A:HEC1004
|
4.3
|
14.6
|
1.0
|
|
C3B
|
A:HEC1004
|
4.3
|
16.8
|
1.0
|
|
C3D
|
A:HEC1004
|
4.3
|
14.1
|
1.0
|
|
C2D
|
A:HEC1004
|
4.3
|
13.8
|
1.0
|
|
NE2
|
A:HIS361
|
4.4
|
17.0
|
1.0
|
|
CD
|
A:LYS188
|
4.4
|
16.2
|
1.0
|
|
O
|
A:HOH883
|
4.5
|
17.4
|
1.0
|
|
OH
|
A:TYR303
|
4.5
|
21.9
|
1.0
|
|
CMD
|
A:HEC1006
|
4.8
|
14.2
|
1.0
|
|
NH2
|
A:ARG131
|
4.9
|
14.3
|
1.0
|
|
O
|
A:HOH874
|
4.9
|
15.9
|
1.0
|
|
Iron binding site 2 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 2 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1005
b:15.6
occ:1.00
|
FE
|
A:HEC1005
|
0.0
|
15.6
|
1.0
|
|
NC
|
A:HEC1005
|
1.9
|
15.1
|
1.0
|
|
NE2
|
A:HIS231
|
2.0
|
15.5
|
1.0
|
|
NA
|
A:HEC1005
|
2.0
|
14.7
|
1.0
|
|
NE2
|
A:HIS398
|
2.0
|
15.5
|
1.0
|
|
ND
|
A:HEC1005
|
2.0
|
13.3
|
1.0
|
|
NB
|
A:HEC1005
|
2.0
|
14.4
|
1.0
|
|
CD2
|
A:HIS398
|
2.9
|
15.8
|
1.0
|
|
CD2
|
A:HIS231
|
2.9
|
14.1
|
1.0
|
|
CE1
|
A:HIS231
|
3.0
|
16.7
|
1.0
|
|
C1C
|
A:HEC1005
|
3.0
|
15.0
|
1.0
|
|
C4D
|
A:HEC1005
|
3.0
|
15.2
|
1.0
|
|
C1D
|
A:HEC1005
|
3.0
|
14.7
|
1.0
|
|
CE1
|
A:HIS398
|
3.0
|
16.4
|
1.0
|
|
C4A
|
A:HEC1005
|
3.0
|
14.2
|
1.0
|
|
C4B
|
A:HEC1005
|
3.0
|
12.1
|
1.0
|
|
C4C
|
A:HEC1005
|
3.0
|
14.6
|
1.0
|
|
C1B
|
A:HEC1005
|
3.0
|
15.5
|
1.0
|
|
C1A
|
A:HEC1005
|
3.0
|
13.5
|
1.0
|
|
CHC
|
A:HEC1005
|
3.4
|
12.9
|
1.0
|
|
CHD
|
A:HEC1005
|
3.4
|
14.0
|
1.0
|
|
CHB
|
A:HEC1005
|
3.4
|
12.6
|
1.0
|
|
CHA
|
A:HEC1005
|
3.4
|
12.6
|
1.0
|
|
ND1
|
A:HIS231
|
4.1
|
15.2
|
1.0
|
|
CG
|
A:HIS231
|
4.1
|
15.9
|
1.0
|
|
CG
|
A:HIS398
|
4.1
|
16.5
|
1.0
|
|
ND1
|
A:HIS398
|
4.1
|
15.4
|
1.0
|
|
C3D
|
A:HEC1005
|
4.2
|
12.2
|
1.0
|
|
C2B
|
A:HEC1005
|
4.2
|
13.8
|
1.0
|
|
C2C
|
A:HEC1005
|
4.2
|
15.3
|
1.0
|
|
C3A
|
A:HEC1005
|
4.2
|
14.4
|
1.0
|
|
C3B
|
A:HEC1005
|
4.2
|
13.9
|
1.0
|
|
C3C
|
A:HEC1005
|
4.2
|
13.8
|
1.0
|
|
C2A
|
A:HEC1005
|
4.2
|
14.8
|
1.0
|
|
C2D
|
A:HEC1005
|
4.2
|
15.1
|
1.0
|
|
Iron binding site 3 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 3 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1006
b:14.4
occ:1.00
|
FE
|
A:HEC1006
|
0.0
|
14.4
|
1.0
|
|
NE2
|
A:HIS119
|
1.9
|
14.7
|
1.0
|
|
NE2
|
A:HIS300
|
1.9
|
14.1
|
1.0
|
|
ND
|
A:HEC1006
|
2.0
|
14.3
|
1.0
|
|
NB
|
A:HEC1006
|
2.0
|
13.4
|
1.0
|
|
NA
|
A:HEC1006
|
2.0
|
13.0
|
1.0
|
|
NC
|
A:HEC1006
|
2.0
|
14.2
|
1.0
|
|
CE1
|
A:HIS119
|
2.9
|
13.4
|
1.0
|
|
CE1
|
A:HIS300
|
2.9
|
13.5
|
1.0
|
|
CD2
|
A:HIS300
|
3.0
|
14.9
|
1.0
|
|
C4A
|
A:HEC1006
|
3.0
|
12.3
|
1.0
|
|
CD2
|
A:HIS119
|
3.0
|
13.4
|
1.0
|
|
C1D
|
A:HEC1006
|
3.0
|
15.8
|
1.0
|
|
C1A
|
A:HEC1006
|
3.0
|
13.8
|
1.0
|
|
C4C
|
A:HEC1006
|
3.0
|
15.4
|
1.0
|
|
C1B
|
A:HEC1006
|
3.0
|
14.6
|
1.0
|
|
C1C
|
A:HEC1006
|
3.1
|
13.5
|
1.0
|
|
C4D
|
A:HEC1006
|
3.1
|
15.6
|
1.0
|
|
C4B
|
A:HEC1006
|
3.1
|
15.4
|
1.0
|
|
CHD
|
A:HEC1006
|
3.4
|
13.9
|
1.0
|
|
CHB
|
A:HEC1006
|
3.4
|
12.7
|
1.0
|
|
CHA
|
A:HEC1006
|
3.4
|
12.2
|
1.0
|
|
CHC
|
A:HEC1006
|
3.5
|
12.7
|
1.0
|
|
ND1
|
A:HIS119
|
4.0
|
14.1
|
1.0
|
|
ND1
|
A:HIS300
|
4.0
|
12.6
|
1.0
|
|
CG
|
A:HIS119
|
4.1
|
14.7
|
1.0
|
|
CG
|
A:HIS300
|
4.1
|
14.8
|
1.0
|
|
C3A
|
A:HEC1006
|
4.2
|
12.9
|
1.0
|
|
C2A
|
A:HEC1006
|
4.2
|
12.4
|
1.0
|
|
C2C
|
A:HEC1006
|
4.2
|
13.3
|
1.0
|
|
C2D
|
A:HEC1006
|
4.3
|
12.8
|
1.0
|
|
C2B
|
A:HEC1006
|
4.3
|
14.4
|
1.0
|
|
C3C
|
A:HEC1006
|
4.3
|
11.6
|
1.0
|
|
C3D
|
A:HEC1006
|
4.3
|
12.5
|
1.0
|
|
C3B
|
A:HEC1006
|
4.3
|
14.6
|
1.0
|
|
CMD
|
A:HEC1004
|
4.9
|
12.0
|
1.0
|
|
CE
|
A:MET122
|
5.0
|
15.4
|
1.0
|
|
Iron binding site 4 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 4 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1007
b:14.9
occ:1.00
|
FE
|
A:HEC1007
|
0.0
|
14.9
|
1.0
|
|
NE2
|
A:HIS491
|
1.9
|
14.0
|
1.0
|
|
NC
|
A:HEC1007
|
1.9
|
14.7
|
1.0
|
|
NE2
|
A:HIS383
|
1.9
|
14.1
|
1.0
|
|
NA
|
A:HEC1007
|
2.0
|
14.5
|
1.0
|
|
NB
|
A:HEC1007
|
2.0
|
14.8
|
1.0
|
|
ND
|
A:HEC1007
|
2.0
|
14.9
|
1.0
|
|
CE1
|
A:HIS491
|
2.8
|
14.7
|
1.0
|
|
CD2
|
A:HIS383
|
2.9
|
15.0
|
1.0
|
|
CE1
|
A:HIS383
|
2.9
|
15.6
|
1.0
|
|
C1C
|
A:HEC1007
|
3.0
|
16.4
|
1.0
|
|
CD2
|
A:HIS491
|
3.0
|
13.9
|
1.0
|
|
C4B
|
A:HEC1007
|
3.0
|
12.4
|
1.0
|
|
C4C
|
A:HEC1007
|
3.0
|
14.4
|
1.0
|
|
C1A
|
A:HEC1007
|
3.0
|
13.9
|
1.0
|
|
C4A
|
A:HEC1007
|
3.0
|
13.3
|
1.0
|
|
C1D
|
A:HEC1007
|
3.0
|
15.2
|
1.0
|
|
C1B
|
A:HEC1007
|
3.0
|
13.8
|
1.0
|
|
C4D
|
A:HEC1007
|
3.0
|
14.8
|
1.0
|
|
CHC
|
A:HEC1007
|
3.4
|
14.1
|
1.0
|
|
CHD
|
A:HEC1007
|
3.4
|
13.6
|
1.0
|
|
CHB
|
A:HEC1007
|
3.4
|
12.2
|
1.0
|
|
CHA
|
A:HEC1007
|
3.4
|
13.6
|
1.0
|
|
ND1
|
A:HIS491
|
4.0
|
14.6
|
1.0
|
|
ND1
|
A:HIS383
|
4.1
|
14.0
|
1.0
|
|
CG
|
A:HIS383
|
4.1
|
15.3
|
1.0
|
|
CG
|
A:HIS491
|
4.1
|
15.3
|
1.0
|
|
C2C
|
A:HEC1007
|
4.2
|
15.9
|
1.0
|
|
C3C
|
A:HEC1007
|
4.2
|
15.2
|
1.0
|
|
C3A
|
A:HEC1007
|
4.2
|
13.5
|
1.0
|
|
C2A
|
A:HEC1007
|
4.2
|
14.4
|
1.0
|
|
C2B
|
A:HEC1007
|
4.2
|
13.9
|
1.0
|
|
C3B
|
A:HEC1007
|
4.2
|
14.3
|
1.0
|
|
C3D
|
A:HEC1007
|
4.3
|
13.4
|
1.0
|
|
C2D
|
A:HEC1007
|
4.3
|
14.3
|
1.0
|
|
CB
|
A:SER487
|
5.0
|
14.6
|
1.0
|
|
Iron binding site 5 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 5 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1008
b:18.3
occ:1.00
|
FE
|
A:HEC1008
|
0.0
|
18.3
|
1.0
|
|
NE2
|
A:HIS415
|
1.9
|
20.0
|
1.0
|
|
NE2
|
A:HIS372
|
1.9
|
17.3
|
1.0
|
|
NB
|
A:HEC1008
|
2.0
|
17.0
|
1.0
|
|
NC
|
A:HEC1008
|
2.0
|
19.3
|
1.0
|
|
ND
|
A:HEC1008
|
2.0
|
19.3
|
1.0
|
|
NA
|
A:HEC1008
|
2.0
|
18.4
|
1.0
|
|
CE1
|
A:HIS415
|
2.8
|
22.9
|
1.0
|
|
CE1
|
A:HIS372
|
2.9
|
18.2
|
1.0
|
|
CD2
|
A:HIS372
|
2.9
|
17.5
|
1.0
|
|
CD2
|
A:HIS415
|
3.0
|
19.3
|
1.0
|
|
C4B
|
A:HEC1008
|
3.0
|
17.1
|
1.0
|
|
C1B
|
A:HEC1008
|
3.0
|
17.5
|
1.0
|
|
C1D
|
A:HEC1008
|
3.0
|
22.2
|
1.0
|
|
C1C
|
A:HEC1008
|
3.0
|
19.8
|
1.0
|
|
C4D
|
A:HEC1008
|
3.0
|
21.6
|
1.0
|
|
C4C
|
A:HEC1008
|
3.0
|
21.5
|
1.0
|
|
C1A
|
A:HEC1008
|
3.1
|
20.9
|
1.0
|
|
C4A
|
A:HEC1008
|
3.1
|
18.5
|
1.0
|
|
CHC
|
A:HEC1008
|
3.4
|
16.5
|
1.0
|
|
CHD
|
A:HEC1008
|
3.4
|
21.1
|
1.0
|
|
CHA
|
A:HEC1008
|
3.4
|
21.5
|
1.0
|
|
CHB
|
A:HEC1008
|
3.4
|
17.1
|
1.0
|
|
ND1
|
A:HIS415
|
4.0
|
21.2
|
1.0
|
|
ND1
|
A:HIS372
|
4.0
|
18.9
|
1.0
|
|
CG
|
A:HIS415
|
4.1
|
19.5
|
1.0
|
|
CG
|
A:HIS372
|
4.1
|
17.6
|
1.0
|
|
C2B
|
A:HEC1008
|
4.2
|
16.6
|
1.0
|
|
C3B
|
A:HEC1008
|
4.2
|
16.3
|
1.0
|
|
C2C
|
A:HEC1008
|
4.2
|
20.5
|
1.0
|
|
C3D
|
A:HEC1008
|
4.3
|
26.4
|
1.0
|
|
C2D
|
A:HEC1008
|
4.3
|
25.5
|
1.0
|
|
C3C
|
A:HEC1008
|
4.3
|
19.9
|
1.0
|
|
C2A
|
A:HEC1008
|
4.3
|
20.5
|
1.0
|
|
C3A
|
A:HEC1008
|
4.3
|
21.3
|
1.0
|
|
CBC
|
A:HEC1007
|
4.9
|
16.8
|
1.0
|
|
Iron binding site 6 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 6 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1002
b:16.9
occ:1.00
|
FE
|
A:HEC1002
|
0.0
|
16.9
|
1.0
|
|
NE2
|
A:HIS39
|
1.9
|
16.0
|
1.0
|
|
NE2
|
A:HIS234
|
1.9
|
15.4
|
1.0
|
|
NA
|
A:HEC1002
|
2.0
|
16.6
|
1.0
|
|
NB
|
A:HEC1002
|
2.0
|
17.2
|
1.0
|
|
ND
|
A:HEC1002
|
2.0
|
17.0
|
1.0
|
|
NC
|
A:HEC1002
|
2.0
|
16.7
|
1.0
|
|
CE1
|
A:HIS234
|
2.9
|
12.6
|
1.0
|
|
CD2
|
A:HIS39
|
2.9
|
15.7
|
1.0
|
|
CE1
|
A:HIS39
|
2.9
|
13.7
|
1.0
|
|
CD2
|
A:HIS234
|
2.9
|
14.9
|
1.0
|
|
C1D
|
A:HEC1002
|
3.0
|
16.7
|
1.0
|
|
C4A
|
A:HEC1002
|
3.0
|
17.2
|
1.0
|
|
C4C
|
A:HEC1002
|
3.0
|
16.6
|
1.0
|
|
C1B
|
A:HEC1002
|
3.0
|
17.3
|
1.0
|
|
C1A
|
A:HEC1002
|
3.1
|
17.2
|
1.0
|
|
C4D
|
A:HEC1002
|
3.1
|
17.6
|
1.0
|
|
C4B
|
A:HEC1002
|
3.1
|
17.5
|
1.0
|
|
C1C
|
A:HEC1002
|
3.1
|
16.0
|
1.0
|
|
CHD
|
A:HEC1002
|
3.3
|
16.6
|
1.0
|
|
CHB
|
A:HEC1002
|
3.4
|
17.8
|
1.0
|
|
CHC
|
A:HEC1002
|
3.5
|
16.5
|
1.0
|
|
CHA
|
A:HEC1002
|
3.5
|
15.8
|
1.0
|
|
ND1
|
A:HIS234
|
4.0
|
14.5
|
1.0
|
|
ND1
|
A:HIS39
|
4.0
|
16.7
|
1.0
|
|
CG
|
A:HIS39
|
4.0
|
15.8
|
1.0
|
|
CG
|
A:HIS234
|
4.0
|
14.9
|
1.0
|
|
C3A
|
A:HEC1002
|
4.2
|
17.8
|
1.0
|
|
C2B
|
A:HEC1002
|
4.2
|
18.0
|
1.0
|
|
C2D
|
A:HEC1002
|
4.2
|
16.5
|
1.0
|
|
C2A
|
A:HEC1002
|
4.3
|
15.6
|
1.0
|
|
C3C
|
A:HEC1002
|
4.3
|
14.8
|
1.0
|
|
C2C
|
A:HEC1002
|
4.3
|
15.3
|
1.0
|
|
C3B
|
A:HEC1002
|
4.3
|
16.7
|
1.0
|
|
C3D
|
A:HEC1002
|
4.3
|
14.5
|
1.0
|
|
Iron binding site 7 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 7 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1003
b:16.2
occ:1.00
|
FE
|
A:HEC1003
|
0.0
|
16.2
|
1.0
|
|
ND
|
A:HEC1003
|
1.9
|
15.3
|
1.0
|
|
NE2
|
A:HIS70
|
2.0
|
14.5
|
1.0
|
|
NB
|
A:HEC1003
|
2.0
|
15.3
|
1.0
|
|
NE2
|
A:HIS30
|
2.0
|
14.1
|
1.0
|
|
NA
|
A:HEC1003
|
2.0
|
15.9
|
1.0
|
|
NC
|
A:HEC1003
|
2.0
|
16.5
|
1.0
|
|
CD2
|
A:HIS70
|
2.9
|
16.1
|
1.0
|
|
CE1
|
A:HIS30
|
2.9
|
16.5
|
1.0
|
|
CE1
|
A:HIS70
|
3.0
|
17.4
|
1.0
|
|
C1B
|
A:HEC1003
|
3.0
|
16.1
|
1.0
|
|
C1D
|
A:HEC1003
|
3.0
|
13.8
|
1.0
|
|
CD2
|
A:HIS30
|
3.0
|
15.8
|
1.0
|
|
C4A
|
A:HEC1003
|
3.0
|
14.5
|
1.0
|
|
C4D
|
A:HEC1003
|
3.0
|
14.0
|
1.0
|
|
C4C
|
A:HEC1003
|
3.0
|
14.2
|
1.0
|
|
C1A
|
A:HEC1003
|
3.0
|
15.3
|
1.0
|
|
C4B
|
A:HEC1003
|
3.0
|
13.0
|
1.0
|
|
C1C
|
A:HEC1003
|
3.0
|
15.3
|
1.0
|
|
CHB
|
A:HEC1003
|
3.4
|
15.8
|
1.0
|
|
CHD
|
A:HEC1003
|
3.4
|
14.9
|
1.0
|
|
CHA
|
A:HEC1003
|
3.4
|
13.2
|
1.0
|
|
CHC
|
A:HEC1003
|
3.4
|
12.2
|
1.0
|
|
ND1
|
A:HIS30
|
4.1
|
15.1
|
1.0
|
|
ND1
|
A:HIS70
|
4.1
|
14.5
|
1.0
|
|
CG
|
A:HIS70
|
4.1
|
14.1
|
1.0
|
|
CG
|
A:HIS30
|
4.1
|
15.8
|
1.0
|
|
C2B
|
A:HEC1003
|
4.2
|
16.4
|
1.0
|
|
C2D
|
A:HEC1003
|
4.2
|
15.4
|
1.0
|
|
C3A
|
A:HEC1003
|
4.2
|
15.4
|
1.0
|
|
C3D
|
A:HEC1003
|
4.2
|
16.3
|
1.0
|
|
C2A
|
A:HEC1003
|
4.2
|
15.8
|
1.0
|
|
C3C
|
A:HEC1003
|
4.3
|
15.2
|
1.0
|
|
C3B
|
A:HEC1003
|
4.3
|
14.6
|
1.0
|
|
C2C
|
A:HEC1003
|
4.3
|
15.4
|
1.0
|
|
CMA
|
A:HEC1005
|
4.9
|
15.2
|
1.0
|
|
Iron binding site 8 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 8 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:17.8
occ:1.00
|
FE
|
A:HEC1001
|
0.0
|
17.8
|
1.0
|
|
NE2
|
A:HIS18
|
1.9
|
16.1
|
1.0
|
|
NE2
|
A:HIS44
|
1.9
|
17.4
|
1.0
|
|
ND
|
A:HEC1001
|
2.0
|
18.2
|
1.0
|
|
NA
|
A:HEC1001
|
2.0
|
17.1
|
1.0
|
|
NC
|
A:HEC1001
|
2.1
|
18.0
|
1.0
|
|
NB
|
A:HEC1001
|
2.1
|
20.0
|
1.0
|
|
CE1
|
A:HIS18
|
2.8
|
17.2
|
1.0
|
|
CE1
|
A:HIS44
|
2.9
|
17.9
|
1.0
|
|
CD2
|
A:HIS44
|
2.9
|
15.0
|
1.0
|
|
CD2
|
A:HIS18
|
3.0
|
15.7
|
1.0
|
|
C1D
|
A:HEC1001
|
3.0
|
20.9
|
1.0
|
|
C4A
|
A:HEC1001
|
3.0
|
18.0
|
1.0
|
|
C4D
|
A:HEC1001
|
3.0
|
21.4
|
1.0
|
|
C1A
|
A:HEC1001
|
3.1
|
18.0
|
1.0
|
|
C4C
|
A:HEC1001
|
3.1
|
19.6
|
1.0
|
|
C1B
|
A:HEC1001
|
3.1
|
20.7
|
1.0
|
|
C1C
|
A:HEC1001
|
3.1
|
19.0
|
1.0
|
|
C4B
|
A:HEC1001
|
3.1
|
19.6
|
1.0
|
|
CHD
|
A:HEC1001
|
3.4
|
18.6
|
1.0
|
|
CHB
|
A:HEC1001
|
3.4
|
17.0
|
1.0
|
|
CHA
|
A:HEC1001
|
3.4
|
20.3
|
1.0
|
|
CHC
|
A:HEC1001
|
3.5
|
19.7
|
1.0
|
|
ND1
|
A:HIS18
|
3.9
|
15.9
|
1.0
|
|
ND1
|
A:HIS44
|
4.0
|
16.6
|
1.0
|
|
CG
|
A:HIS18
|
4.0
|
17.6
|
1.0
|
|
CG
|
A:HIS44
|
4.0
|
16.6
|
1.0
|
|
C2D
|
A:HEC1001
|
4.2
|
20.4
|
1.0
|
|
C3A
|
A:HEC1001
|
4.3
|
16.6
|
1.0
|
|
C2A
|
A:HEC1001
|
4.3
|
16.2
|
1.0
|
|
C3D
|
A:HEC1001
|
4.3
|
20.8
|
1.0
|
|
C2B
|
A:HEC1001
|
4.3
|
18.3
|
1.0
|
|
C2C
|
A:HEC1001
|
4.3
|
18.9
|
1.0
|
|
C3B
|
A:HEC1001
|
4.3
|
18.3
|
1.0
|
|
C3C
|
A:HEC1001
|
4.3
|
18.2
|
1.0
|
|
CMA
|
A:HEC1002
|
4.9
|
16.7
|
1.0
|
|
Iron binding site 9 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 9 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1004
b:14.7
occ:1.00
|
FE
|
B:HEC1004
|
0.0
|
14.7
|
1.0
|
|
N
|
B:NO21
|
1.8
|
15.3
|
1.0
|
|
NZ
|
B:LYS188
|
1.9
|
15.7
|
1.0
|
|
NC
|
B:HEC1004
|
2.0
|
14.0
|
1.0
|
|
ND
|
B:HEC1004
|
2.0
|
13.7
|
1.0
|
|
NA
|
B:HEC1004
|
2.0
|
14.6
|
1.0
|
|
NB
|
B:HEC1004
|
2.0
|
15.1
|
1.0
|
|
O2
|
B:NO21
|
2.8
|
16.9
|
1.0
|
|
O1
|
B:NO21
|
2.9
|
16.9
|
1.0
|
|
C1C
|
B:HEC1004
|
2.9
|
14.5
|
1.0
|
|
C4B
|
B:HEC1004
|
3.0
|
15.2
|
1.0
|
|
C1D
|
B:HEC1004
|
3.0
|
14.4
|
1.0
|
|
C1A
|
B:HEC1004
|
3.0
|
15.5
|
1.0
|
|
C4C
|
B:HEC1004
|
3.0
|
13.8
|
1.0
|
|
CE
|
B:LYS188
|
3.0
|
16.3
|
1.0
|
|
C4D
|
B:HEC1004
|
3.0
|
14.5
|
1.0
|
|
C4A
|
B:HEC1004
|
3.1
|
14.5
|
1.0
|
|
C1B
|
B:HEC1004
|
3.1
|
15.4
|
1.0
|
|
CHC
|
B:HEC1004
|
3.3
|
15.1
|
1.0
|
|
CHA
|
B:HEC1004
|
3.4
|
14.9
|
1.0
|
|
CHB
|
B:HEC1004
|
3.4
|
14.9
|
1.0
|
|
CHD
|
B:HEC1004
|
3.4
|
13.3
|
1.0
|
|
C2C
|
B:HEC1004
|
4.2
|
12.6
|
1.0
|
|
C2D
|
B:HEC1004
|
4.2
|
13.2
|
1.0
|
|
C3A
|
B:HEC1004
|
4.2
|
15.6
|
1.0
|
|
C3C
|
B:HEC1004
|
4.2
|
13.0
|
1.0
|
|
C2A
|
B:HEC1004
|
4.2
|
14.3
|
1.0
|
|
C3B
|
B:HEC1004
|
4.2
|
14.7
|
1.0
|
|
C3D
|
B:HEC1004
|
4.3
|
12.8
|
1.0
|
|
C2B
|
B:HEC1004
|
4.3
|
15.6
|
1.0
|
|
CD
|
B:LYS188
|
4.4
|
14.7
|
1.0
|
|
OH
|
B:TYR303
|
4.5
|
20.8
|
1.0
|
|
NE2
|
B:HIS361
|
4.5
|
15.7
|
1.0
|
|
O
|
B:HOH900
|
4.5
|
17.9
|
1.0
|
|
CMD
|
B:HEC1006
|
4.8
|
13.2
|
1.0
|
|
NH2
|
B:ARG131
|
4.9
|
16.0
|
1.0
|
|
O
|
B:HOH891
|
4.9
|
16.3
|
1.0
|
|
O
|
B:HOH1089
|
5.0
|
15.6
|
1.0
|
|
Iron binding site 10 out
of 16 in 3rkh
Go back to
Iron Binding Sites List in 3rkh
Iron binding site 10 out
of 16 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite (Full Occupancy)
 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 A Complex with Nitrite (Full Occupancy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1005
b:14.9
occ:1.00
|
FE
|
B:HEC1005
|
0.0
|
14.9
|
1.0
|
|
NE2
|
B:HIS231
|
1.9
|
12.6
|
1.0
|
|
NE2
|
B:HIS398
|
2.0
|
14.5
|
1.0
|
|
NA
|
B:HEC1005
|
2.0
|
14.6
|
1.0
|
|
NB
|
B:HEC1005
|
2.0
|
16.6
|
1.0
|
|
ND
|
B:HEC1005
|
2.0
|
14.8
|
1.0
|
|
NC
|
B:HEC1005
|
2.0
|
15.4
|
1.0
|
|
CD2
|
B:HIS398
|
2.9
|
13.0
|
1.0
|
|
CD2
|
B:HIS231
|
2.9
|
13.7
|
1.0
|
|
CE1
|
B:HIS231
|
3.0
|
14.1
|
1.0
|
|
C4A
|
B:HEC1005
|
3.0
|
14.0
|
1.0
|
|
CE1
|
B:HIS398
|
3.0
|
16.5
|
1.0
|
|
C1D
|
B:HEC1005
|
3.0
|
12.2
|
1.0
|
|
C1B
|
B:HEC1005
|
3.0
|
14.6
|
1.0
|
|
C4B
|
B:HEC1005
|
3.0
|
13.9
|
1.0
|
|
C4C
|
B:HEC1005
|
3.0
|
14.0
|
1.0
|
|
C1C
|
B:HEC1005
|
3.0
|
13.1
|
1.0
|
|
C4D
|
B:HEC1005
|
3.0
|
13.8
|
1.0
|
|
C1A
|
B:HEC1005
|
3.1
|
13.9
|
1.0
|
|
CHB
|
B:HEC1005
|
3.4
|
13.6
|
1.0
|
|
CHD
|
B:HEC1005
|
3.4
|
12.8
|
1.0
|
|
CHC
|
B:HEC1005
|
3.4
|
12.9
|
1.0
|
|
CHA
|
B:HEC1005
|
3.5
|
12.8
|
1.0
|
|
ND1
|
B:HIS231
|
4.1
|
13.5
|
1.0
|
|
CG
|
B:HIS231
|
4.1
|
14.3
|
1.0
|
|
ND1
|
B:HIS398
|
4.1
|
16.4
|
1.0
|
|
CG
|
B:HIS398
|
4.1
|
16.3
|
1.0
|
|
C3A
|
B:HEC1005
|
4.2
|
13.6
|
1.0
|
|
C2B
|
B:HEC1005
|
4.2
|
14.5
|
1.0
|
|
C3B
|
B:HEC1005
|
4.2
|
13.6
|
1.0
|
|
C2A
|
B:HEC1005
|
4.2
|
13.8
|
1.0
|
|
C2C
|
B:HEC1005
|
4.2
|
15.0
|
1.0
|
|
C3D
|
B:HEC1005
|
4.2
|
13.1
|
1.0
|
|
C2D
|
B:HEC1005
|
4.2
|
13.9
|
1.0
|
|
C3C
|
B:HEC1005
|
4.3
|
12.4
|
1.0
|
|
Reference:
A.A.Trofimov,
K.M.Polyakov,
T.V.Tikhonova,
A.V.Tikhonov,
T.N.Safonova,
K.M.Boyko,
P.V.Dorovatovskii,
V.O.Popov.
Covalent Modifications of the Catalytic Tyrosine in Octahaem Cytochrome C Nitrite Reductase and Their Effect on the Enzyme Activity. Acta Crystallogr.,Sect.D V. 68 144 2012.
ISSN: ISSN 0907-4449
PubMed: 22281743
DOI: 10.1107/S0907444911052632
Page generated: Sun Aug 4 19:19:54 2024
|
