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PyDISH No: 07028

PDB: 3rkh,
chainID: A, resSeq: 1004
heme type: C

distortion

Protein data

function: oxidoreductase
experiment: X-RAY DIFFRACTION
resolution: 1.83 Å

axial ligand #1: LYS

chainID: A,
resSeq: 188,
Coordination distance[Å]: 1.908
molecule: Eight-heme nitrite reductase
Organism: Thioalkalivibrio nitratireducens

axial ligand #2: NO2

chainID: A,
resSeq: 1,
Coordination distance[Å]: 1.817
molecule: NITRITE ION

List of other hemes in pdb:3rkh

ID of heme Distortion Axial ligands on heme Function & structure
3rkh-A-1005
sad. +1.07
ruf. -0.37
dom. -0.00
bre. +0.14
HIS chainID: A,
resSeq: 231,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 456.0 Å3
d(Fe-oop): 0.039 Å
HIS chainID: A, resSeq: 398,
molecule: Eight-heme nitrite reductase
3rkh-A-1006
sad. -0.25
ruf. -0.78
dom. +0.25
bre. -0.04
HIS chainID: A,
resSeq: 119,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 391.0 Å3
d(Fe-oop): 0.030 Å
HIS chainID: A, resSeq: 300,
molecule: Eight-heme nitrite reductase
3rkh-A-1007
sad. +0.78
ruf. -0.64
dom. -0.12
bre. +0.08
HIS chainID: A,
resSeq: 383,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 399.0 Å3
d(Fe-oop): 0.020 Å
HIS chainID: A, resSeq: 491,
molecule: Eight-heme nitrite reductase
3rkh-A-1008
sad. -0.35
ruf. -0.99
dom. +0.24
bre. +0.00
HIS chainID: A,
resSeq: 372,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 513.0 Å3
d(Fe-oop): 0.053 Å
HIS chainID: A, resSeq: 415,
molecule: Eight-heme nitrite reductase
3rkh-A-1002
sad. -0.14
ruf. -0.44
dom. +0.03
bre. -0.05
HIS chainID: A,
resSeq: 39,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 337.0 Å3
d(Fe-oop): 0.037 Å
HIS chainID: A, resSeq: 234,
molecule: Eight-heme nitrite reductase
3rkh-A-1003
sad. +0.38
ruf. -0.49
dom. +0.00
bre. +0.07
HIS chainID: A,
resSeq: 30,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 487.0 Å3
d(Fe-oop): 0.033 Å
HIS chainID: A, resSeq: 70,
molecule: Eight-heme nitrite reductase
3rkh-A-1001
sad. +0.02
ruf. -0.38
dom. +0.02
bre. -0.17
HIS chainID: A,
resSeq: 18,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 413.0 Å3
d(Fe-oop): 0.059 Å
HIS chainID: A, resSeq: 44,
molecule: Eight-heme nitrite reductase
3rkh-B-1004
sad. +0.54
ruf. -0.53
dom. +0.12
bre. +0.01
LYS chainID: B,
resSeq: 188,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 377.0 Å3
d(Fe-oop): 0.020 Å
NO2 chainID: B, resSeq: 1,
molecule: NITRITE ION
3rkh-B-1005
sad. +1.14
ruf. -0.39
dom. -0.01
bre. +0.11
HIS chainID: B,
resSeq: 231,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 472.0 Å3
d(Fe-oop): 0.041 Å
HIS chainID: B, resSeq: 398,
molecule: Eight-heme nitrite reductase
3rkh-B-1006
sad. -0.23
ruf. -0.81
dom. +0.22
bre. +0.07
HIS chainID: B,
resSeq: 119,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 409.0 Å3
d(Fe-oop): 0.030 Å
HIS chainID: B, resSeq: 300,
molecule: Eight-heme nitrite reductase
3rkh-B-1007
sad. +0.76
ruf. -0.68
dom. -0.10
bre. +0.06
HIS chainID: B,
resSeq: 383,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 405.0 Å3
d(Fe-oop): 0.049 Å
HIS chainID: B, resSeq: 491,
molecule: Eight-heme nitrite reductase
3rkh-B-1008
sad. -0.32
ruf. -0.96
dom. +0.22
bre. +0.12
HIS chainID: B,
resSeq: 372,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 526.0 Å3
d(Fe-oop): 0.051 Å
HIS chainID: B, resSeq: 415,
molecule: Eight-heme nitrite reductase
3rkh-B-1002
sad. -0.16
ruf. -0.48
dom. +0.03
bre. -0.06
HIS chainID: B,
resSeq: 39,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 334.0 Å3
d(Fe-oop): 0.031 Å
HIS chainID: B, resSeq: 234,
molecule: Eight-heme nitrite reductase
3rkh-B-1003
sad. +0.34
ruf. -0.48
dom. +0.02
bre. +0.13
HIS chainID: B,
resSeq: 30,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 501.0 Å3
d(Fe-oop): 0.015 Å
HIS chainID: B, resSeq: 70,
molecule: Eight-heme nitrite reductase
3rkh-B-1001
sad. -0.13
ruf. -0.39
dom. -0.03
bre. -0.19
HIS chainID: B,
resSeq: 18,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 392.0 Å3
d(Fe-oop): 0.010 Å
HIS chainID: B, resSeq: 44,
molecule: Eight-heme nitrite reductase