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PyDISH No: 05329

PDB: 3d1i,
chainID: A, resSeq: 1002
heme type: C

distortion

Protein data

function: oxidoreductase
experiment: X-RAY DIFFRACTION
resolution: 1.8 Å

axial ligand #1: HIS

chainID: A,
resSeq: 39,
Coordination distance[Å]: 1.918
molecule: Eight-heme nitrite reductase
Organism: Thioalkalivibrio nitratireducens

axial ligand #2: HIS

chainID: A,
resSeq: 234,
Coordination distance[Å]: 1.918
molecule: same as ligand #1

List of other hemes in pdb:3d1i

ID of heme Distortion Axial ligands on heme Function & structure
3d1i-A-1004
sad. +0.60
ruf. -0.39
dom. +0.08
bre. -0.04
LYS chainID: A,
resSeq: 188,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 414.0 Å3
d(Fe-oop): 0.019 Å
NO2 chainID: A, resSeq: 528,
molecule: NITRITE ION
3d1i-A-1005
sad. +1.11
ruf. -0.34
dom. -0.01
bre. +0.06
HIS chainID: A,
resSeq: 231,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 469.0 Å3
d(Fe-oop): 0.017 Å
HIS chainID: A, resSeq: 398,
molecule: Eight-heme nitrite reductase
3d1i-A-1006
sad. -0.18
ruf. -0.79
dom. +0.20
bre. -0.01
HIS chainID: A,
resSeq: 119,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 403.0 Å3
d(Fe-oop): 0.001 Å
HIS chainID: A, resSeq: 300,
molecule: Eight-heme nitrite reductase
3d1i-A-1007
sad. +0.74
ruf. -0.66
dom. -0.12
bre. +0.07
HIS chainID: A,
resSeq: 383,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 443.0 Å3
d(Fe-oop): 0.026 Å
HIS chainID: A, resSeq: 491,
molecule: Eight-heme nitrite reductase
3d1i-A-1008
sad. -0.34
ruf. -0.82
dom. +0.17
bre. +0.17
HIS chainID: A,
resSeq: 372,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 547.0 Å3
d(Fe-oop): 0.072 Å
HIS chainID: A, resSeq: 415,
molecule: Eight-heme nitrite reductase
3d1i-A-1003
sad. +0.45
ruf. -0.48
dom. +0.01
bre. +0.06
HIS chainID: A,
resSeq: 30,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 498.0 Å3
d(Fe-oop): 0.047 Å
HIS chainID: A, resSeq: 70,
molecule: Eight-heme nitrite reductase
3d1i-A-1001
sad. +0.07
ruf. -0.34
dom. -0.02
bre. -0.12
HIS chainID: A,
resSeq: 18,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 406.0 Å3
d(Fe-oop): 0.031 Å
HIS chainID: A, resSeq: 44,
molecule: Eight-heme nitrite reductase
3d1i-B-1004
sad. +0.55
ruf. -0.44
dom. +0.14
bre. -0.07
LYS chainID: B,
resSeq: 188,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 404.0 Å3
d(Fe-oop): 0.022 Å
NO2 chainID: B, resSeq: 528,
molecule: NITRITE ION
3d1i-B-1005
sad. +1.10
ruf. -0.33
dom. -0.01
bre. +0.07
HIS chainID: B,
resSeq: 231,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 486.0 Å3
d(Fe-oop): 0.030 Å
HIS chainID: B, resSeq: 398,
molecule: Eight-heme nitrite reductase
3d1i-B-1006
sad. -0.21
ruf. -0.84
dom. +0.23
bre. +0.06
HIS chainID: B,
resSeq: 119,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 411.0 Å3
d(Fe-oop): 0.008 Å
HIS chainID: B, resSeq: 300,
molecule: Eight-heme nitrite reductase
3d1i-B-1007
sad. +0.79
ruf. -0.68
dom. -0.14
bre. +0.07
HIS chainID: B,
resSeq: 383,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 432.0 Å3
d(Fe-oop): 0.026 Å
HIS chainID: B, resSeq: 491,
molecule: Eight-heme nitrite reductase
3d1i-B-1008
sad. -0.34
ruf. -0.80
dom. +0.18
bre. +0.12
HIS chainID: B,
resSeq: 372,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 547.0 Å3
d(Fe-oop): 0.040 Å
HIS chainID: B, resSeq: 415,
molecule: Eight-heme nitrite reductase
3d1i-B-1002
sad. -0.08
ruf. -0.39
dom. -0.01
bre. -0.08
HIS chainID: B,
resSeq: 39,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 352.0 Å3
d(Fe-oop): 0.048 Å
HIS chainID: B, resSeq: 234,
molecule: Eight-heme nitrite reductase
3d1i-B-1003
sad. +0.33
ruf. -0.50
dom. +0.01
bre. +0.06
HIS chainID: B,
resSeq: 30,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 498.0 Å3
d(Fe-oop): 0.026 Å
HIS chainID: B, resSeq: 70,
molecule: Eight-heme nitrite reductase
3d1i-B-1001
sad. -0.15
ruf. -0.39
dom. -0.05
bre. -0.11
HIS chainID: B,
resSeq: 18,
molecule: Eight-heme nitrite reductase
oxidoreductase
oligomeric count: 6
pocket vol.: 409.0 Å3
d(Fe-oop): 0.045 Å
HIS chainID: B, resSeq: 44,
molecule: Eight-heme nitrite reductase