SMTL ID : 3wkp.1

C135A mutant of Geobacillus thermodenitrificans copper-containing nitrite reductase in complex with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

12 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.95, A:H.143 CU.2: 6 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, H.294 Ligands: NO2.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.100, A:H.134, B:H.294 CU.3: 2 residues within 4Å: Chain A: H.42, H.83 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.7, H2O.8 CU.4: 1 residues within 4Å: Chain A: H.39 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.39 CU.8: 5 residues within 4Å: Chain B: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.95, B:H.143 CU.9: 6 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, H.294 Ligands: NO2.12 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.100, B:H.134, C:H.294 CU.10: 2 residues within 4Å: Chain B: H.42, H.83 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.16, H2O.18 CU.11: 1 residues within 4Å: Chain B: H.39 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.39 CU.15: 5 residues within 4Å: Chain C: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.95, C:H.143 CU.16: 6 residues within 4Å: Chain A: H.244, H.294 Chain C: D.98, H.100, H.134 Ligands: NO2.19 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.100, C:H.134, A:H.294 CU.17: 2 residues within 4Å: Chain C: H.42, H.83 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.25, H2O.27 CU.18: 1 residues within 4Å: Chain C: H.39 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.39

3 x NO2: NITRITE ION(Non-covalent)

NO2.5: 9 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, V.246, V.292, H.294, F.296 Ligands: CU.2 No protein-ligand interaction detected (PLIP) NO2.12: 9 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, V.246, V.292, H.294, F.296 Ligands: CU.9 No protein-ligand interaction detected (PLIP) NO2.19: 9 residues within 4Å: Chain A: H.244, V.246, V.292, H.294, F.296 Chain C: D.98, H.100, H.134 Ligands: CU.16 No protein-ligand interaction detected (PLIP)

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 6 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.163, A:V.166 Hydrogen bonds: A:E.169 MPD.13: 6 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.163, B:V.166 Hydrogen bonds: B:E.169 MPD.20: 6 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.163, C:V.166 Hydrogen bonds: C:E.169

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain A: K.32, M.33, E.34, H.42, I.43, E.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.34, A:I.43 PEG.14: 6 residues within 4Å: Chain B: K.32, M.33, E.34, H.42, I.43, E.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.34, B:I.43 PEG.21: 6 residues within 4Å: Chain C: K.32, M.33, E.34, H.42, I.43, E.44 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.34, C:I.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., C135A mutant of Geobacillus thermodenitrificans copper-containing nitrite reductase in complex with nitrite. to be published

Release Date

2013-12-11

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase

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