SMTL ID : 3wnj.1

1.20 A resolution crystal structure of dioxygen bound copper-containing nitrite reductase from Geobacillus thermodenitrificans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.95, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.95, A:C.135, A:H.143 CU.2: 6 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, H.294 Ligands: OXY.8 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.134, B:H.294, H2O.13, H2O.14 CU.3: 2 residues within 4Å: Chain A: H.42, H.83 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.12 CU.4: 1 residues within 4Å: Chain A: H.39 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.39 CU.5: 1 residues within 4Å: Chain A: E.239 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.239, H2O.5, H2O.13, H2O.25 CU.6: 1 residues within 4Å: Chain A: D.167 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.167, H2O.8, H2O.10, H2O.12, H2O.14 CU.19: 4 residues within 4Å: Chain B: H.95, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.95, B:C.135, B:H.143 CU.20: 6 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, H.294 Ligands: OXY.26 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.294, B:H.100, B:H.134, H2O.27, H2O.28 CU.21: 2 residues within 4Å: Chain B: H.42, H.83 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.26 CU.22: 1 residues within 4Å: Chain B: H.39 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.39 CU.23: 1 residues within 4Å: Chain B: E.239 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.239, H2O.19, H2O.26, H2O.38 CU.24: 1 residues within 4Å: Chain B: D.167 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.167, H2O.22, H2O.23, H2O.26, H2O.27 CU.37: 4 residues within 4Å: Chain C: H.95, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.95, C:C.135, C:H.143 CU.38: 6 residues within 4Å: Chain A: H.244, H.294 Chain C: D.98, H.100, H.134 Ligands: OXY.44 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.100, C:H.134, A:H.294, H2O.40, H2O.42 CU.39: 2 residues within 4Å: Chain C: H.42, H.83 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.39 CU.40: 1 residues within 4Å: Chain C: H.39 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.39 CU.41: 1 residues within 4Å: Chain C: E.239 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.239, H2O.11, H2O.33, H2O.40 CU.42: 1 residues within 4Å: Chain C: D.167 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.167, H2O.35, H2O.37, H2O.40, H2O.41

3 x NA: SODIUM ION(Non-functional Binders)

NA.7: 1 residues within 4Å: Chain A: D.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.40 Water bridges: A:D.40 NA.25: 1 residues within 4Å: Chain B: D.40 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.40, B:D.40 NA.43: 1 residues within 4Å: Chain C: D.40 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.40 Water bridges: C:D.40

3 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.8: 8 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, V.246, H.294, F.296 Ligands: CU.2 No protein-ligand interaction detected (PLIP) OXY.26: 8 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, V.246, H.294, F.296 Ligands: CU.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.98 OXY.44: 8 residues within 4Å: Chain A: H.244, V.246, H.294, F.296 Chain C: D.98, H.100, H.134 Ligands: CU.38 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.98

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

MPD.9: 6 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.163, A:V.166 Hydrogen bonds: A:E.169 Water bridges: A:E.169, A:E.169, A:R.229, A:Y.231 MPD.27: 6 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.163, B:V.166 Hydrogen bonds: B:E.169 Water bridges: B:E.169, B:E.169, B:R.229, B:Y.231 MPD.45: 6 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:D.163, C:V.166 Hydrogen bonds: C:E.169 Water bridges: C:E.169, C:E.169, C:R.229, C:Y.231

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 3 residues within 4Å: Chain A: P.139, M.183 Chain B: Q.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.300 EDO.11: 4 residues within 4Å: Chain A: N.158, G.159, Y.160, D.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.163 Water bridges: A:N.158, A:Y.160 EDO.28: 3 residues within 4Å: Chain B: P.139, M.183 Chain C: Q.300 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.300 EDO.29: 4 residues within 4Å: Chain B: N.158, G.159, Y.160, D.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.163 Water bridges: B:N.158, B:Y.160 EDO.46: 3 residues within 4Å: Chain A: Q.300 Chain C: P.139, M.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.300 EDO.47: 4 residues within 4Å: Chain C: N.158, G.159, Y.160, D.163 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.163 Water bridges: C:N.158, C:Y.160

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 7 residues within 4Å: Chain A: N.261, H.262, L.263 Chain B: H.262, L.263 Ligands: SO4.30, SO4.48 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.262 Water bridges: A:N.260, A:H.262, B:H.262 SO4.13: 3 residues within 4Å: Chain A: M.270 Ligands: SO4.31, SO4.49 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:M.270, A:M.270 SO4.14: 3 residues within 4Å: Chain A: K.22, G.23, K.61 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.23 Water bridges: A:K.61, A:K.61, A:K.61 Salt bridges: A:K.61 SO4.30: 7 residues within 4Å: Chain B: N.261, H.262, L.263 Chain C: H.262, L.263 Ligands: SO4.12, SO4.48 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.262 Water bridges: B:N.260, B:H.262, C:H.262 SO4.31: 3 residues within 4Å: Chain B: M.270 Ligands: SO4.13, SO4.49 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:M.270, C:M.270 SO4.32: 3 residues within 4Å: Chain B: K.22, G.23, K.61 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.23 Water bridges: B:K.61, B:K.61, B:K.61 Salt bridges: B:K.61 SO4.48: 7 residues within 4Å: Chain A: H.262, L.263 Chain C: N.261, H.262, L.263 Ligands: SO4.12, SO4.30 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:H.262, C:N.260, C:H.262 Hydrogen bonds: C:H.262 SO4.49: 3 residues within 4Å: Chain C: M.270 Ligands: SO4.13, SO4.31 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:M.270, C:M.270 SO4.50: 3 residues within 4Å: Chain C: K.22, G.23, K.61 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.23 Water bridges: C:K.61, C:K.61, C:K.61 Salt bridges: C:K.61

12 x ACY: ACETIC ACID(Non-functional Binders)

ACY.15: 4 residues within 4Å: Chain A: V.140 Chain B: P.290, V.292, F.296 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.290 ACY.16: 4 residues within 4Å: Chain A: D.55, K.56, T.212, F.213 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.56, A:F.213 Hydrogen bonds: A:K.56, A:T.212 ACY.17: 5 residues within 4Å: Chain A: K.127, P.128, N.258, N.260 Chain B: Q.264 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.264, A:N.258, A:N.260 Water bridges: B:D.251, A:E.78 Hydrophobic interactions: A:K.127 Salt bridges: A:K.127 ACY.18: 6 residues within 4Å: Chain A: R.168, L.221, A.222, T.312, G.313, E.314 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.314 Hydrogen bonds: A:E.314 Salt bridges: A:R.168 ACY.33: 4 residues within 4Å: Chain B: V.140 Chain C: P.290, V.292, F.296 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.290 ACY.34: 4 residues within 4Å: Chain B: D.55, K.56, T.212, F.213 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.56, B:F.213 Hydrogen bonds: B:K.56, B:T.212 ACY.35: 5 residues within 4Å: Chain B: K.127, P.128, N.258, N.260 Chain C: Q.264 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:K.127 Hydrogen bonds: B:N.258, B:N.260, C:Q.264 Water bridges: B:E.78, C:D.251 Salt bridges: B:K.127 ACY.36: 6 residues within 4Å: Chain B: R.168, L.221, A.222, T.312, G.313, E.314 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.314 Hydrogen bonds: B:E.314 Salt bridges: B:R.168 ACY.51: 4 residues within 4Å: Chain A: P.290, V.292, F.296 Chain C: V.140 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.290 ACY.52: 4 residues within 4Å: Chain C: D.55, K.56, T.212, F.213 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.56, C:F.213 Hydrogen bonds: C:K.56, C:T.212 ACY.53: 5 residues within 4Å: Chain A: Q.264 Chain C: K.127, P.128, N.258, N.260 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:K.127 Hydrogen bonds: C:N.258, C:N.260, A:Q.264 Water bridges: C:E.78, A:D.251 Salt bridges: C:K.127 ACY.54: 6 residues within 4Å: Chain C: R.168, L.221, A.222, T.312, G.313, E.314 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.314 Hydrogen bonds: C:E.314 Salt bridges: C:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Crystallographic evidence for side-on dioxygen trapped on type 2 copper in copper-containing nitrite reductase. To be Published

Release Date

2014-12-10

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase

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