SMTL ID : 1gq1.1

CYTOCHROME CD1 NITRITE REDUCTASE, Y25S mutant, OXIDISED FORM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: D.16, H.17, N.23, R.64, C.65, C.68, H.69, G.78, K.79, L.81, L.89, Y.93, L.94, F.97, S.102, P.103, L.127 Ligands: GOL.4 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:D.16, A:N.23, A:L.81, A:L.81, A:L.94, A:F.97, A:P.103, A:L.127 Hydrogen bonds: A:K.79 Water bridges: A:K.79, A:K.79 Salt bridges: A:K.79 Metal complexes: A:H.17, A:H.69 HEC.8: 19 residues within 4Å: Chain B: D.16, H.17, N.23, R.64, C.65, C.68, H.69, G.78, K.79, L.81, L.89, Y.93, L.94, F.97, I.98, S.102, P.103, M.123 Ligands: GOL.11 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:D.16, B:N.23, B:K.79, B:L.81, B:L.81, B:L.94, B:F.97, B:I.98, B:P.103 Hydrogen bonds: B:K.79, B:Y.93 Water bridges: B:K.79, B:A.80 Salt bridges: B:K.79 Metal complexes: B:H.17, B:H.69

2 x DHE: HEME D(Non-covalent)

DHE.2: 26 residues within 4Å: Chain A: S.25, P.27, S.28, M.106, W.109, R.174, H.200, I.201, R.203, R.216, R.243, S.244, I.245, Y.263, A.301, A.302, I.303, H.345, R.391, F.444, Q.507, W.522, T.554, G.555, F.557 Ligands: SO4.3 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:W.109, A:I.201, A:I.201, A:R.243, A:R.243, A:F.444, A:F.444, A:W.522, A:T.554, A:F.557 Hydrogen bonds: A:S.28, A:I.245, A:Y.263, A:Y.263, A:I.303, A:Q.507 Water bridges: A:R.174, A:R.174, A:R.203, A:R.203, A:R.203, A:R.203, A:K.446, A:K.446, A:K.446, A:G.555 Salt bridges: A:R.174, A:H.200, A:H.200, A:R.203, A:R.203, A:R.216, A:R.243, A:R.391, A:K.446 Metal complexes: A:H.200 DHE.9: 27 residues within 4Å: Chain B: S.25, E.26, P.27, S.28, M.106, W.109, R.174, H.200, I.201, R.203, R.216, R.243, S.244, I.245, Y.263, A.301, A.302, I.303, H.345, R.391, F.444, Q.507, W.522, T.554, G.555, F.557 Ligands: SO4.10 36 PLIP interactions: 36 interactions with chain B, Hydrophobic interactions: B:W.109, B:I.201, B:I.201, B:R.243, B:R.243, B:F.444, B:F.444, B:W.522, B:T.554, B:F.557 Hydrogen bonds: B:S.28, B:I.245, B:Y.263, B:I.303, B:Q.507, B:T.554 Water bridges: B:R.174, B:R.174, B:R.203, B:R.203, B:R.203, B:R.203, B:K.446, B:K.446, B:K.446, B:G.555 Salt bridges: B:R.174, B:H.200, B:H.200, B:R.203, B:R.203, B:R.216, B:R.243, B:R.391, B:K.446 Metal complexes: B:H.200

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

SO4.3: 4 residues within 4Å: Chain A: S.25, H.345, H.388 Ligands: DHE.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.345, A:H.388 SO4.6: 6 residues within 4Å: Chain A: Y.289, D.290, E.291, Q.292 Chain B: M.139, R.143 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.292, B:R.143 Water bridges: B:K.279 SO4.7: 3 residues within 4Å: Chain A: Q.35, K.237, S.240 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.35, A:S.240 Water bridges: A:S.240, A:S.240, A:S.240 Salt bridges: A:K.237 SO4.10: 4 residues within 4Å: Chain B: S.25, H.345, H.388 Ligands: DHE.9 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.25, B:D.346 Salt bridges: B:H.345, B:H.388 SO4.12: 3 residues within 4Å: Chain B: Y.308, R.354, K.372 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.308, B:Y.308 Water bridges: B:R.354, B:R.354, B:R.354 Salt bridges: B:R.354, B:K.372 SO4.13: 4 residues within 4Å: Chain B: N.31, Q.35, K.237, S.240 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.31, B:Q.35, B:S.240 Water bridges: B:N.31, B:Q.34, B:S.240, B:S.240 Salt bridges: B:K.237 SO4.14: 3 residues within 4Å: Chain B: F.395, V.396, P.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.396 Water bridges: B:P.449 SO4.15: 4 residues within 4Å: Chain B: G.439, G.440, N.461, I.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.440, B:N.461 Water bridges: B:D.412

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 13 residues within 4Å: Chain A: N.23, R.24, S.25, E.26, P.27, S.28, E.63, R.64, P.103, A.104, G.105, T.111 Ligands: HEC.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.23, A:E.26, A:E.26 Water bridges: A:S.28, A:G.67, A:M.106 GOL.5: 5 residues within 4Å: Chain A: F.395, V.396, P.449, S.451, I.475 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.396, A:P.449 GOL.11: 12 residues within 4Å: Chain B: N.23, R.24, S.25, E.26, P.27, E.63, R.64, P.103, A.104, G.105, T.111 Ligands: HEC.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.23, B:E.26, B:E.26 Water bridges: B:S.28, B:M.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gordon, E.H.J. et al., Structure and Kinetic Properties of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase with the D1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine. J.Biol.Chem. (2003)

Release Date

2002-11-28

Peptides

CYTOCHROME CD1 NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYTOCHROME CD1 NITRITE REDUCTASE