SMTL ID : 5nc0.1

The 0.91 A resolution structure of the L16G mutant of cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitric oxide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.91 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 24 residues within 4Å: Chain A: R.12, Q.13, G.16, T.17, M.19, A.20, W.56, F.59, A.68, I.72, F.79, K.82, Q.83, F.86, S.115, C.116, C.119, H.120, Y.123, R.124 Ligands: NO.2, NO3.3, NO2.4, SO4.7 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.20, A:W.56, A:W.56, A:F.59, A:A.68, A:I.72, A:F.79, A:K.82, A:F.86, A:F.86, A:R.124 Hydrogen bonds: A:T.17, A:T.17 Water bridges: A:R.124 pi-Cation interactions: A:R.124 Metal complexes: A:H.120, NO.2 HEC.13: 24 residues within 4Å: Chain B: R.12, Q.13, G.16, T.17, M.19, A.20, W.56, F.59, A.68, I.72, F.79, K.82, Q.83, F.86, S.115, C.116, C.119, H.120, Y.123, R.124 Ligands: NO.14, NO3.15, NO2.16, SO4.19 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.20, B:W.56, B:W.56, B:F.59, B:A.68, B:I.72, B:F.79, B:K.82, B:F.86, B:F.86, B:R.124 Hydrogen bonds: B:T.17 Water bridges: B:T.17, B:R.124 pi-Cation interactions: B:R.124 Metal complexes: B:H.120, NO.14

2 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 7 residues within 4Å: Chain A: G.16, M.19, P.55, W.56, H.120 Ligands: HEC.1, NO2.4 No protein-ligand interaction detected (PLIP) NO.14: 7 residues within 4Å: Chain B: G.16, M.19, P.55, W.56, H.120 Ligands: HEC.13, NO2.16 No protein-ligand interaction detected (PLIP)

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 9 residues within 4Å: Chain A: V.9, R.12, Q.13, G.65, G.66, D.67, A.68 Ligands: HEC.1, SO4.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.9, A:R.12, A:Q.13, A:G.65, A:D.67, A:A.68 NO3.15: 9 residues within 4Å: Chain B: V.9, R.12, Q.13, G.65, G.66, D.67, A.68 Ligands: HEC.13, SO4.19 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.9, B:R.12, B:Q.13, B:G.65, B:D.67, B:A.68

4 x NO2: NITRITE ION(Non-covalent)

NO2.4: 7 residues within 4Å: Chain A: R.12, Q.13, G.16, P.55, F.59 Ligands: HEC.1, NO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.16 NO2.9: 3 residues within 4Å: Chain A: Q.81, Q.84, A.85 No protein-ligand interaction detected (PLIP) NO2.16: 7 residues within 4Å: Chain B: R.12, Q.13, G.16, P.55, F.59 Ligands: HEC.13, NO.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.16 NO2.21: 3 residues within 4Å: Chain B: Q.81, Q.84, A.85 No protein-ligand interaction detected (PLIP)

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

SO4.5: 3 residues within 4Å: Chain A: R.69, P.70, E.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.71 Salt bridges: A:R.69 SO4.6: 2 residues within 4Å: Chain A: D.103, R.106 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.103 Salt bridges: A:R.106 SO4.7: 4 residues within 4Å: Chain A: D.67, R.124 Ligands: HEC.1, NO3.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.67 Water bridges: A:R.124, A:R.124, A:K.125 Salt bridges: A:R.124 SO4.8: 4 residues within 4Å: Chain A: K.117, H.120, D.121, R.124 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.120, A:R.124 SO4.17: 3 residues within 4Å: Chain B: R.69, P.70, E.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.71 Salt bridges: B:R.69 SO4.18: 2 residues within 4Å: Chain B: D.103, R.106 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.103 Salt bridges: B:R.106 SO4.19: 4 residues within 4Å: Chain B: D.67, R.124 Ligands: HEC.13, NO3.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.67 Water bridges: B:R.124, B:R.124, B:K.125 Salt bridges: B:R.124 SO4.20: 4 residues within 4Å: Chain B: K.117, H.120, D.121, R.124 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.120, B:R.124

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

EDO.10: 3 residues within 4Å: Chain A: K.49, T.50, A.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.49, A:K.49 Water bridges: A:T.50, A:T.50 EDO.11: 2 residues within 4Å: Chain A: K.82, Y.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.82, A:K.82 Water bridges: A:Y.123, A:Y.123 EDO.12: 4 residues within 4Å: Chain A: E.46, K.49, S.94, D.98 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.49 EDO.22: 3 residues within 4Å: Chain B: K.49, T.50, A.53 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.49, B:K.49 Water bridges: B:T.50 EDO.23: 2 residues within 4Å: Chain B: K.82, Y.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.82, B:K.82 Water bridges: B:Y.123 EDO.24: 4 residues within 4Å: Chain B: E.46, K.49, S.94, D.98 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nilsson, Z.N. et al., Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory. Inorg Chem (2017)

Release Date

2018-01-10

Peptides

Cytochrome c': AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome c'

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