SMTL ID : 4yio.1

X-ray structure of the iron/manganese cambialistic superoxide dismutase from Streptococcus thermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.27, H.81, D.163, H.167 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.27, A:H.81, A:D.163, A:H.167, H2O.3 FE.9: 4 residues within 4Å: Chain B: H.27, H.81, D.163, H.167 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.27, B:H.81, B:D.163, B:H.167, H2O.13

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

SO4.2: 2 residues within 4Å: Chain A: R.124, P.146 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.124 SO4.3: 3 residues within 4Å: Chain A: E.61, A.65, R.68 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.68 SO4.4: 3 residues within 4Å: Chain A: K.30 Chain B: N.175, V.176 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:T.34, B:N.175 Salt bridges: A:K.30 Hydrogen bonds: B:N.175 SO4.5: 2 residues within 4Å: Chain A: E.141, K.156 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.154, A:K.156 Salt bridges: A:K.156 SO4.10: 2 residues within 4Å: Chain B: R.124, P.146 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.144, B:S.144 Salt bridges: B:R.124 SO4.11: 2 residues within 4Å: Chain B: A.65, R.68 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.65, B:R.68 Salt bridges: B:R.68

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: D.20, E.22, L.171, K.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.20, A:K.172 Water bridges: A:E.22 GOL.7: 4 residues within 4Å: Chain A: N.104, S.109, F.110, E.111 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.104, A:S.109, A:F.110, A:E.111 Water bridges: A:S.109 GOL.8: 3 residues within 4Å: Chain A: A.11, Y.12, D.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.12, A:D.13, A:D.13 Water bridges: A:D.13 GOL.12: 5 residues within 4Å: Chain B: S.120, T.123, V.142, V.143, S.144 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.144, B:S.144 Water bridges: B:T.123, B:R.124, B:V.142 GOL.13: 3 residues within 4Å: Chain B: A.11, Y.12, D.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.12, B:D.13, B:D.13 Water bridges: B:Y.10 GOL.14: 7 residues within 4Å: Chain B: K.92, Q.93, E.94, P.95, F.110, F.185, W.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.92, B:F.185 GOL.15: 4 residues within 4Å: Chain B: D.20, E.22, L.171, K.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.22, B:E.22 Water bridges: B:E.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Russo Krauss, I. et al., Fine tuning of metal-specific activity in the Mn-like group of cambialistic superoxide dismutases. Rsc Adv (2015)

Release Date

2016-01-13

Peptides

Superoxide dismutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Superoxide dismutase