SMTL ID : 5sw4.1

Crystal structure of native catalase-peroxidase KatG at pH8.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 27 residues within 4Å: Chain A: G.84, L.85, I.87, R.88, X.91, V.219, P.221, I.237, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, T.264, H.265, T.303, S.304, L.306, W.310, L.366, T.368, F.396, W.400 Ligands: OXY.3 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:I.87, A:R.88, A:P.221, A:I.237, A:F.241, A:L.254, A:I.255, A:T.264, A:L.306, A:W.310, A:L.366, A:F.396, A:W.400 Hydrogen bonds: A:K.263, A:H.265, A:S.304 Water bridges: A:D.78, A:D.78, A:G.84, A:R.88, A:R.88, A:H.265 Salt bridges: A:R.88, A:H.265, A:H.265 Metal complexes: A:H.259 HEM.8: 24 residues within 4Å: Chain B: G.84, L.85, I.87, R.88, X.91, V.219, P.221, F.241, L.254, I.255, G.258, H.259, F.261, G.262, K.263, T.264, H.265, T.303, S.304, W.310, L.366, T.368, F.396, W.400 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:I.87, B:P.221, B:F.241, B:L.254, B:I.255, B:I.255, B:T.264, B:W.310, B:L.366, B:F.396, B:W.400 Hydrogen bonds: B:K.263, B:H.265, B:T.303, B:S.304 Water bridges: B:G.84, B:R.88, B:R.88, B:H.265 Salt bridges: B:R.88, B:H.265, B:H.265 Metal complexes: B:H.259

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

NA.2: 4 residues within 4Å: Chain A: G.102, R.103, G.104, S.474 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.104, A:D.407 Water bridges: A:G.104, A:E.108 NA.9: 4 residues within 4Å: Chain B: G.102, R.103, G.104, S.474 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.102 Water bridges: B:G.104

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 5 residues within 4Å: Chain A: R.88, X.91, H.92, D.121 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.88, A:R.88, A:H.92

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 2 residues within 4Å: Chain A: Y.181, D.599 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.103, A:R.103 PO4.10: 2 residues within 4Å: Chain B: Y.181, L.596 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.103, B:R.103, B:D.599

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

MPD.5: 5 residues within 4Å: Chain A: P.120, A.123, L.189, T.303, S.304 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.189 Hydrogen bonds: A:T.303 MPD.6: 4 residues within 4Å: Chain A: D.63, P.134, I.135, K.138 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.138 Hydrogen bonds: A:P.134 MPD.11: 5 residues within 4Å: Chain B: P.120, A.270, V.273, T.303, S.304 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.270, B:V.273 Water bridges: B:W.289

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 9 residues within 4Å: Chain A: A.100, D.101, R.472, V.573, L.574, E.575, P.576, K.600, L.603 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.100, A:R.472, A:R.472, A:K.600, A:K.600 Water bridges: A:V.577, A:V.577 TRS.12: 9 residues within 4Å: Chain B: A.100, D.101, R.472, V.573, L.574, E.575, P.576, K.600, L.603 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.100, B:R.472, B:R.472, B:K.600 Water bridges: B:S.469, B:K.600

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carpena, X. et al., A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases. EMBO Rep. (2005)

Release Date

2016-08-24

Peptides

Catalase-peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Catalase-peroxidase

Related Entries With Identical Sequence