SMTL ID : 1e7l.1

Endonuclease VII (EndoVII) N62D mutant from phage T4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: H.41, D.42, H.43, E.44, R.54, K.69 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.41, A:H.43, A:E.44 Water bridges: A:R.54, A:R.54, A:R.54, A:E.65, A:E.65 Salt bridges: A:H.43, A:R.54, A:K.69 SO4.2: 3 residues within 4Å: Chain A: G.120, K.121, K.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.121 Water bridges: A:E.122, A:E.122 Salt bridges: A:K.141 SO4.3: 3 residues within 4Å: Chain A: H.41, H.43 Chain B: N.107 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:D.40, A:H.41, A:H.41 Salt bridges: A:H.41, A:H.43 Hydrogen bonds: B:N.107 SO4.4: 3 residues within 4Å: Chain A: H.70, N.73, R.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.73 Salt bridges: A:H.70, A:R.74 SO4.5: 3 residues within 4Å: Chain A: K.121, T.140, K.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.141 Water bridges: A:T.142 Salt bridges: A:K.121 SO4.6: 3 residues within 4Å: Chain A: E.44, L.45, N.46 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.45, A:N.46, A:N.46 Water bridges: B:E.115, B:E.115 SO4.7: 3 residues within 4Å: Chain A: H.70, K.71, R.74 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.70, A:K.71, A:R.74 SO4.9: 4 residues within 4Å: Chain B: Y.8, K.12, H.38, L.39 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.8, B:L.39 Water bridges: B:N.37 Salt bridges: B:K.12, B:H.38 SO4.10: 3 residues within 4Å: Chain B: V.109, K.149, R.153 4 PLIP interactions: 4 interactions with chain B Water bridges: B:P.106, B:G.110 Salt bridges: B:K.149, B:R.153 SO4.11: 6 residues within 4Å: Chain B: H.41, D.42, H.43, R.54, E.65, K.69 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.43, B:E.65 Water bridges: B:E.44, B:R.54, B:R.54, B:K.69, B:K.69 Salt bridges: B:H.43, B:R.54, B:K.69 SO4.12: 4 residues within 4Å: Chain A: N.107 Chain B: H.38, H.41, H.43 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:H.38, B:H.41 Salt bridges: B:H.41, B:H.43 Hydrogen bonds: A:N.107 SO4.13: 3 residues within 4Å: Chain B: G.120, K.121, K.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.121 Salt bridges: B:K.141 SO4.14: 3 residues within 4Å: Chain B: K.121, T.140, K.141 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.141 Water bridges: B:T.142 Salt bridges: B:K.121 SO4.15: 3 residues within 4Å: Chain B: H.70, N.73, R.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.73 Water bridges: B:H.70 Salt bridges: B:H.70, B:R.74

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.23, A:C.26, A:C.58, A:C.61 ZN.16: 4 residues within 4Å: Chain B: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.23, B:C.26, B:C.58, B:C.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raaijmakers, H.C.A. et al., Conformational Flexibility in T4 Endonuclease Vii Revealed by Crystallography: Implications for Substrate Binding and Cleavage. J.Mol.Biol. (2001)

Release Date

2001-05-04

Peptides

RECOMBINATION ENDONUCLEASE VII: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RECOMBINATION ENDONUCLEASE VII

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