SMTL ID : 4qh0.5 (5 other biounits)

Crystal structure of NucA from Streptococcus agalactiae with magnesium ion bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.143, N.154, E.157 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: N.143, E.157 No protein-ligand interaction detected (PLIP)

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

SO4.2: 3 residues within 4Å: Chain A: K.123, G.124, W.125 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.124 Water bridges: A:K.123, A:K.123, A:W.125, A:W.125 Salt bridges: A:K.123 SO4.3: 5 residues within 4Å: Chain A: H.103, Y.104, S.145, N.146, Q.147 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.104, A:Y.104, A:N.146, A:Q.147, A:Q.147 Salt bridges: A:H.103 SO4.4: 2 residues within 4Å: Chain A: N.31, R.151 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.31 Water bridges: A:N.39, A:R.151, A:R.151, A:R.151 Salt bridges: A:R.151 SO4.5: 1 residues within 4Å: Chain A: H.96 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.96 SO4.6: 3 residues within 4Å: Chain A: N.101, D.102, H.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.103 Salt bridges: A:H.103 SO4.10: 4 residues within 4Å: Chain A: T.56, T.65 Chain B: N.59, Q.60 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.59, B:Q.60 Water bridges: B:N.59, A:T.65, A:T.65, A:N.67, A:N.67, A:N.67 SO4.11: 6 residues within 4Å: Chain B: H.103, Y.104, Q.144, S.145, N.146, Q.147 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.104, B:N.146, B:Q.147, B:Q.147 Salt bridges: B:H.103 SO4.12: 3 residues within 4Å: Chain B: I.57, D.58, N.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.59 Water bridges: B:N.59, B:S.64 SO4.13: 2 residues within 4Å: Chain B: W.95, Q.97 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.97, B:Q.97 Salt bridges: B:K.91 SO4.14: 4 residues within 4Å: Chain B: R.80, A.112, A.115, Y.116 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.116 Water bridges: B:R.80, B:A.112, B:A.117, B:N.143, B:N.143, B:N.143, B:N.143 Salt bridges: B:R.80 SO4.15: 2 residues within 4Å: Chain B: E.35, R.151 8 PLIP interactions: 8 interactions with chain B Water bridges: B:E.35, B:N.39, B:N.39, B:R.151, B:R.151, B:Y.155, B:Y.156 Salt bridges: B:R.151

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: Y.104, H.141, Q.210, A.211 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.72 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: N.44, R.171 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: K.168, R.169, Q.196, D.197 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Moon, A.F. et al., Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-11-19

Peptides

DNA-entry nuclease (Competence-specific nuclease): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

DNA-entry nuclease (Competence-specific nuclease)

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