SMTL ID : 3mqy.1

SgrAI with cleaved DNA and Magnesium bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x DG- DA- DG- DT- DC- DC- DA: DNA (5'-D(*GP*AP*GP*TP*CP*CP*A)-3')(Non-covalent)

DG-DA-DG-DT-DC-DC-DA.1: 16 residues within 4Å: Chain A: R.245, S.246, D.247 Chain B: R.28, R.30, R.151, S.152 Chain C: C.1 Chain D: G.4, T.5, G.6, G.7, A.8, C.9, T.10, C.11 34 PLIP interactions: 9 interactions with chain A, 25 interactions with chain B Hydrogen bonds: A:N.91, A:N.91, A:D.247, A:D.247, B:R.151, B:R.242, B:S.243, B:R.248, B:R.30, B:R.30, B:T.32, B:Q.35, B:L.36, B:Q.38, B:Q.39, B:Q.39, B:N.91, B:N.91, B:N.91, B:N.91, B:K.95, B:K.95, B:K.95, B:K.95, B:R.212, B:D.247, B:D.247, A:R.242, A:S.243, A:R.245, A:R.248 Water bridges: B:D.187, B:D.187, B:F.240, B:F.240, B:K.241, B:K.241, B:K.241, B:K.241, B:K.241, B:K.241, B:S.31, B:S.31, B:T.32, B:A.37, B:D.89, B:D.247, A:N.91, A:K.241, A:K.241, A:K.241 Salt bridges: B:R.242, A:R.242 DG-DA-DG-DT-DC-DC-DA.2: 17 residues within 4Å: Chain A: R.30, R.151, S.152 Chain B: R.245, S.246, D.247, G.283, N.285 Chain C: G.4, T.5, G.6, G.7, A.8, C.9, T.10, C.11 Chain D: C.1 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.187, F.240 Chain D: C.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.187, A:F.240, H2O.1, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: E.102, N.148, L.149, D.187 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.102, A:L.149, A:D.187, H2O.3 MG.5: 3 residues within 4Å: Chain B: D.187, F.240 Chain C: C.1 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.187, B:F.240, H2O.6, H2O.6, H2O.6 MG.6: 4 residues within 4Å: Chain B: E.102, N.148, L.149, D.187 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.102, B:L.149, B:D.187, H2O.7 MG.7: 2 residues within 4Å: Chain B: D.187 Chain C: C.1 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.187, H2O.7, H2O.11, H2O.11, H2O.11 MG.8: 2 residues within 4Å: Chain A: D.187 Chain D: C.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.187, H2O.3, H2O.3, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Little, E.J. et al., New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA. Acta Crystallogr.,Sect.D (2011)

Release Date

2010-11-24

Peptides

SgraIR restriction enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SgraIR restriction enzyme

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