SMTL ID : 5tgq.1

Restriction-modification system Type II R.SwaI, DNA free

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.76, D.93, F.94 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.76, A:D.93, A:F.94, H2O.2, H2O.3 CA.8: 3 residues within 4Å: Chain B: D.76, D.93, F.94 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.76, B:D.93, B:F.94, H2O.5, H2O.6

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

CL.2: 6 residues within 4Å: Chain A: R.162, I.163, N.164, P.165, S.196, R.199 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: G.109, T.110, K.113 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: F.3, T.181, R.182 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: R.162, I.163, N.164, P.165, S.196, R.199 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: G.109, T.110, K.113 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: F.3, T.181, R.182 Ligand excluded by PLIP

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

TRS.5: 8 residues within 4Å: Chain A: D.42, E.45, A.66, P.67, K.68, K.70, T.71, D.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.42, A:A.66, A:T.71, A:D.76, A:D.76 TRS.12: 8 residues within 4Å: Chain B: D.42, E.45, A.66, P.67, K.68, K.70, T.71, D.76 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.42, B:A.66, B:T.71, B:D.76 Water bridges: B:D.42, B:D.42

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: K.82, F.83, M.84, D.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.85 Salt bridges: A:K.82 ACT.7: 3 residues within 4Å: Chain A: N.112, V.115, K.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.112 ACT.13: 4 residues within 4Å: Chain B: K.82, F.83, M.84, D.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.85, B:D.85 Salt bridges: B:K.82 ACT.14: 3 residues within 4Å: Chain B: N.112, V.115, K.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, B.W. et al., DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Nucleic Acids Res. (2017)

Release Date

2016-12-21

Peptides

R.SwaI protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

R.SwaI protein

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