SMTL ID : 3s1s.1

Characterization and crystal structure of the type IIG restriction endonuclease BpuSI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 24 residues within 4Å: Chain A: H.284, H.293, E.294, G.295, P.328, A.329, A.330, G.331, S.332, G.333, N.334, L.335, D.355, I.356, E.357, F.360, D.388, V.389, N.406, P.408, K.421, F.422, F.447 Ligands: IOD.59 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:H.284, A:S.332, A:S.332, A:G.333, A:N.334, A:L.335, A:I.356, A:D.388, A:V.389, A:K.421 Water bridges: A:H.293, A:D.327, A:L.336, A:N.406 pi-Stacking: A:F.447

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: E.588, W.589, N.592, N.593 Ligand excluded by PLIP EDO.3: 1 residues within 4Å: Chain A: Y.224 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: M.347, R.349, N.380 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: V.215, E.216, V.376, S.377 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: S.82, D.277, N.334, A.337, T.338, R.367, L.371 Ligands: EDO.17 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: R.228, P.229, G.230, E.249 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: V.697, K.703, K.704 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: P.138, I.139, V.140, R.272 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: E.204, D.221, A.222, I.223, V.260, L.263, S.264 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: R.317, G.458 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: T.87, R.88, L.91 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: D.240, F.241, N.242, V.243, S.365, A.381, P.382, I.384 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: R.433 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: E.30, H.50 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: G.486, N.487, G.517 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: Y.17, T.80, S.82, K.305, T.338 Ligands: EDO.6, IOD.60 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: F.438, G.439, N.475 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: G.617, A.618, S.619 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: E.234, R.237, F.245 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: L.53, G.55, M.852 Ligands: IOD.27 Ligand excluded by PLIP

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.22: 4 residues within 4Å: Chain A: E.21, D.60, E.76, V.77 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.21, A:D.60, A:E.76, A:V.77, H2O.5, H2O.9

38 x IOD: IODIDE ION(Non-functional Binders)

IOD.23: 4 residues within 4Å: Chain A: Q.468, P.871, E.872, Q.875 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: F.695, K.699 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain A: Y.173 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: T.147, V.148 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain A: S.56, R.834, V.835 Ligands: EDO.21 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain A: H.538, K.541, R.542 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: K.64, K.103 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain A: V.602, L.608, Q.800 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain A: E.567 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain A: R.88, G.500, L.501 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain A: R.237, N.242 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain A: E.726 Ligand excluded by PLIP IOD.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.36: 4 residues within 4Å: Chain A: R.736, R.737, S.738, R.740 Ligand excluded by PLIP IOD.37: 1 residues within 4Å: Chain A: E.395 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain A: H.826, R.836 Ligand excluded by PLIP IOD.39: 3 residues within 4Å: Chain A: F.372, P.373, Q.374 Ligand excluded by PLIP IOD.40: 4 residues within 4Å: Chain A: R.610, R.733, L.755, K.796 Ligand excluded by PLIP IOD.41: 3 residues within 4Å: Chain A: L.643, E.660, R.666 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain A: H.424, K.425, Q.428 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain A: L.437 Ligand excluded by PLIP IOD.44: 2 residues within 4Å: Chain A: V.650, N.753 Ligand excluded by PLIP IOD.45: 3 residues within 4Å: Chain A: R.736, G.790, E.791 Ligand excluded by PLIP IOD.46: 4 residues within 4Å: Chain A: A.618, Y.692, F.705, K.707 Ligand excluded by PLIP IOD.47: 3 residues within 4Å: Chain A: V.410, D.415, I.418 Ligand excluded by PLIP IOD.48: 4 residues within 4Å: Chain A: S.176, T.177, L.266, L.269 Ligand excluded by PLIP IOD.49: 2 residues within 4Å: Chain A: V.217, P.218 Ligand excluded by PLIP IOD.50: 4 residues within 4Å: Chain A: R.498, E.499, E.504, V.505 Ligand excluded by PLIP IOD.51: 2 residues within 4Å: Chain A: H.107, H.122 Ligand excluded by PLIP IOD.52: 1 residues within 4Å: Chain A: N.539 Ligand excluded by PLIP IOD.53: 3 residues within 4Å: Chain A: S.176, N.179, L.262 Ligand excluded by PLIP IOD.54: 3 residues within 4Å: Chain A: R.207, R.211, N.267 Ligand excluded by PLIP IOD.55: 2 residues within 4Å: Chain A: E.795, S.798 Ligand excluded by PLIP IOD.56: 2 residues within 4Å: Chain A: A.158, N.161 Ligand excluded by PLIP IOD.57: 3 residues within 4Å: Chain A: E.247, P.248, E.249 Ligand excluded by PLIP IOD.58: 2 residues within 4Å: Chain A: S.12, Y.13 Ligand excluded by PLIP IOD.59: 4 residues within 4Å: Chain A: D.300, L.335, N.406 Ligands: SAH.1 Ligand excluded by PLIP IOD.60: 4 residues within 4Å: Chain A: Y.17, K.81, S.82 Ligands: EDO.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, B.W. et al., Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI. Nucleic Acids Res. (2011)

Release Date

2011-07-13

Peptides

restriction endonuclease BpuSI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

restriction endonuclease BpuSI