SMTL ID : 1ux1.1

Bacillus subtilis cytidine deaminase with a Cys53His and an Arg56Gln substitution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

4 x THU: TETRAHYDRODEOXYURIDINE(Non-covalent)

THU.1: 16 residues within 4Å: Chain A: S.22, F.24, V.26, N.42, E.44, H.53, A.54, E.55, P.85, C.86, C.89 Chain B: F.125 Chain C: A.46, A.47, Y.48 Ligands: ZN.2 8 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:F.125 Hydrogen bonds: A:N.42, A:E.44, A:A.54, A:E.55, A:C.86, C:A.46, C:Y.48 THU.4: 16 residues within 4Å: Chain A: F.125, L.130 Chain B: S.22, F.24, V.26, N.42, E.44, H.53, A.54, E.55, P.85, C.86, C.89 Chain D: A.46, Y.48 Ligands: ZN.5 7 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:N.42, B:A.54, B:E.55, B:C.86, D:A.46, D:Y.48 Hydrophobic interactions: A:F.125 THU.6: 16 residues within 4Å: Chain A: A.46, A.47, Y.48 Chain C: S.22, F.24, V.26, N.42, E.44, H.53, A.54, E.55, P.85, C.86, C.89 Chain D: F.125 Ligands: ZN.7 8 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: D:F.125 Hydrogen bonds: C:N.42, C:E.44, C:A.54, C:E.55, C:C.86, A:A.46, A:Y.48 THU.8: 16 residues within 4Å: Chain B: A.46, A.47, Y.48 Chain C: F.125 Chain D: S.22, F.24, V.26, N.42, E.44, H.53, A.54, E.55, P.85, C.86, C.89 Ligands: ZN.9 7 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: C:F.125 Hydrogen bonds: D:N.42, D:A.54, D:E.55, D:C.86, B:A.46, B:Y.48

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.53, E.55, C.86, C.89 Ligands: THU.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.53, A:C.86, A:C.89 ZN.5: 5 residues within 4Å: Chain B: H.53, E.55, C.86, C.89 Ligands: THU.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.53, B:C.86, B:C.89 ZN.7: 5 residues within 4Å: Chain C: H.53, E.55, C.86, C.89 Ligands: THU.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.53, C:C.86, C:C.89 ZN.9: 5 residues within 4Å: Chain D: H.53, E.55, C.86, C.89 Ligands: THU.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.53, D:C.86, D:C.89

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

TRS.3: 3 residues within 4Å: Chain A: D.15, A.17, Q.25 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.17, A:Q.25 Water bridges: A:D.15, A:A.19, A:Q.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, E. et al., Structural, Kinetic, and Mutational Studies of the Zinc Ion Environment in Tetrameric Cytidine Deaminase. Biochemistry (2004)

Release Date

2004-05-20

Peptides

CYTIDINE DEAMINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CYTIDINE DEAMINASE