Zinc in PDB 4la2: Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq

The structure of Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq, PDB code: 4la2 was solved by Y.Zhang, C.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.34 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.383, 85.303, 87.457, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 21.6

The binding sites of Zinc atom in the Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq (pdb code 4la2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq, PDB code: 4la2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:22.3 occ:1.00 NE2 A:HIS163 2.2 17.9 1.0 NE2 A:HIS125 2.2 18.4 1.0 OE1 A:GLU129 2.2 19.0 1.0 OE2 A:GLU129 2.3 16.9 1.0 O1S A:MES202 2.4 38.9 1.0 O2S A:MES202 2.4 39.3 1.0 S A:MES202 2.5 54.6 1.0 OH A:TYR131 2.5 18.4 0.4 CD A:GLU129 2.6 17.4 1.0 CE1 A:HIS163 3.0 19.6 1.0 CD2 A:HIS125 3.1 16.6 1.0 CD2 A:HIS163 3.2 19.5 1.0 CE1 A:HIS125 3.2 16.8 1.0 CZ A:TYR131 3.5 17.7 0.4 O3S A:MES202 3.8 38.8 1.0 C8 A:MES202 4.0 40.4 1.0 CE1 A:TYR131 4.0 17.8 0.6 CE2 A:TYR131 4.0 17.8 0.4 NE2 A:HIS123 4.0 22.2 1.0 CG A:GLU129 4.0 18.1 1.0 CD2 A:HIS123 4.1 22.1 1.0 ND1 A:HIS163 4.2 18.2 1.0 CG A:HIS163 4.3 17.2 1.0 CG A:HIS125 4.3 16.2 1.0 ND1 A:HIS125 4.3 16.7 1.0 CD2 A:HIS157 4.4 19.6 1.0 OH A:TYR131 4.4 16.8 0.6 NE1 A:TRP178 4.5 15.5 1.0 CE1 A:TYR131 4.6 18.4 0.4 O A:HOH463 4.6 41.1 1.0 CB A:GLU129 4.7 18.1 1.0 CZ A:TYR131 4.7 17.6 0.6 C7 A:MES202 4.9 43.5 1.0 CD1 A:TYR131 4.9 16.7 0.6 CZ2 A:TRP178 5.0 16.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dimethylsulphoniopropionate (Dmsp) Lyase Dddq within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:23.0 occ:1.00 OE2 B:GLU129 2.2 19.9 1.0 NE2 B:HIS163 2.2 18.9 1.0 NE2 B:HIS125 2.2 19.8 1.0 OE1 B:GLU129 2.3 16.1 1.0 O1S B:MES202 2.4 46.8 1.0 OH B:TYR131 2.5 18.9 0.4 CD B:GLU129 2.5 17.9 1.0 S B:MES202 2.6 58.9 1.0 O2S B:MES202 2.6 50.5 1.0 CE1 B:HIS163 3.1 22.5 1.0 CD2 B:HIS125 3.2 16.6 1.0 CD2 B:HIS163 3.2 19.9 1.0 CE1 B:HIS125 3.2 16.3 1.0 CZ B:TYR131 3.5 19.4 0.4 O3S B:MES202 3.7 49.5 1.0 C8 B:MES202 3.8 47.4 1.0 CE1 B:TYR131 3.9 19.6 0.6 NE2 B:HIS123 3.9 22.4 1.0 CG B:GLU129 4.0 16.1 1.0 CE1 B:TYR131 4.1 20.5 0.4 CD2 B:HIS123 4.2 22.4 1.0 ND1 B:HIS163 4.2 19.8 1.0 CG B:HIS163 4.3 17.3 1.0 ND1 B:HIS125 4.3 16.2 1.0 CG B:HIS125 4.3 17.1 1.0 CD2 B:HIS157 4.4 21.2 1.0 CE2 B:TYR131 4.4 19.9 0.4 OH B:TYR131 4.4 19.5 0.6 NE1 B:TRP178 4.5 17.5 1.0 O B:HOH428 4.5 41.1 1.0 CB B:GLU129 4.6 15.0 1.0 CZ B:TYR131 4.7 19.4 0.6 CD1 B:TYR131 4.9 19.9 0.6 CZ2 B:TRP178 5.0 17.6 1.0 NE2 B:HIS157 5.0 27.4 1.0

C.Li, T.Wei, S.Zhang, X.Chen, X.Gao, P.Wang, B.Xie, H.Su, Q.Qin, X.Zhang, J.Yu, H.Zhang, B.Zhou, G.Yang, Y.Zhang. Molecular Insight Into Bacterial Cleavage of Oceanic Dimethylsulfoniopropionate Into Dimethyl Sulfide Proc.Natl.Acad.Sci.Usa V. 111 1026 2014.
ISSN: ISSN 0027-8424
PubMed: 24395783
DOI: 10.1073/PNAS.1312354111