Zinc in PDB 3fdk: Crystal Structure of Hydrolase DR0930 with Promiscuous Catalytic Activity

The structure of Crystal Structure of Hydrolase DR0930 with Promiscuous Catalytic Activity, PDB code: 3fdk was solved by A.A.Fedorov, L.V.Fedorov, D.F.Xiang, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.83 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.505, 61.505, 205.943, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 27.7

The binding sites of Zinc atom in the Crystal Structure of Hydrolase DR0930 with Promiscuous Catalytic Activity (pdb code 3fdk). 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 Hydrolase DR0930 with Promiscuous Catalytic Activity, PDB code: 3fdk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Hydrolase DR0930 with Promiscuous Catalytic Activity


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 Hydrolase DR0930 with Promiscuous Catalytic Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.7 occ:1.00 O A:HOH363 1.8 19.3 1.0 NE2 A:HIS23 2.0 21.9 1.0 OD1 A:ASP264 2.1 22.1 1.0 OQ1 A:KCX143 2.2 21.2 1.0 NE2 A:HIS21 2.2 23.4 1.0 CX A:KCX143 2.9 23.0 1.0 CD2 A:HIS23 3.0 24.3 1.0 CE1 A:HIS23 3.0 19.3 1.0 CG A:ASP264 3.1 19.4 1.0 CD2 A:HIS21 3.1 22.2 1.0 OQ2 A:KCX143 3.2 22.7 1.0 CE1 A:HIS21 3.2 23.7 1.0 ZN A:ZN402 3.4 25.7 1.0 OD2 A:ASP264 3.4 23.9 1.0 NZ A:KCX143 4.1 21.5 1.0 ND1 A:HIS23 4.1 24.0 1.0 CG A:HIS23 4.1 22.8 1.0 CE1 A:HIS204 4.2 23.9 1.0 NE2 A:HIS204 4.2 26.9 1.0 CG A:HIS21 4.3 22.5 1.0 ND1 A:HIS21 4.3 20.9 1.0 CB A:ASP264 4.4 19.0 1.0 CB A:ALA67 4.5 22.4 1.0 O A:HOH374 4.7 39.8 1.0 CA A:ASP264 4.8 19.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Hydrolase DR0930 with Promiscuous Catalytic Activity


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 Hydrolase DR0930 with Promiscuous Catalytic Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:25.7 occ:1.00 OQ2 A:KCX143 1.9 22.7 1.0 ND1 A:HIS176 2.0 27.6 1.0 NE2 A:HIS204 2.1 26.9 1.0 O A:HOH363 2.1 19.3 1.0 CD2 A:HIS204 3.0 24.1 1.0 CX A:KCX143 3.0 23.0 1.0 CE1 A:HIS176 3.0 26.6 1.0 CG A:HIS176 3.0 27.1 1.0 CE1 A:HIS204 3.1 23.9 1.0 CB A:HIS176 3.4 25.9 1.0 ZN A:ZN401 3.4 24.7 1.0 OQ1 A:KCX143 3.5 21.2 1.0 NH2 A:ARG228 3.5 31.0 1.0 OH A:TYR97 3.9 36.6 1.0 CE1 A:TYR97 4.0 29.1 1.0 OD2 A:ASP264 4.1 23.9 1.0 NE2 A:HIS176 4.1 28.1 1.0 NE2 A:HIS21 4.1 23.4 1.0 CE1 A:HIS21 4.1 23.7 1.0 CD2 A:HIS176 4.2 27.0 1.0 NZ A:KCX143 4.2 21.5 1.0 CG A:HIS204 4.2 25.3 1.0 ND1 A:HIS204 4.2 24.6 1.0 CA A:HIS176 4.2 25.2 1.0 CZ A:ARG228 4.4 32.4 1.0 CZ A:TYR97 4.5 30.2 1.0 CE A:KCX143 4.6 24.7 1.0 OD1 A:ASP264 4.6 22.1 1.0 CG A:ASP264 4.7 19.4 1.0 NE A:ARG228 4.7 31.2 1.0

D.F.Xiang, P.Kolb, A.A.Fedorov, M.M.Meier, L.V.Fedorov, T.T.Nguyen, R.Sterner, S.C.Almo, B.K.Shoichet, F.M.Raushel. Functional Annotation and Three-Dimensional Structure of DR0930 From Deinococcus Radiodurans, A Close Relative of Phosphotriesterase in the Amidohydrolase Superfamily. Biochemistry V. 48 2237 2009.
ISSN: ISSN 0006-2960
PubMed: 19159332
DOI: 10.1021/BI802274F