Zinc in PDB 2w8s: Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli

The structure of Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli, PDB code: 2w8s was solved by S.Jonas, B.Van Loo, M.Hyvonen, F.Hollfelder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.62 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.700, 200.100, 211.700, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.9

The structure of Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli (pdb code 2w8s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli, PDB code: 2w8s:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


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 A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1515 b:28.4 occ:0.30 FE A:FE1516 0.0 27.7 0.3 OD2 A:ASP324 2.1 28.2 1.0 OD1 A:ASP12 2.1 26.9 1.0 NE2 A:HIS325 2.2 28.4 1.0 OD2 A:ASP12 2.3 27.9 1.0 CG A:ASP12 2.5 25.4 1.0 OG2 A:CYS57 2.6 32.0 0.2 SG A:CYS57 2.8 36.4 0.8 CG A:ASP324 2.9 27.4 1.0 OG1 A:CYS57 3.0 31.4 0.2 CD2 A:HIS325 3.0 27.4 1.0 CE1 A:HIS325 3.0 28.8 1.0 CB A:CYS57 3.1 30.2 0.8 OD1 A:ASP324 3.2 29.0 1.0 CB A:CYS57 3.2 32.1 0.2 CA A:CYS57 3.7 29.4 0.8 CA A:CYS57 3.7 32.2 0.2 CB A:ASP12 3.9 23.8 1.0 ND1 A:HIS325 4.1 28.0 1.0 CG A:HIS325 4.1 27.2 1.0 N A:CYS57 4.2 32.3 0.2 NH2 A:ARG61 4.3 33.4 1.0 N A:CYS57 4.3 27.6 0.8 CD2 A:HIS218 4.3 23.4 1.0 CB A:ASP324 4.4 26.4 1.0 NE A:ARG61 4.5 31.1 1.0 CA A:ASP12 4.5 23.2 1.0 OE1 A:GLN13 4.5 25.5 1.0 N A:GLN13 4.6 22.3 1.0 OH A:TYR105 4.7 29.3 1.0 CZ A:ARG61 4.9 31.7 1.0 NZ A:LYS337 4.9 27.1 1.0 C A:ASP12 4.9 22.8 1.0 NE2 A:HIS218 4.9 23.9 1.0 C A:CYS57 5.0 28.7 0.8

Zinc binding site 2 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


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 A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1515 b:30.7 occ:0.30 FE B:FE1516 0.0 30.0 0.3 OD2 B:ASP324 2.0 31.5 1.0 NE2 B:HIS325 2.1 27.9 1.0 OD1 B:ASP12 2.2 28.2 1.0 OG2 B:CYS57 2.3 39.2 0.2 SG B:CYS57 2.4 35.6 0.8 OD2 B:ASP12 2.4 27.1 1.0 CG B:ASP12 2.6 26.2 1.0 CD2 B:HIS325 2.9 28.7 1.0 CG B:ASP324 3.0 24.9 1.0 CE1 B:HIS325 3.2 29.9 1.0 OD1 B:ASP324 3.2 24.0 1.0 CB B:CYS57 3.2 39.5 0.2 CB B:CYS57 3.3 27.0 0.8 OG1 B:CYS57 3.4 39.1 0.2 CA B:CYS57 3.7 39.6 0.2 CA B:CYS57 3.7 26.2 0.8 NH2 B:ARG61 3.8 34.6 1.0 CB B:ASP12 4.0 24.5 1.0 CG B:HIS325 4.1 26.6 1.0 ND1 B:HIS325 4.2 28.7 1.0 N B:CYS57 4.3 24.0 0.8 NE B:ARG61 4.3 30.4 1.0 CB B:ASP324 4.4 22.7 1.0 N B:CYS57 4.4 39.5 0.2 CD2 B:HIS218 4.5 25.2 1.0 CZ B:ARG61 4.6 32.0 1.0 CA B:ASP12 4.6 24.4 1.0 OE1 B:GLN13 4.6 29.6 1.0 CE B:LYS337 4.6 18.9 1.0 NZ B:LYS337 4.6 15.2 1.0 N B:GLN13 4.8 24.9 1.0 OH B:TYR105 4.9 30.1 1.0 C B:CYS57 4.9 39.8 0.2

Zinc binding site 3 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1515 b:20.4 occ:0.30 FE C:FE1516 0.0 19.2 0.3 NE2 C:HIS325 2.0 21.8 1.0 OD2 C:ASP324 2.1 22.3 1.0 OD1 C:ASP12 2.3 21.2 1.0 OG1 C:CYS57 2.4 35.9 0.2 SG C:CYS57 2.4 35.1 0.8 OD2 C:ASP12 2.5 22.6 1.0 CG C:ASP12 2.7 19.6 1.0 CD2 C:HIS325 2.9 18.9 1.0 CG C:ASP324 2.9 20.8 1.0 OD1 C:ASP324 3.0 23.5 1.0 CE1 C:HIS325 3.0 21.4 1.0 CB C:CYS57 3.2 36.0 0.2 CB C:CYS57 3.3 26.3 0.8 CA C:CYS57 3.4 36.0 0.2 OG2 C:CYS57 3.4 35.8 0.2 CA C:CYS57 3.6 25.8 0.8 N C:CYS57 3.9 36.0 0.2 NH2 C:ARG61 3.9 28.2 1.0 CG C:HIS325 4.0 19.1 1.0 N C:CYS57 4.0 23.6 0.8 ND1 C:HIS325 4.0 19.7 1.0 CB C:ASP12 4.1 19.3 1.0 CB C:ASP324 4.4 19.1 1.0 NE C:ARG61 4.4 27.8 1.0 NZ C:LYS337 4.4 15.5 1.0 CE C:LYS337 4.5 18.7 1.0 OE1 C:GLN13 4.5 18.6 1.0 CD2 C:HIS218 4.5 27.1 1.0 CA C:ASP12 4.6 19.1 1.0 CZ C:ARG61 4.6 28.4 1.0 N C:GLN13 4.7 19.2 1.0 C C:CYS57 4.8 36.1 0.2 C C:ASP12 5.0 18.6 1.0 C C:CYS57 5.0 24.4 0.8

Zinc binding site 4 out of 4 in the Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Catalytically Promiscuous Phosphonate Monoester Hydrolase From Burkholderia Caryophylli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1515 b:28.4 occ:0.30 FE D:FE1516 0.1 28.1 0.3 NE2 D:HIS325 2.0 26.8 1.0 OD2 D:ASP324 2.1 31.7 1.0 OD1 D:ASP12 2.2 27.0 1.0 OD2 D:ASP12 2.3 24.8 1.0 CG D:ASP12 2.6 22.1 1.0 OG2 D:CYS57 2.7 28.7 0.2 CD2 D:HIS325 2.9 25.0 1.0 SG D:CYS57 3.0 33.6 0.8 CE1 D:HIS325 3.0 25.7 1.0 CG D:ASP324 3.1 27.7 1.0 CB D:CYS57 3.1 23.4 0.8 OD1 D:ASP324 3.4 29.1 1.0 CB D:CYS57 3.4 28.7 0.2 OG1 D:CYS57 3.5 27.9 0.2 CA D:CYS57 3.6 28.7 0.2 CA D:CYS57 3.7 23.0 0.8 NH2 D:ARG61 4.0 27.8 1.0 CB D:ASP12 4.0 20.2 1.0 CG D:HIS325 4.0 23.7 1.0 ND1 D:HIS325 4.1 24.6 1.0 N D:CYS57 4.2 29.0 0.2 N D:CYS57 4.3 20.8 0.8 CE D:LYS337 4.4 19.9 1.0 CD2 D:HIS218 4.4 25.9 1.0 CB D:ASP324 4.4 24.5 1.0 NZ D:LYS337 4.5 19.0 1.0 OE1 D:GLN13 4.5 18.3 1.0 NE D:ARG61 4.6 28.5 1.0 CA D:ASP12 4.6 20.5 1.0 CZ D:ARG61 4.7 27.1 1.0 N D:GLN13 4.8 20.2 1.0 OH D:TYR105 4.8 28.4 1.0 C D:CYS57 4.9 28.8 0.2 C D:ASP12 5.0 20.5 1.0

B.Van Loo, S.Jonas, A.C.Babtie, A.Benjdia, O.Berteau, M.Hyvonen, F.Hollfelder. An Efficient, Multiply Promiscuous Hydrolase in the Alkaline Phosphatase Superfamily. Proc.Natl.Acad.Sci.Usa V. 107 2740 2010.
ISSN: ISSN 0027-8424
PubMed: 20133613
DOI: 10.1073/PNAS.0903951107