Zinc in PDB 1r44: Crystal Structure of Vanx

The structure of Crystal Structure of Vanx, PDB code: 1r44 was solved by S.D.Pratt, L.Katz, J.M.Severin, T.Holzman, C.H.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.597, 44.694, 169.428, 90.00, 103.76, 90.00
R / Rfree (%)	25.4 / 30.1

The binding sites of Zinc atom in the Crystal Structure of Vanx (pdb code 1r44). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Vanx, PDB code: 1r44:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Vanx


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 Vanx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:13.7 occ:1.00 OD1 A:ASP123 2.3 11.3 1.0 NE2 A:HIS116 2.4 2.0 1.0 ND1 A:HIS184 2.5 2.0 1.0 O A:HOH205 2.5 5.2 1.0 CG A:ASP123 3.0 6.1 1.0 OD2 A:ASP123 3.1 6.0 1.0 CD2 A:HIS116 3.3 2.0 1.0 CE1 A:HIS116 3.3 2.0 1.0 CG A:HIS184 3.4 7.6 1.0 CE1 A:HIS184 3.4 6.6 1.0 CB A:HIS184 3.5 3.1 1.0 CA A:HIS184 4.0 4.7 1.0 NH2 A:ARG71 4.3 3.3 1.0 CD1 A:TRP183 4.3 2.0 1.0 CB A:ASP123 4.4 2.6 1.0 O A:ILE122 4.4 11.3 1.0 NE1 A:TRP183 4.4 2.0 1.0 CG A:HIS116 4.4 2.0 1.0 ND1 A:HIS116 4.5 4.5 1.0 OE2 A:GLU181 4.5 21.6 1.0 NE2 A:HIS184 4.6 13.9 1.0 CD2 A:HIS184 4.6 9.6 1.0 C A:ILE122 4.7 8.1 1.0 N A:ASP123 4.7 7.7 1.0 CA A:ASP123 4.8 2.0 1.0 N A:HIS184 4.8 4.9 1.0 O A:HOH204 4.8 13.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vanx


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 Vanx within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:6.1 occ:1.00 NE2 B:HIS116 2.4 2.0 1.0 OD1 B:ASP123 2.4 18.1 1.0 ND1 B:HIS184 2.4 4.6 1.0 O B:HOH204 2.6 2.0 1.0 CG B:ASP123 3.1 11.9 1.0 OD2 B:ASP123 3.2 11.3 1.0 CD2 B:HIS116 3.3 2.0 1.0 CG B:HIS184 3.3 7.6 1.0 CE1 B:HIS184 3.4 6.1 1.0 CE1 B:HIS116 3.4 6.1 1.0 CB B:HIS184 3.5 2.0 1.0 CA B:HIS184 4.0 4.0 1.0 NH2 B:ARG71 4.2 2.0 1.0 CD1 B:TRP183 4.3 2.0 1.0 NE1 B:TRP183 4.4 2.0 1.0 CG B:HIS116 4.4 2.4 1.0 OE2 B:GLU181 4.5 18.1 1.0 O B:ILE122 4.5 7.6 1.0 CB B:ASP123 4.5 8.5 1.0 ND1 B:HIS116 4.5 6.0 1.0 CD2 B:HIS184 4.5 13.2 1.0 NE2 B:HIS184 4.5 14.7 1.0 C B:ILE122 4.8 3.7 1.0 N B:ASP123 4.8 7.4 1.0 CA B:ASP123 4.9 3.5 1.0 N B:HIS184 4.9 5.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vanx


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 Vanx within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:14.0 occ:1.00 NE2 C:HIS116 2.3 2.0 1.0 ND1 C:HIS184 2.4 6.2 1.0 OD1 C:ASP123 2.4 15.9 1.0 CG C:ASP123 3.1 12.2 1.0 OD2 C:ASP123 3.1 16.1 1.0 CD2 C:HIS116 3.2 3.8 1.0 O C:HOH205 3.2 14.4 1.0 CE1 C:HIS184 3.4 2.7 1.0 CG C:HIS184 3.4 8.6 1.0 CE1 C:HIS116 3.4 2.0 1.0 CB C:HIS184 3.6 6.5 1.0 CA C:HIS184 4.1 2.7 1.0 NH2 C:ARG71 4.2 2.0 1.0 CG C:HIS116 4.4 3.5 1.0 CD1 C:TRP183 4.4 6.6 1.0 NE1 C:TRP183 4.4 2.0 1.0 OE2 C:GLU181 4.5 11.8 1.0 O C:ILE122 4.5 9.9 1.0 ND1 C:HIS116 4.5 2.7 1.0 CB C:ASP123 4.5 11.2 1.0 NE2 C:HIS184 4.6 13.4 1.0 CD2 C:HIS184 4.6 11.6 1.0 C C:ILE122 4.8 8.2 1.0 N C:ASP123 4.9 9.0 1.0 CA C:ASP123 4.9 9.8 1.0 N C:HIS184 5.0 5.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vanx


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 Vanx within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:16.1 occ:1.00 ND1 D:HIS184 2.4 5.4 1.0 OD1 D:ASP123 2.4 16.5 1.0 NE2 D:HIS116 2.4 2.0 1.0 O D:HOH204 2.6 11.5 1.0 CG D:ASP123 3.1 6.7 1.0 OD2 D:ASP123 3.1 2.7 1.0 CG D:HIS184 3.3 10.3 1.0 CD2 D:HIS116 3.3 2.0 1.0 CE1 D:HIS184 3.3 11.8 1.0 CE1 D:HIS116 3.5 2.0 1.0 CB D:HIS184 3.5 6.4 1.0 CA D:HIS184 4.0 4.8 1.0 CD1 D:TRP183 4.3 2.0 1.0 O D:ILE122 4.3 8.1 1.0 NE1 D:TRP183 4.4 2.0 1.0 NH2 D:ARG71 4.4 3.6 1.0 OE2 D:GLU181 4.4 13.5 1.0 CG D:HIS116 4.5 2.0 1.0 CB D:ASP123 4.5 3.2 1.0 CD2 D:HIS184 4.5 10.2 1.0 NE2 D:HIS184 4.5 15.5 1.0 ND1 D:HIS116 4.6 6.9 1.0 O D:HOH205 4.7 15.7 1.0 C D:ILE122 4.7 8.2 1.0 N D:HIS184 4.8 4.8 1.0 N D:ASP123 4.8 11.2 1.0 CA D:ASP123 4.9 3.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vanx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Vanx within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn203 b:17.4 occ:1.00 NE2 E:HIS116 2.3 2.4 1.0 OD1 E:ASP123 2.4 8.1 1.0 ND1 E:HIS184 2.4 7.3 1.0 O E:HOH205 2.6 2.5 1.0 CG E:ASP123 3.1 8.8 1.0 OD2 E:ASP123 3.1 3.9 1.0 CD2 E:HIS116 3.3 4.1 1.0 CG E:HIS184 3.3 10.0 1.0 CE1 E:HIS184 3.3 12.2 1.0 CE1 E:HIS116 3.4 2.0 1.0 CB E:HIS184 3.5 2.0 1.0 CA E:HIS184 4.0 2.5 1.0 O E:HOH204 4.1 17.2 1.0 NH2 E:ARG71 4.2 2.0 1.0 CD1 E:TRP183 4.4 2.0 1.0 CG E:HIS116 4.4 2.0 1.0 O E:ILE122 4.4 9.5 1.0 NE1 E:TRP183 4.4 2.0 1.0 CB E:ASP123 4.5 7.9 1.0 ND1 E:HIS116 4.5 2.0 1.0 NE2 E:HIS184 4.5 14.3 1.0 CD2 E:HIS184 4.5 11.9 1.0 OE2 E:GLU181 4.5 17.0 1.0 C E:ILE122 4.7 8.6 1.0 N E:ASP123 4.8 12.1 1.0 CA E:ASP123 4.9 8.2 1.0 N E:HIS184 4.9 4.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vanx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Vanx within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn203 b:13.7 occ:1.00 NE2 F:HIS116 2.3 4.4 1.0 OD1 F:ASP123 2.4 7.5 1.0 ND1 F:HIS184 2.4 7.1 1.0 O F:HOH205 2.7 2.0 1.0 CG F:ASP123 3.0 3.2 1.0 OD2 F:ASP123 3.1 2.0 1.0 CD2 F:HIS116 3.2 5.1 1.0 CE1 F:HIS184 3.3 7.6 1.0 CG F:HIS184 3.3 5.3 1.0 CE1 F:HIS116 3.4 2.0 1.0 CB F:HIS184 3.5 2.3 1.0 CA F:HIS184 4.0 5.9 1.0 NH2 F:ARG71 4.2 2.0 1.0 O F:ILE122 4.4 4.4 1.0 CD1 F:TRP183 4.4 2.0 1.0 CG F:HIS116 4.4 2.0 1.0 NE1 F:TRP183 4.4 2.0 1.0 CB F:ASP123 4.4 2.0 1.0 OE2 F:GLU181 4.5 21.8 1.0 ND1 F:HIS116 4.5 2.0 1.0 NE2 F:HIS184 4.5 13.9 1.0 CD2 F:HIS184 4.5 11.3 1.0 C F:ILE122 4.7 8.9 1.0 N F:ASP123 4.8 7.0 1.0 CA F:ASP123 4.8 4.3 1.0 N F:HIS184 4.9 7.0 1.0

D.E.Bussiere, S.D.Pratt, L.Katz, J.M.Severin, T.Holzman, C.H.Park. The Structure of Vanx Reveals A Novel Amino-Dipeptidase Involved in Mediating Transposon-Based Vancomycin Resistance Mol.Cell V. 2 75 1998.
ISSN: ISSN 1097-2765
PubMed: 9702193
DOI: 10.1016/S1097-2765(00)80115-X