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Zinc in PDB 1r44: Crystal Structure of Vanx

Protein crystallography data

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

Zinc Binding Sites:

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 1r44

Go back to Zinc Binding Sites List in 1r44
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 1r44

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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 1r44

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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 1r44

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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 1r44

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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 1r44

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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

Reference:

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
Page generated: Wed Dec 16 03:02:28 2020

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