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Zinc in PDB 3giq: Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate.

Enzymatic activity of Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate.

All present enzymatic activity of Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate.:
3.5.1.82;

Protein crystallography data

The structure of Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate., PDB code: 3giq was solved by A.A.Fedorov, E.V.Fedorov, J.Cummings, 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) 24.99 / 1.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.291, 91.291, 507.584, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 20.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate. (pdb code 3giq). 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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate., PDB code: 3giq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3giq

Go back to Zinc Binding Sites List in 3giq
Zinc binding site 1 out of 4 in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate.


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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn482

b:12.6
occ:1.00
 ND1 A:HIS218 2.0 9.6 1.0
OPB A:G01481 2.0 12.0 1.0
NE2 A:HIS248 2.2 11.2 1.0
SG A:CYS95 2.3 11.5 1.0
CE1 A:HIS218 2.8 11.7 1.0
CG A:HIS218 3.0 11.2 1.0
P A:G01481 3.0 11.3 1.0
OPA A:G01481 3.0 10.6 1.0
CD2 A:HIS248 3.1 10.1 1.0
CE1 A:HIS248 3.2 11.1 1.0
CB A:CYS95 3.2 11.3 1.0
CB A:HIS218 3.4 10.6 1.0
ZN A:ZN483 3.5 14.9 1.0
NE2 A:HIS218 3.9 11.6 1.0
CD2 A:HIS218 4.0 10.4 1.0
N A:G01481 4.0 9.6 1.0
CA A:G01481 4.1 10.5 1.0
CE2 A:TYR190 4.2 20.9 1.0
OH A:TYR190 4.3 15.7 1.0
ND1 A:HIS248 4.3 11.3 1.0
CG A:HIS248 4.3 11.4 1.0
C6 A:G01481 4.3 11.0 1.0
CA A:CYS95 4.4 11.0 1.0
NE2 A:HIS66 4.5 12.5 1.0
CA A:HIS218 4.5 10.8 1.0
CE1 A:HIS66 4.6 12.5 1.0
CZ A:TYR190 4.7 19.4 1.0
CB A:G01481 4.9 10.7 1.0

Zinc binding site 2 out of 4 in 3giq

Go back to Zinc Binding Sites List in 3giq
Zinc binding site 2 out of 4 in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate.


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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn483

b:14.9
occ:1.00
 NE2 A:HIS68 2.0 9.8 1.0
OPA A:G01481 2.0 10.6 1.0
NE2 A:HIS66 2.1 12.5 1.0
SG A:CYS95 2.4 11.5 1.0
OD1 A:ASP365 2.9 14.1 1.0
CE1 A:HIS68 2.9 10.7 1.0
CD2 A:HIS68 3.0 9.5 1.0
CD2 A:HIS66 3.1 12.3 1.0
CE1 A:HIS66 3.1 12.5 1.0
P A:G01481 3.3 11.3 1.0
ZN A:ZN482 3.5 12.6 1.0
CG A:ASP365 3.6 15.3 1.0
CB A:CYS95 3.7 11.3 1.0
OPB A:G01481 3.7 12.0 1.0
OD2 A:ASP365 3.7 11.2 1.0
C6 A:G01481 3.8 11.0 1.0
CD2 A:HIS248 4.0 10.1 1.0
ND1 A:HIS68 4.0 11.2 1.0
CG A:HIS68 4.1 9.4 1.0
ND1 A:HIS66 4.2 11.6 1.0
CG A:HIS66 4.2 10.9 1.0
NE2 A:HIS248 4.3 11.2 1.0
CB A:ASN94 4.3 11.5 1.0
N A:G01481 4.6 9.6 1.0
N A:CYS95 4.7 11.3 1.0
C A:ASN94 4.7 11.5 1.0
CA A:CYS95 4.8 11.0 1.0
CB A:ASP365 4.9 12.6 1.0
O A:ASN94 5.0 11.5 1.0

Zinc binding site 3 out of 4 in 3giq

Go back to Zinc Binding Sites List in 3giq
Zinc binding site 3 out of 4 in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate.


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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn482

b:12.3
occ:1.00
 ND1 B:HIS218 2.0 10.9 1.0
OPB B:G01481 2.1 10.6 1.0
NE2 B:HIS248 2.2 10.1 1.0
SG B:CYS95 2.2 11.1 1.0
OPA B:G01481 2.8 11.0 1.0
P B:G01481 2.9 10.4 1.0
CE1 B:HIS218 3.0 11.3 1.0
CG B:HIS218 3.0 11.4 1.0
CD2 B:HIS248 3.1 10.1 1.0
CE1 B:HIS248 3.2 10.6 1.0
CB B:CYS95 3.3 9.8 1.0
CB B:HIS218 3.4 12.2 1.0
ZN B:ZN483 3.4 13.9 1.0
N B:G01481 4.0 9.9 1.0
NE2 B:HIS218 4.0 10.3 1.0
CA B:G01481 4.1 10.1 1.0
CD2 B:HIS218 4.1 10.5 1.0
ND1 B:HIS248 4.3 8.8 1.0
CE2 B:TYR190 4.3 17.8 1.0
CG B:HIS248 4.3 11.1 1.0
OH B:TYR190 4.3 16.3 1.0
C6 B:G01481 4.4 11.4 1.0
CA B:CYS95 4.4 9.9 1.0
NE2 B:HIS66 4.4 13.1 1.0
CA B:HIS218 4.5 10.8 1.0
CE1 B:HIS66 4.6 14.1 1.0
CZ B:TYR190 4.8 18.5 1.0
CB B:G01481 5.0 9.2 1.0

Zinc binding site 4 out of 4 in 3giq

Go back to Zinc Binding Sites List in 3giq
Zinc binding site 4 out of 4 in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate.


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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc and Phosphonate Inhibitor, A Mimic of the Reaction Tetrahedral Intermediate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn483

b:13.9
occ:1.00
 OPA B:G01481 2.0 11.0 1.0
NE2 B:HIS68 2.0 11.1 1.0
NE2 B:HIS66 2.1 13.1 1.0
SG B:CYS95 2.5 11.1 1.0
CE1 B:HIS68 2.9 10.1 1.0
OD1 B:ASP365 2.9 13.1 1.0
CD2 B:HIS68 3.0 8.7 1.0
CD2 B:HIS66 3.1 12.7 1.0
CE1 B:HIS66 3.1 14.1 1.0
P B:G01481 3.2 10.4 1.0
ZN B:ZN482 3.4 12.3 1.0
CG B:ASP365 3.6 11.8 1.0
CB B:CYS95 3.7 9.8 1.0
C6 B:G01481 3.7 11.4 1.0
OPB B:G01481 3.7 10.6 1.0
OD2 B:ASP365 3.8 12.2 1.0
ND1 B:HIS68 4.0 8.8 1.0
CD2 B:HIS248 4.0 10.1 1.0
CG B:HIS68 4.1 9.5 1.0
ND1 B:HIS66 4.2 12.1 1.0
CG B:HIS66 4.2 12.2 1.0
CB B:ASN94 4.3 10.7 1.0
NE2 B:HIS248 4.3 10.1 1.0
N B:G01481 4.5 9.9 1.0
N B:CYS95 4.6 9.2 1.0
C B:ASN94 4.7 10.8 1.0
CA B:CYS95 4.8 9.9 1.0
CB B:ASP365 4.9 10.0 1.0
O B:ASN94 4.9 9.7 1.0

Reference:

J.A.Cummings, A.A.Fedorov, C.Xu, S.Brown, E.Fedorov, P.C.Babbitt, S.C.Almo, F.M.Raushel. Annotating Enzymes of Uncertain Function: the Deacylation of D-Amino Acids By Members of the Amidohydrolase Superfamily. Biochemistry V. 48 6469 2009.
ISSN: ISSN 0006-2960
PubMed: 19518059
DOI: 10.1021/BI900661B
Page generated: Thu Oct 24 13:42:31 2024

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