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Zinc in PDB 9qi6: Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid

Enzymatic activity of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid

All present enzymatic activity of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid:
3.5.2.6;

Protein crystallography data

The structure of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid, PDB code: 9qi6 was solved by A.Chikunova, M.Radojkovic, M.Ubbink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.99 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.495, 41.351, 269.672, 90, 90, 90
R / Rfree (%) 18.6 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid (pdb code 9qi6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid, PDB code: 9qi6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 9qi6

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Zinc binding site 1 out of 5 in the Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:37.4
occ:1.00
 O A:HOH475 2.2 26.3 1.0
OD2 A:ASP31 2.4 22.4 1.0
OD1 A:ASP31 2.6 30.6 1.0
CG A:ASP31 2.8 25.1 1.0
OD1 A:ASP28 3.9 37.0 1.0
CB A:ASP31 4.3 21.2 1.0
CG A:ASP28 4.6 44.9 1.0
O A:HOH522 4.6 30.8 1.0
N A:ASP28 4.8 46.3 1.0
OD2 A:ASP28 4.8 45.5 1.0

Zinc binding site 2 out of 5 in 9qi6

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Zinc binding site 2 out of 5 in the Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:55.1
occ:1.00
 OD1 A:ASP141 2.2 16.7 1.0
CE1 A:HIS90 2.3 15.0 1.0
O A:HOH584 2.3 28.2 1.0
OD2 A:ASP141 2.6 13.9 1.0
CG A:ASP141 2.7 14.1 1.0
NE2 A:HIS90 2.7 14.5 1.0
ND1 A:HIS90 3.5 17.6 1.0
CD2 A:HIS90 4.0 13.8 1.0
O A:HOH499 4.1 16.9 1.0
CD A:LYS93 4.1 27.5 1.0
O A:ASP141 4.1 15.6 1.0
CB A:ASP141 4.1 14.9 1.0
O A:HOH583 4.2 39.0 1.0
OD1 A:ASN86 4.3 13.9 1.0
CG A:HIS90 4.4 15.5 1.0
O A:HOH469 4.4 19.5 1.0
CE A:LYS93 4.5 34.1 1.0
CA A:ASP141 4.6 14.9 1.0
C A:ASP141 4.7 14.4 1.0
ND2 A:ASN86 4.8 17.5 1.0
CD1 A:ILE119 4.8 17.0 1.0
CG A:ASN86 4.8 16.8 1.0

Zinc binding site 3 out of 5 in 9qi6

Go back to Zinc Binding Sites List in 9qi6
Zinc binding site 3 out of 5 in the Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:39.0
occ:1.00
 OD1 A:ASP63 2.0 13.6 1.0
ND1 A:HIS184 2.1 22.1 1.0
O A:HOH404 2.2 23.1 1.0
OD2 A:ASP63 2.4 14.2 1.0
CG A:ASP63 2.5 13.0 1.0
CE1 A:HIS184 2.9 21.8 1.0
CG A:HIS184 3.2 18.1 1.0
CB A:HIS184 3.6 16.0 1.0
CB A:ASP63 4.0 13.0 1.0
NE2 A:HIS184 4.1 22.1 1.0
O A:HOH448 4.2 11.6 1.0
CD2 A:HIS184 4.3 18.6 1.0
OE2 A:GLU59 4.4 43.7 1.0
CA A:ASP63 4.6 14.2 1.0
O A:HOH604 4.7 31.4 1.0
N A:ASP63 4.7 12.9 1.0
C A:ALA62 4.8 13.4 1.0
O A:ALA62 4.8 11.5 1.0
CB A:ALA62 4.8 15.3 1.0

Zinc binding site 4 out of 5 in 9qi6

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Zinc binding site 4 out of 5 in the Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:41.9
occ:1.00
 ND1 B:HIS184 2.2 29.4 1.0
OD1 B:ASP63 2.4 26.4 1.0
OD2 B:ASP63 2.5 32.1 1.0
OE1 B:GLU59 2.6 40.6 1.0
CG B:ASP63 2.7 29.3 1.0
CE1 B:HIS184 3.1 28.9 1.0
CG B:HIS184 3.2 24.8 1.0
CB B:HIS184 3.5 20.1 1.0
CD B:GLU59 3.8 39.5 1.0
CB B:ALA62 4.1 19.8 1.0
CB B:ASP63 4.2 22.3 1.0
NE2 B:HIS184 4.2 29.5 1.0
CD2 B:HIS184 4.3 26.7 1.0
OE2 B:GLU59 4.3 45.9 1.0
C B:ALA62 4.4 17.7 1.0
N B:ASP63 4.4 17.9 1.0
CE1 B:TYR47 4.4 25.8 1.0
O B:ALA62 4.6 17.2 1.0
CA B:ASP63 4.7 21.3 1.0
CD1 B:TYR47 4.7 20.9 1.0
CA B:ALA62 4.9 18.1 1.0
CG B:GLU59 4.9 34.5 1.0
CA B:HIS184 5.0 18.6 1.0

Zinc binding site 5 out of 5 in 9qi6

Go back to Zinc Binding Sites List in 9qi6
Zinc binding site 5 out of 5 in the Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of I105R Blac From Mycobacterium Tuberculosis Bound to the Trans-Enamine Adduct of Clavulanic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:77.0
occ:1.00
 CE1 B:HIS90 2.3 27.6 1.0
OD1 B:ASP141 2.3 26.2 1.0
NE2 B:HIS90 2.8 25.0 1.0
OD2 B:ASP141 2.9 22.0 1.0
CG B:ASP141 2.9 23.8 1.0
ND1 B:HIS90 3.5 23.1 1.0
CD2 B:HIS90 4.1 23.8 1.0
CD B:LYS93 4.1 38.8 1.0
OD1 B:ASN86 4.1 33.5 1.0
O B:ASP141 4.3 20.3 1.0
CB B:ASP141 4.3 21.7 1.0
CE B:LYS93 4.3 46.2 1.0
CG B:HIS90 4.4 23.7 1.0
O B:HOH445 4.5 32.2 1.0
CA B:ASP141 4.7 21.8 1.0
CG B:ASN86 4.8 30.0 1.0
C B:ASP141 4.8 24.2 1.0
ND2 B:ASN86 4.9 29.1 1.0
CD1 B:ILE119 5.0 17.0 1.0

Reference:

M.Radojkovic, S.F.Koene, A.Chikunova, M.Timmer, S.V.Natarajan, M.Ubbink. High-Resolution Activity and Inhibitor Profiling of Residue 105 in Class A Beta-Lactamases To Be Published.
Page generated: Fri Aug 22 18:56:28 2025

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