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Zinc in PDB 2yz3: Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor

Enzymatic activity of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor

All present enzymatic activity of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor, PDB code: 2yz3 was solved by Y.Yamaguchi, Y.Yamagata, Y.Arakawa, H.Kurosaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.80 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.184, 90.749, 128.977, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor (pdb code 2yz3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor, PDB code: 2yz3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2yz3

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Zinc binding site 1 out of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:35.4
occ:1.00
 ND1 A:HIS96 2.0 36.3 1.0
NE2 A:HIS159 2.2 37.6 1.0
NE2 A:HIS94 2.2 35.2 1.0
S1 A:M5P401 2.5 39.3 1.0
CE1 A:HIS96 2.9 33.9 1.0
CD2 A:HIS159 2.9 37.9 1.0
CG A:HIS96 3.0 36.1 1.0
CD2 A:HIS94 3.1 34.8 1.0
CE1 A:HIS94 3.1 34.2 1.0
CE1 A:HIS159 3.3 37.2 1.0
C11 A:M5P401 3.3 40.2 1.0
CB A:HIS96 3.4 35.0 1.0
ZN A:ZN302 3.8 24.9 0.8
NE2 A:HIS96 4.0 35.2 1.0
CB A:CYS178 4.0 34.3 1.0
CG A:HIS159 4.1 36.1 1.0
CD2 A:HIS96 4.1 34.7 1.0
OD2 A:ASP98 4.1 35.2 1.0
ND1 A:HIS94 4.2 33.3 1.0
CG A:HIS94 4.2 33.6 1.0
C10 A:M5P401 4.2 44.6 1.0
ND1 A:HIS159 4.2 37.5 1.0
SG A:CYS178 4.4 31.4 1.0
OD1 A:ASP98 4.5 31.2 1.0
C12 A:M5P401 4.5 46.6 1.0
CG A:ASP98 4.7 33.9 1.0
O1 A:M5P401 4.8 48.8 1.0
CA A:HIS96 4.8 34.9 1.0
O2 A:M5P401 4.9 49.7 1.0

Zinc binding site 2 out of 4 in 2yz3

Go back to Zinc Binding Sites List in 2yz3
Zinc binding site 2 out of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:24.9
occ:0.80
 OD1 A:ASP98 1.9 31.2 1.0
S1 A:M5P401 2.1 39.3 1.0
NE2 A:HIS220 2.1 35.8 1.0
SG A:CYS178 2.2 31.4 1.0
CD2 A:HIS220 3.0 33.5 1.0
CG A:ASP98 3.1 33.9 1.0
CE1 A:HIS220 3.2 32.4 1.0
CB A:CYS178 3.3 34.3 1.0
C11 A:M5P401 3.5 40.2 1.0
NH2 A:ARG99 3.6 30.8 1.0
OD2 A:ASP98 3.6 35.2 1.0
ZN A:ZN301 3.8 35.4 1.0
NE A:ARG99 4.0 27.6 1.0
CZ A:ARG99 4.2 28.5 1.0
CE1 A:HIS94 4.2 34.2 1.0
CG A:HIS220 4.2 33.8 1.0
ND1 A:HIS220 4.2 31.6 1.0
NE2 A:HIS94 4.3 35.2 1.0
CB A:ASP98 4.3 29.9 1.0
O A:HOH531 4.3 29.4 1.0
C8 A:M5P401 4.5 38.9 1.0
CA A:CYS178 4.6 36.9 1.0
C10 A:M5P401 4.6 44.6 1.0
O A:HOH538 4.7 45.7 1.0
O A:GLY219 4.9 34.2 1.0
NE2 A:HIS159 5.0 37.6 1.0

Zinc binding site 3 out of 4 in 2yz3

Go back to Zinc Binding Sites List in 2yz3
Zinc binding site 3 out of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:27.2
occ:1.00
 NE2 B:HIS94 2.1 25.0 1.0
ND1 B:HIS96 2.2 29.5 1.0
NE2 B:HIS159 2.2 28.5 1.0
S1 B:M5P402 2.2 32.7 1.0
CE1 B:HIS94 3.0 24.8 1.0
CD2 B:HIS159 3.0 29.0 1.0
CG B:HIS96 3.1 27.7 1.0
CE1 B:HIS96 3.1 28.2 1.0
CD2 B:HIS94 3.2 25.9 1.0
CE1 B:HIS159 3.2 28.9 1.0
CB B:HIS96 3.4 25.5 1.0
C11 B:M5P402 3.4 39.7 1.0
ZN B:ZN304 3.7 19.5 0.8
OD2 B:ASP98 4.1 26.2 1.0
ND1 B:HIS94 4.1 26.1 1.0
CB B:CYS178 4.1 28.2 1.0
NE2 B:HIS96 4.1 29.1 1.0
CD2 B:HIS96 4.2 26.4 1.0
CG B:HIS94 4.2 26.7 1.0
CG B:HIS159 4.2 30.2 1.0
C10 B:M5P402 4.2 43.9 1.0
ND1 B:HIS159 4.3 29.2 1.0
C12 B:M5P402 4.3 45.9 1.0
SG B:CYS178 4.3 27.5 1.0
O1 B:M5P402 4.5 49.5 1.0
OD1 B:ASP98 4.5 22.4 1.0
O2 B:M5P402 4.7 50.8 1.0
CG B:ASP98 4.7 26.3 1.0
CA B:HIS96 4.8 27.5 1.0

Zinc binding site 4 out of 4 in 2yz3

Go back to Zinc Binding Sites List in 2yz3
Zinc binding site 4 out of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:19.5
occ:0.80
 OD1 B:ASP98 2.0 22.4 1.0
NE2 B:HIS220 2.1 24.7 1.0
S1 B:M5P402 2.2 32.7 1.0
SG B:CYS178 2.3 27.5 1.0
CE1 B:HIS220 3.0 25.5 1.0
CD2 B:HIS220 3.1 25.1 1.0
CG B:ASP98 3.1 26.3 1.0
C11 B:M5P402 3.3 39.7 1.0
CB B:CYS178 3.4 28.2 1.0
NH2 B:ARG99 3.5 26.6 1.0
OD2 B:ASP98 3.6 26.2 1.0
ZN B:ZN303 3.7 27.2 1.0
NE B:ARG99 3.9 26.4 1.0
CZ B:ARG99 4.1 29.3 1.0
ND1 B:HIS220 4.1 25.0 1.0
CG B:HIS220 4.2 26.4 1.0
CE1 B:HIS94 4.2 24.8 1.0
CB B:ASP98 4.3 23.9 1.0
C10 B:M5P402 4.4 43.9 1.0
NE2 B:HIS94 4.5 25.0 1.0
O B:HOH612 4.5 56.9 1.0
CA B:CYS178 4.6 29.3 1.0
C8 B:M5P402 4.6 39.8 1.0
O B:HOH523 4.6 29.0 1.0
NE2 B:HIS159 4.7 28.5 1.0
OG B:SER49 4.8 24.1 1.0
O B:GLY219 5.0 26.6 1.0

Reference:

Y.Yamaguchi, W.Jin, K.Matsunaga, S.Ikemizu, Y.Yamagata, J.Wachino, N.Shibata, Y.Arakawa, H.Kurosaki. Crystallographic Investigation of the Inhibition Mode of A Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa By A Mercaptocarboxylate Inhibitor. J.Med.Chem. V. 50 6647 2007.
ISSN: ISSN 0022-2623
PubMed: 18052313
DOI: 10.1021/JM701031N
Page generated: Wed Dec 16 04:03:49 2020

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