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Zinc in PDB 5b3r: Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa, PDB code: 5b3r was solved by A.Shimizu-Ibuka, Y.Ishii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.550, 87.380, 105.750, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa (pdb code 5b3r). 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 Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa, PDB code: 5b3r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5b3r

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Zinc binding site 1 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa


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 Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:26.4
occ:1.00
ND1 A:HIS97 2.0 24.4 1.0
O5 A:CIT2003 2.0 27.2 1.0
NE2 A:HIS157 2.1 32.0 1.0
NE2 A:HIS95 2.2 22.2 1.0
C6 A:CIT2003 2.7 30.0 1.0
O6 A:CIT2003 2.7 27.9 1.0
CE1 A:HIS97 3.0 25.2 1.0
CG A:HIS97 3.0 24.4 1.0
CD2 A:HIS95 3.0 21.8 1.0
CD2 A:HIS157 3.1 31.0 1.0
CE1 A:HIS157 3.2 31.0 1.0
CB A:HIS97 3.3 25.2 1.0
CE1 A:HIS95 3.4 24.6 1.0
ZN A:ZN2002 3.6 18.4 0.5
OD1 A:ASP99 3.7 25.6 1.0
SG A:CYS176 3.9 27.2 1.0
NE2 A:HIS97 4.1 25.3 1.0
O4 A:CIT2003 4.1 33.2 1.0
CB A:CYS176 4.1 26.4 1.0
CD2 A:HIS97 4.1 24.4 1.0
C3 A:CIT2003 4.2 30.9 1.0
CG A:HIS95 4.2 22.0 1.0
CG A:HIS157 4.2 31.0 1.0
ND1 A:HIS157 4.3 30.7 1.0
OD2 A:ASP99 4.4 25.8 1.0
ND1 A:HIS95 4.4 23.6 1.0
CG A:ASP99 4.5 26.4 1.0
C5 A:CIT2003 4.5 32.8 1.0
CG2 A:THR158 4.7 27.3 1.0
O7 A:CIT2003 4.7 31.2 1.0
CA A:HIS97 4.8 25.6 1.0
C4 A:CIT2003 4.9 32.0 1.0

Zinc binding site 2 out of 4 in 5b3r

Go back to Zinc Binding Sites List in 5b3r
Zinc binding site 2 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa


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 Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:18.4
occ:0.50
NE2 A:HIS215 1.9 21.0 1.0
O5 A:CIT2003 2.0 27.2 1.0
O4 A:CIT2003 2.1 33.2 1.0
OD2 A:ASP99 2.2 25.8 1.0
O7 A:CIT2003 2.2 31.2 1.0
SG A:CYS176 2.3 27.2 1.0
CE1 A:HIS215 2.7 25.0 1.0
C6 A:CIT2003 2.7 30.0 1.0
C3 A:CIT2003 2.9 30.9 1.0
CD2 A:HIS215 3.0 25.1 1.0
C5 A:CIT2003 3.1 32.8 1.0
CG A:ASP99 3.3 26.4 1.0
C4 A:CIT2003 3.4 32.0 1.0
CB A:CYS176 3.5 26.4 1.0
ZN A:ZN2001 3.6 26.4 1.0
OD1 A:ASP99 3.7 25.6 1.0
O6 A:CIT2003 3.9 27.9 1.0
ND1 A:HIS215 3.9 24.0 1.0
CG A:HIS215 4.0 24.2 1.0
O3 A:CIT2003 4.3 29.2 1.0
C2 A:CIT2003 4.3 34.5 1.0
O1 A:CIT2003 4.3 38.5 1.0
NE2 A:HIS157 4.3 32.0 1.0
CB A:SER214 4.4 25.2 1.0
NE2 A:HIS95 4.4 22.2 1.0
CA A:CYS176 4.5 25.6 1.0
CE1 A:HIS95 4.6 24.6 1.0
CB A:ASP99 4.6 25.6 1.0
C1 A:CIT2003 4.7 36.9 1.0
OG A:SER214 4.7 27.0 1.0
CE1 A:HIS157 4.7 31.0 1.0
CD A:LYS51 4.8 21.1 1.0
CE A:LYS51 4.9 21.1 1.0

Zinc binding site 3 out of 4 in 5b3r

Go back to Zinc Binding Sites List in 5b3r
Zinc binding site 3 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa


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 Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:22.2
occ:1.00
O5 B:CIT2003 1.9 25.6 1.0
ND1 B:HIS97 2.0 20.5 1.0
NE2 B:HIS157 2.0 24.1 1.0
NE2 B:HIS95 2.2 20.6 1.0
C6 B:CIT2003 2.7 25.9 1.0
O6 B:CIT2003 2.8 23.3 1.0
CE1 B:HIS97 3.0 21.7 1.0
CD2 B:HIS95 3.0 19.6 1.0
CE1 B:HIS157 3.0 24.6 1.0
CG B:HIS97 3.1 20.6 1.0
CD2 B:HIS157 3.1 23.6 1.0
CE1 B:HIS95 3.3 21.2 1.0
CB B:HIS97 3.4 20.2 1.0
OD1 B:ASP99 3.8 23.5 1.0
SG B:CYS176 4.0 21.1 1.0
NE2 B:HIS97 4.1 21.1 1.0
O3 B:CIT2003 4.1 21.6 1.0
CB B:CYS176 4.1 19.3 1.0
ZN B:ZN2002 4.1 29.4 1.0
ND1 B:HIS157 4.1 24.0 1.0
C3 B:CIT2003 4.1 25.4 1.0
CD2 B:HIS97 4.1 20.9 1.0
CG B:HIS157 4.2 24.1 1.0
CG B:HIS95 4.2 19.4 1.0
ND1 B:HIS95 4.3 20.1 1.0
C5 B:CIT2003 4.5 23.6 1.0
O7 B:CIT2003 4.6 25.4 1.0
CG B:ASP99 4.6 22.8 1.0
CG2 B:THR158 4.6 21.9 1.0
OD2 B:ASP99 4.7 24.7 1.0
CA B:HIS97 4.8 20.9 1.0
C4 B:CIT2003 4.9 24.3 1.0

Zinc binding site 4 out of 4 in 5b3r

Go back to Zinc Binding Sites List in 5b3r
Zinc binding site 4 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa


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 Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:29.4
occ:1.00
NE2 B:HIS215 2.1 23.3 1.0
O3 B:CIT2003 2.1 21.6 1.0
O7 B:CIT2003 2.1 25.4 1.0
SG B:CYS176 2.3 21.1 1.0
OD2 B:ASP99 2.7 24.7 1.0
O5 B:CIT2003 2.7 25.6 1.0
C3 B:CIT2003 2.9 25.4 1.0
CE1 B:HIS215 3.0 23.9 1.0
C5 B:CIT2003 3.0 23.6 1.0
CD2 B:HIS215 3.1 24.2 1.0
C6 B:CIT2003 3.1 25.9 1.0
C4 B:CIT2003 3.2 24.3 1.0
CB B:CYS176 3.4 19.3 1.0
CG B:ASP99 3.7 22.8 1.0
OD1 B:ASP99 4.1 23.5 1.0
ZN B:ZN2001 4.1 22.2 1.0
ND1 B:HIS215 4.1 24.9 1.0
CB B:SER214 4.2 22.2 1.0
O4 B:CIT2003 4.2 24.2 1.0
CG B:HIS215 4.2 24.3 1.0
O2 B:CIT2003 4.3 32.1 1.0
O6 B:CIT2003 4.3 23.3 1.0
C2 B:CIT2003 4.3 28.4 1.0
CA B:CYS176 4.4 20.6 1.0
OG B:SER214 4.6 22.9 1.0
NE2 B:HIS157 4.6 24.1 1.0
CE B:LYS179 4.7 22.4 1.0
CE1 B:HIS157 4.8 24.6 1.0
NZ B:LYS179 4.8 22.0 1.0
C1 B:CIT2003 4.8 30.5 1.0
NE2 B:HIS95 4.9 20.6 1.0
CD B:LYS51 4.9 20.0 1.0
CB B:ASP99 5.0 22.8 1.0

Reference:

T.Furuyama, H.Nonomura, Y.Ishii, N.D.Hanson, A.Shimizu-Ibuka. Structural and Mutagenic Analysis of Metallo-Beta-Lactamase Imp-18 Antimicrob. Agents V. 60 5521 2016CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 27381398
DOI: 10.1128/AAC.00985-16
Page generated: Wed Dec 16 06:04:29 2020

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