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Zinc in PDB 5y5b: Crystal Structure of Imp-1 Metallo-Beta-Lactamase

Enzymatic activity of Crystal Structure of Imp-1 Metallo-Beta-Lactamase

All present enzymatic activity of Crystal Structure of Imp-1 Metallo-Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Imp-1 Metallo-Beta-Lactamase, PDB code: 5y5b was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.53 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.010, 57.730, 101.060, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase (pdb code 5y5b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase, PDB code: 5y5b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5y5b

Go back to Zinc Binding Sites List in 5y5b
Zinc binding site 1 out of 2 in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase


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 Imp-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.1
occ:1.00
O A:HOH551 1.9 10.8 1.0
NE2 A:HIS139 2.0 7.6 1.0
NE2 A:HIS77 2.0 8.3 1.0
ND1 A:HIS79 2.0 8.9 1.0
CD2 A:HIS77 3.0 7.9 1.0
CE1 A:HIS79 3.0 9.4 1.0
CE1 A:HIS139 3.0 7.6 1.0
CD2 A:HIS139 3.0 7.6 1.0
CG A:HIS79 3.1 9.4 1.0
CE1 A:HIS77 3.1 9.4 1.0
CB A:HIS79 3.4 8.6 1.0
ZN A:ZN302 3.4 15.4 1.0
O A:HOH409 3.5 24.2 1.0
SG A:CYS158 3.7 10.7 1.0
OD1 A:ASP81 3.8 14.5 1.0
CB A:CYS158 3.8 10.3 1.0
O3 A:SO4303 3.9 14.9 1.0
NE2 A:HIS79 4.1 10.6 1.0
ND1 A:HIS139 4.1 7.5 1.0
CG A:HIS77 4.2 7.7 1.0
ND1 A:HIS77 4.2 8.4 1.0
CG A:HIS139 4.2 8.1 1.0
CD2 A:HIS79 4.2 10.6 1.0
OD2 A:ASP81 4.4 11.7 1.0
CG A:ASP81 4.5 12.4 1.0
CG2 A:THR140 4.7 7.8 1.0
O A:HOH425 4.7 21.9 1.0
CA A:HIS79 4.8 8.3 1.0
S A:SO4303 4.8 20.9 1.0
O4 A:SO4303 4.9 23.2 1.0

Zinc binding site 2 out of 2 in 5y5b

Go back to Zinc Binding Sites List in 5y5b
Zinc binding site 2 out of 2 in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase


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 Imp-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:15.4
occ:1.00
OD2 A:ASP81 2.1 11.7 1.0
O A:HOH551 2.1 10.8 1.0
NE2 A:HIS197 2.1 10.4 1.0
O3 A:SO4303 2.3 14.9 1.0
SG A:CYS158 2.4 10.7 1.0
O A:HOH425 2.5 21.9 1.0
CD2 A:HIS197 3.1 11.8 1.0
CG A:ASP81 3.1 12.4 1.0
CE1 A:HIS197 3.1 12.6 1.0
ZN A:ZN301 3.4 9.1 1.0
OD1 A:ASP81 3.5 14.5 1.0
S A:SO4303 3.5 20.9 1.0
CB A:CYS158 3.5 10.3 1.0
O4 A:SO4303 3.7 23.2 1.0
O1 A:SO4303 4.1 24.8 1.0
O A:HOH409 4.2 24.2 1.0
O A:HOH461 4.2 35.2 1.0
ND1 A:HIS197 4.2 12.1 1.0
CG A:HIS197 4.2 11.8 1.0
NE2 A:HIS139 4.3 7.6 1.0
NE2 A:HIS77 4.4 8.3 1.0
CB A:ASP81 4.4 9.5 1.0
CE1 A:HIS77 4.4 9.4 1.0
CB A:SER196 4.6 10.1 1.0
O2 A:SO4303 4.7 20.9 1.0
CA A:CYS158 4.7 10.1 1.0
CE1 A:HIS139 4.7 7.6 1.0
OG A:SER196 4.8 9.6 1.0
CD A:LYS33 4.8 10.2 1.0
CE A:LYS33 4.9 9.8 1.0

Reference:

J.Wachino, J.Wachino. N/A N/A.
Page generated: Wed Dec 16 11:22:12 2020

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