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Zinc in PDB 3l6n: Crystal Structure of Metallo-Beta-Lactamase Ind-7

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Ind-7

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Ind-7:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Ind-7, PDB code: 3l6n was solved by Y.Yamaguchi, H.Kurosaki, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.28 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.599, 74.313, 47.374, 90.00, 99.38, 90.00
R / Rfree (%) 17.7 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Ind-7 (pdb code 3l6n). 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 Metallo-Beta-Lactamase Ind-7, PDB code: 3l6n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3l6n

Go back to Zinc Binding Sites List in 3l6n
Zinc binding site 1 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Ind-7


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 Ind-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.3
occ:1.00
O A:HOH625 1.9 10.5 1.0
NE2 A:HIS159 2.0 5.1 1.0
ND1 A:HIS98 2.0 6.9 1.0
NE2 A:HIS96 2.1 5.0 1.0
O A:HOH800 2.6 49.9 1.0
CE1 A:HIS98 2.9 7.4 1.0
CD2 A:HIS159 3.0 6.1 1.0
CE1 A:HIS159 3.0 8.6 1.0
CE1 A:HIS96 3.1 5.2 1.0
CG A:HIS98 3.1 5.2 1.0
CD2 A:HIS96 3.1 5.8 1.0
CB A:HIS98 3.5 5.5 1.0
ZN A:ZN302 3.6 12.2 0.7
O A:HOH801 3.8 29.5 1.0
NE2 A:HIS98 4.1 8.0 1.0
ND1 A:HIS159 4.1 7.4 1.0
CG A:HIS159 4.1 6.2 1.0
OD1 A:ASP100 4.1 6.9 1.0
CD2 A:HIS98 4.1 7.6 1.0
ND1 A:HIS96 4.2 4.0 1.0
CG A:HIS96 4.2 3.6 1.0
CB A:CYS178 4.3 7.3 0.3
CB A:CYS178 4.3 7.1 0.7
CG2 A:THR160 4.4 5.9 1.0
SG A:CYS178 4.4 7.5 0.3
SG A:CYS178 4.4 5.3 0.7
O A:HOH691 4.7 24.2 1.0
OD2 A:ASP100 4.8 10.9 1.0
CG A:ARG101 4.8 5.7 0.7
CA A:HIS98 4.9 6.0 1.0
CG A:ASP100 4.9 7.4 1.0
CG A:ARG101 4.9 4.2 0.3

Zinc binding site 2 out of 2 in 3l6n

Go back to Zinc Binding Sites List in 3l6n
Zinc binding site 2 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Ind-7


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 Ind-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.2
occ:0.70
SG A:CYS178 2.0 7.5 0.3
OD2 A:ASP100 2.0 10.9 1.0
O A:HOH625 2.1 10.5 1.0
NE2 A:HIS220 2.1 9.0 0.7
SG A:CYS178 2.2 5.3 0.7
NE2 A:HIS220 2.9 8.3 0.3
CG A:ASP100 3.0 7.4 1.0
CE1 A:HIS220 3.0 9.5 0.7
CD2 A:HIS220 3.1 9.1 0.7
CE1 A:HIS220 3.3 8.1 0.3
CB A:CYS178 3.3 7.1 0.7
OD1 A:ASP100 3.3 6.9 1.0
CB A:CYS178 3.4 7.3 0.3
NE A:ARG101 3.5 3.6 0.3
O A:HOH801 3.5 29.5 1.0
ZN A:ZN301 3.6 9.3 1.0
NH2 A:ARG101 3.6 3.6 0.3
CD2 A:HIS220 3.7 8.3 0.3
CZ A:ARG101 4.0 2.4 0.3
ND1 A:HIS220 4.1 8.6 0.3
ND1 A:HIS220 4.1 10.1 0.7
CG A:HIS220 4.2 9.6 0.7
CE1 A:HIS96 4.2 5.2 1.0
NE2 A:HIS159 4.3 5.1 1.0
NE2 A:HIS96 4.4 5.0 1.0
CG A:HIS220 4.4 9.2 0.3
CB A:ASP100 4.4 5.9 1.0
O A:HOH800 4.5 49.9 1.0
CD A:ARG101 4.5 7.2 0.7
CG A:ARG101 4.5 5.7 0.7
CG A:ARG101 4.6 4.2 0.3
CD A:ARG101 4.6 3.1 0.3
CA A:CYS178 4.6 6.8 0.7
CA A:CYS178 4.6 7.1 0.3
NE A:ARG101 4.7 8.2 0.7
CE1 A:HIS159 4.7 8.6 1.0
O A:HOH564 4.8 27.4 1.0
O A:HOH553 4.9 15.0 1.0

Reference:

Y.Yamaguchi, N.Takashio, J.-I.Wachino, Y.Yamagata, Y.Arakawa, K.Matsuda, H.Kurosaki. Structure of Metallo-Beta-Lactamase Ind-7 From A Chryseobacterium Indologenes Clinical Isolate at 1.65-A Resolution J.Biochem. V. 147 905 2010.
ISSN: ISSN 0021-924X
PubMed: 20305272
DOI: 10.1093/JB/MVQ029
Page generated: Sat Oct 26 08:24:10 2024

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