Zinc in PDB 3l6n: 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;

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

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 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 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

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