Zinc in PDB 2doo: The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe

All present enzymatic activity of The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe:
3.5.2.6;

The structure of The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe, PDB code: 2doo was solved by H.Kurosaki, Y.Yamaguchi, H.Yasuzawa, W.Jin, Y.Yamagata, Y.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.517, 88.416, 115.064, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.5

The binding sites of Zinc atom in the The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe (pdb code 2doo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe, PDB code: 2doo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:10.6 occ:1.00 ND1 A:HIS79 2.0 7.3 1.0 NE2 A:HIS77 2.1 7.3 1.0 S25 A:C4H601 2.1 14.9 0.5 NE2 A:HIS139 2.1 6.3 1.0 S25 A:C4H601 2.2 14.9 0.5 CD2 A:HIS77 2.8 7.2 1.0 CD2 A:HIS139 2.9 7.3 1.0 CG A:HIS79 3.0 8.8 1.0 CE1 A:HIS79 3.0 7.1 1.0 CE1 A:HIS139 3.2 7.1 1.0 CE1 A:HIS77 3.2 9.1 1.0 C24 A:C4H601 3.3 14.7 0.5 CB A:HIS79 3.3 8.4 1.0 C24 A:C4H601 3.7 16.5 0.5 ZN A:ZN502 3.7 11.3 1.0 SG A:CYS158 3.9 9.4 1.0 CB A:CYS158 3.9 7.3 1.0 NE2 A:HIS79 4.0 7.0 1.0 CD2 A:HIS79 4.0 7.5 1.0 CG A:HIS77 4.1 6.8 1.0 OD1 A:ASP81 4.1 8.3 1.0 CG A:HIS139 4.1 8.8 1.0 ND1 A:HIS77 4.2 9.1 1.0 ND1 A:HIS139 4.2 8.7 1.0 CG2 A:THR140 4.4 10.9 1.0 O A:HOH746 4.4 30.9 1.0 OD2 A:ASP81 4.6 9.5 1.0 C23 A:C4H601 4.7 15.5 0.5 CA A:HIS79 4.7 8.5 1.0 CG A:ASP81 4.7 7.8 1.0 C23 A:C4H601 4.7 17.4 0.5 N A:HIS79 5.0 8.1 1.0

Zinc binding site 2 out of 4 in the The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:11.3 occ:1.00 OD2 A:ASP81 2.0 9.5 1.0 NE2 A:HIS197 2.1 11.7 1.0 SG A:CYS158 2.2 9.4 1.0 S25 A:C4H601 2.4 14.9 0.5 S25 A:C4H601 2.4 14.9 0.5 CE1 A:HIS197 3.0 11.5 1.0 CG A:ASP81 3.0 7.8 1.0 CD2 A:HIS197 3.2 9.8 1.0 C24 A:C4H601 3.2 16.5 0.5 C24 A:C4H601 3.5 14.7 0.5 OD1 A:ASP81 3.5 8.3 1.0 CB A:CYS158 3.5 7.3 1.0 C23 A:C4H601 3.7 15.5 0.5 ZN A:ZN501 3.7 10.6 1.0 ND1 A:HIS197 4.1 11.5 1.0 O22 A:C4H601 4.2 17.3 0.5 C23 A:C4H601 4.2 17.4 0.5 CE1 A:HIS77 4.2 9.1 1.0 NE2 A:HIS77 4.2 7.3 1.0 CG A:HIS197 4.2 10.1 1.0 CB A:ASP81 4.3 7.4 1.0 CB A:SER196 4.4 11.0 1.0 C21 A:C4H601 4.4 17.2 0.5 C21 A:C4H601 4.4 14.6 0.5 O A:HOH695 4.5 18.3 1.0 CD A:LYS33 4.5 7.6 1.0 CE A:LYS33 4.6 6.1 1.0 CA A:CYS158 4.6 8.2 1.0 NE2 A:HIS139 4.7 6.3 1.0 OG A:SER196 4.8 11.7 1.0 N20 A:C4H601 4.9 15.1 0.5

Zinc binding site 3 out of 4 in the The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:13.8 occ:1.00 ND1 B:HIS79 2.0 7.8 1.0 NE2 B:HIS139 2.1 11.1 1.0 NE2 B:HIS77 2.1 10.5 1.0 S25 B:C4H602 2.4 1.0 0.5 S25 B:C4H602 2.4 24.0 0.5 CD2 B:HIS77 2.9 10.8 1.0 CD2 B:HIS139 2.9 11.1 1.0 CE1 B:HIS79 3.0 7.3 1.0 CG B:HIS79 3.0 8.6 1.0 CE1 B:HIS139 3.2 11.3 1.0 CE1 B:HIS77 3.2 12.0 1.0 C24 B:C4H602 3.2 26.6 0.5 C24 B:C4H602 3.3 3.9 0.5 CB B:HIS79 3.3 8.3 1.0 ZN B:ZN504 3.7 13.3 1.0 SG B:CYS158 3.9 14.6 1.0 CB B:CYS158 3.9 11.3 1.0 NE2 B:HIS79 4.1 9.0 1.0 OD1 B:ASP81 4.1 8.8 1.0 CD2 B:HIS79 4.1 9.6 1.0 CG B:HIS77 4.1 10.4 1.0 CG B:HIS139 4.1 10.0 1.0 O B:HOH663 4.2 37.1 1.0 ND1 B:HIS139 4.2 10.1 1.0 ND1 B:HIS77 4.2 12.0 1.0 CG2 B:THR140 4.3 13.3 1.0 C23 B:C4H602 4.4 28.8 0.5 C23 B:C4H602 4.7 7.1 0.5 OD2 B:ASP81 4.7 8.0 1.0 CA B:HIS79 4.8 7.7 1.0 CG B:ASP81 4.8 8.2 1.0 O B:HOH675 4.9 17.0 1.0

Zinc binding site 4 out of 4 in the The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Imp-1 Complexed with the Detecting Reagent (DANSYLC4SH) By A Fluorescent Probe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:13.3 occ:1.00 OD2 B:ASP81 1.9 8.0 1.0 NE2 B:HIS197 2.1 17.8 1.0 S25 B:C4H602 2.2 24.0 0.5 SG B:CYS158 2.2 14.6 1.0 S25 B:C4H602 2.3 1.0 0.5 CG B:ASP81 2.9 8.2 1.0 CE1 B:HIS197 3.0 16.7 1.0 CD2 B:HIS197 3.1 18.1 1.0 OD1 B:ASP81 3.3 8.8 1.0 C24 B:C4H602 3.4 3.9 0.5 CB B:CYS158 3.5 11.3 1.0 ZN B:ZN503 3.7 13.8 1.0 C24 B:C4H602 3.8 26.6 0.5 C23 B:C4H602 3.9 7.1 0.5 CE1 B:HIS77 4.1 12.0 1.0 O22 B:C4H602 4.1 30.9 0.5 C21 B:C4H602 4.1 29.7 0.5 ND1 B:HIS197 4.1 17.8 1.0 NE2 B:HIS77 4.2 10.5 1.0 C23 B:C4H602 4.2 28.8 0.5 CB B:ASP81 4.2 6.9 1.0 CG B:HIS197 4.2 17.5 1.0 CB B:SER196 4.3 13.5 1.0 O B:HOH675 4.4 17.0 1.0 CE B:LYS33 4.4 4.3 1.0 CD B:LYS33 4.6 6.5 1.0 CA B:CYS158 4.6 10.5 1.0 C21 B:C4H602 4.6 6.6 0.5 OG B:SER196 4.7 14.1 1.0 NE2 B:HIS139 4.7 11.1 1.0 N20 B:C4H602 4.8 6.1 0.5 N20 B:C4H602 4.9 29.0 0.5

H.Kurosaki, Y.Yamaguchi, H.Yasuzawa, W.Jin, Y.Yamagata, Y.Arakawa. Probing, Inhibition, and Crystallographic Characterization of Metallo-Beta-Lactamase (Imp-1) with Fluorescent Agents Containing Dansyl and Thiol Groups Chemmedchem V. 1 969 2006.
ISSN: ISSN 1860-7179
PubMed: 16937423
DOI: 10.1002/CMDC.200600115