Zinc in PDB 5grr: Crystal Structure of Mcr-1

The structure of Crystal Structure of Mcr-1, PDB code: 5grr was solved by G.Ma, Y.Zhu, Z.Yu, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.314, 62.696, 104.831, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.7

The binding sites of Zinc atom in the Crystal Structure of Mcr-1 (pdb code 5grr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Mcr-1, PDB code: 5grr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Mcr-1


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 Mcr-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:14.2 occ:1.00 OD2 A:ASP465 1.9 14.1 1.0 OE2 A:GLU246 2.0 15.0 1.0 OG1 A:THR285 2.0 17.0 1.0 NE2 A:HIS466 2.1 12.8 1.0 O A:HOH703 2.1 51.5 0.8 OE1 A:GLU246 2.6 15.7 1.0 CD A:GLU246 2.6 14.7 1.0 CG A:ASP465 2.8 13.3 1.0 OD1 A:ASP465 3.0 13.2 1.0 CD2 A:HIS466 3.0 12.6 1.0 CE1 A:HIS466 3.0 12.3 1.0 CB A:THR285 3.1 16.3 1.0 N A:THR285 3.5 16.2 1.0 CA A:THR285 3.5 15.8 1.0 CG2 A:THR285 3.7 16.2 1.0 O A:HOH704 3.7 23.7 1.0 ND1 A:HIS466 4.0 12.5 1.0 CG A:HIS466 4.1 12.2 1.0 CG A:GLU246 4.1 13.9 1.0 O A:HOH798 4.1 15.4 1.0 CB A:ASP465 4.2 12.8 1.0 C A:SER284 4.2 16.1 1.0 OG1 A:THR247 4.3 13.8 1.0 ZN A:ZN602 4.3 16.3 1.0 NE2 A:HIS478 4.3 12.5 1.0 N A:THR247 4.6 12.9 1.0 CD2 A:HIS395 4.6 14.8 1.0 CD2 A:HIS478 4.7 12.8 1.0 O A:HOH763 4.7 33.3 1.0 CA A:GLU246 4.7 12.8 1.0 CA A:SER284 4.9 16.6 1.0 CB A:GLU246 4.9 13.2 1.0 O A:SER284 4.9 16.0 1.0 CE1 A:HIS478 4.9 12.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Mcr-1


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 Mcr-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:16.3 occ:1.00 NE2 A:HIS478 2.0 12.5 1.0 O A:HOH704 2.1 23.7 1.0 NE2 A:HIS395 2.1 15.3 1.0 O A:HOH703 2.2 51.5 0.8 CE1 A:HIS478 2.9 12.8 1.0 CD2 A:HIS395 3.0 14.8 1.0 CE1 A:HIS395 3.1 15.7 1.0 CD2 A:HIS478 3.2 12.8 1.0 OG1 A:THR285 3.7 17.0 1.0 ND1 A:HIS478 4.1 12.6 1.0 ND1 A:HIS395 4.2 15.6 1.0 O A:HOH763 4.2 33.3 1.0 CG A:HIS395 4.2 14.6 1.0 CG A:HIS478 4.2 12.4 1.0 ZN A:ZN601 4.3 14.2 1.0 OE2 A:GLU246 4.4 15.0 1.0 NE2 A:HIS466 4.6 12.8 1.0 CE1 A:HIS466 4.7 12.3 1.0 CB A:THR285 4.9 16.3 1.0 N A:THR285 4.9 16.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Mcr-1


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 Mcr-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:16.3 occ:0.33 SG A:CYS291 1.7 15.9 0.0 SG A:CYS291 2.0 17.7 1.0 SG A:CYS281 2.2 16.5 0.3 O A:HOH942 2.4 24.2 1.0 CB A:CYS281 2.5 17.2 0.3 CB A:CYS281 2.6 15.8 0.4 CB A:CYS281 2.6 16.8 0.3 SG A:CYS281 2.6 16.1 0.4 CB A:CYS291 2.8 15.6 0.0 SG A:CYS281 2.9 17.3 0.3 CB A:CYS291 3.0 16.4 1.0 CB A:HIS515 3.5 13.1 1.0 C A:CYS291 3.5 15.0 1.0 O A:CYS291 3.5 15.0 1.0 CA A:CYS291 3.7 15.5 0.0 CA A:CYS281 3.8 16.3 0.4 CA A:CYS291 3.8 15.8 1.0 CA A:CYS281 3.9 16.9 0.3 OD1 A:ASP516 3.9 19.0 1.0 CA A:CYS281 3.9 16.7 0.3 N A:MET292 4.0 13.9 1.0 ND1 A:HIS515 4.1 13.7 1.0 CG A:HIS515 4.3 13.1 1.0 N A:CYS281 4.3 15.9 1.0 CB A:ALA298 4.4 21.5 1.0 CA A:ALA298 4.5 21.9 1.0 N A:ALA298 4.5 21.5 1.0 C A:HIS515 4.5 13.3 1.0 CA A:MET292 4.6 13.5 1.0 CA A:HIS515 4.6 13.0 1.0 N A:ASP516 4.7 14.1 1.0 O A:SER288 4.8 14.1 1.0 O A:HIS515 4.9 13.6 1.0 N A:CYS291 5.0 15.5 1.0

G.Ma, Y.Zhu, Z.Yu, A.Ahmad, H.Zhang. High Resolution Crystal Structure of the Catalytic Domain of Mcr-1 Sci Rep V. 6 39540 2016.
ISSN: ESSN 2045-2322
PubMed: 28000749
DOI: 10.1038/SREP39540