Zinc in PDB 5xko: Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis

The structure of Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis, PDB code: 5xko was solved by V.M.Gaded, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.80 / 1.89
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.262, 108.335, 53.261, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 17.8

The structure of Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis (pdb code 5xko). 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 Native MSMEG3575 Deaminase From Mycobacterium Smegmatis, PDB code: 5xko:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis


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 Native MSMEG3575 Deaminase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:12.2 occ:0.77 O1 A:CAC201 1.9 8.3 1.0 ND1 A:HIS56 2.1 10.2 1.0 SG A:CYS89 2.3 9.6 1.0 SG A:CYS86 2.3 8.2 1.0 CE1 A:HIS56 3.0 10.4 1.0 CG A:HIS56 3.2 10.0 1.0 CB A:CYS89 3.3 8.2 1.0 AS A:CAC201 3.3 9.8 1.0 CB A:CYS86 3.4 8.1 1.0 CB A:HIS56 3.5 9.5 1.0 O2 A:CAC201 3.8 9.9 1.0 N A:CYS86 3.8 7.5 1.0 N A:CYS89 4.0 8.1 1.0 C1 A:CAC201 4.0 10.2 1.0 CA A:CYS86 4.1 7.8 1.0 NE2 A:HIS56 4.2 9.8 1.0 CE A:MET88 4.2 10.0 1.0 CA A:CYS89 4.2 7.8 1.0 CD2 A:HIS56 4.3 9.6 1.0 OE1 A:GLU58 4.3 10.2 1.0 O A:CYS86 4.4 6.6 1.0 C A:CYS86 4.5 7.9 1.0 CB A:MET88 4.5 8.4 1.0 C2 A:CAC201 4.9 9.2 1.0 C A:HIS85 4.9 7.4 1.0 NE1 B:TRP95 4.9 8.4 1.0 C A:MET88 5.0 7.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis


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 Native MSMEG3575 Deaminase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:11.2 occ:0.80 O1 B:CAC201 2.0 7.7 1.0 ND1 B:HIS56 2.1 8.7 1.0 SG B:CYS89 2.3 8.3 1.0 SG B:CYS86 2.3 7.1 1.0 CE1 B:HIS56 3.0 9.2 1.0 CG B:HIS56 3.2 8.8 1.0 CB B:CYS89 3.2 7.7 1.0 AS B:CAC201 3.3 8.2 1.0 CB B:CYS86 3.4 8.0 1.0 CB B:HIS56 3.6 8.7 1.0 N B:CYS86 3.8 7.3 1.0 O2 B:CAC201 3.8 8.0 1.0 N B:CYS89 3.9 7.2 1.0 C1 B:CAC201 4.0 8.4 1.0 CA B:CYS86 4.1 7.5 1.0 NE2 B:HIS56 4.2 9.4 1.0 CE B:MET88 4.2 9.9 1.0 CA B:CYS89 4.2 7.6 1.0 OE1 B:GLU58 4.2 9.2 1.0 CD2 B:HIS56 4.3 9.5 1.0 O B:CYS86 4.5 6.8 1.0 C B:CYS86 4.5 7.3 1.0 CB B:MET88 4.6 8.1 1.0 NE1 A:TRP95 4.9 8.0 1.0 C B:HIS85 4.9 6.7 1.0 C2 B:CAC201 4.9 8.2 1.0 C B:MET88 5.0 7.6 1.0 CD B:GLU58 5.0 10.1 1.0

V.Gaded, R.Anand. Selective Deamination of Mutagens By A Mycobacterial Enzyme J. Am. Chem. Soc. V. 139 10762 2017.
ISSN: ESSN 1520-5126
PubMed: 28708393
DOI: 10.1021/JACS.7B04967