Zinc in PDB 5xkq: Crystal Structure of MSMEG3575 in Complex with Ammeline

The structure of Crystal Structure of MSMEG3575 in Complex with Ammeline, PDB code: 5xkq 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)	109.41 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.679, 61.392, 109.406, 90.00, 89.95, 90.00
R / Rfree (%)	19.3 / 25.3

The binding sites of Zinc atom in the Crystal Structure of MSMEG3575 in Complex with Ammeline (pdb code 5xkq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of MSMEG3575 in Complex with Ammeline, PDB code: 5xkq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Ammeline


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 MSMEG3575 in Complex with Ammeline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:36.4 occ:1.00 O A:HOH307 2.0 36.3 1.0 ND1 A:HIS56 2.1 46.5 1.0 SG A:CYS86 2.3 31.9 1.0 SG A:CYS89 2.3 32.2 1.0 CE1 A:HIS56 3.1 44.9 1.0 CG A:HIS56 3.2 47.2 1.0 CB A:CYS86 3.4 31.9 1.0 CB A:CYS89 3.4 32.6 1.0 CB A:HIS56 3.6 49.0 1.0 N A:CYS86 3.8 31.9 1.0 NAE A:6AM202 3.8 86.5 1.0 NAA A:6AM202 3.8 72.2 1.0 CAG A:6AM202 4.0 83.7 1.0 N A:CYS89 4.0 30.9 1.0 CA A:CYS86 4.1 32.8 1.0 CE A:MET88 4.2 29.9 1.0 NE2 A:HIS56 4.2 45.5 1.0 CD2 A:HIS56 4.3 48.5 1.0 OE1 A:GLU58 4.3 56.7 1.0 CA A:CYS89 4.3 32.4 1.0 O A:CYS86 4.5 38.5 1.0 C A:CYS86 4.5 35.8 1.0 CAI A:6AM202 4.6 87.4 1.0 CB A:MET88 4.7 31.0 1.0 CD A:GLU58 4.7 57.1 1.0 NAD A:6AM202 4.8 88.5 1.0 C A:HIS85 4.9 32.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Ammeline


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 MSMEG3575 in Complex with Ammeline within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:33.0 occ:0.98 O B:HOH305 2.0 24.8 1.0 ND1 B:HIS56 2.2 30.3 1.0 SG B:CYS86 2.3 30.4 1.0 SG B:CYS89 2.3 35.0 1.0 CE1 B:HIS56 3.0 29.3 1.0 CG B:HIS56 3.2 29.5 1.0 CB B:CYS86 3.3 30.1 1.0 CB B:CYS89 3.4 33.2 1.0 CB B:HIS56 3.6 31.3 1.0 N B:CYS86 3.8 29.8 1.0 NAB B:6AM202 3.8 66.7 1.0 N B:CYS89 4.0 32.1 1.0 CA B:CYS86 4.1 29.7 1.0 NAF B:6AM202 4.1 80.2 1.0 CE B:MET88 4.2 31.4 1.0 CAH B:6AM202 4.2 70.0 1.0 NE2 B:HIS56 4.2 28.8 1.0 OE1 B:GLU58 4.3 45.0 1.0 CD2 B:HIS56 4.3 28.5 1.0 CA B:CYS89 4.3 31.9 1.0 O B:CYS86 4.5 29.1 1.0 C B:CYS86 4.5 28.1 1.0 CB B:MET88 4.7 33.8 1.0 CD B:GLU58 4.7 43.3 1.0 C B:HIS85 4.9 30.5 1.0 NE1 A:TRP95 5.0 41.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Ammeline


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 MSMEG3575 in Complex with Ammeline within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:37.2 occ:0.96 O C:HOH304 2.0 41.3 1.0 ND1 C:HIS56 2.2 46.7 1.0 SG C:CYS86 2.3 36.9 1.0 SG C:CYS89 2.3 34.5 1.0 CE1 C:HIS56 3.1 44.9 1.0 CG C:HIS56 3.2 45.7 1.0 CB C:CYS86 3.4 34.0 1.0 CB C:CYS89 3.4 33.1 1.0 CB C:HIS56 3.6 46.5 1.0 N C:CYS86 3.8 31.9 1.0 NAB C:6AM201 3.8 70.6 1.0 NAF C:6AM201 4.0 79.4 1.0 N C:CYS89 4.0 31.5 1.0 CAH C:6AM201 4.0 77.5 1.0 CA C:CYS86 4.1 34.1 1.0 CE C:MET88 4.2 33.9 1.0 NE2 C:HIS56 4.2 43.8 1.0 CD2 C:HIS56 4.3 47.0 1.0 CA C:CYS89 4.3 32.9 1.0 OE1 C:GLU58 4.3 61.6 1.0 O C:CYS86 4.5 37.7 1.0 C C:CYS86 4.5 36.0 1.0 CB C:MET88 4.6 30.2 1.0 CD C:GLU58 4.8 61.5 1.0 CAI C:6AM201 4.8 77.1 1.0 NAD C:6AM201 4.8 76.3 1.0 C C:HIS85 4.9 32.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Ammeline


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of MSMEG3575 in Complex with Ammeline within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:32.9 occ:0.95 O D:HOH308 2.0 26.9 1.0 ND1 D:HIS56 2.2 30.8 1.0 SG D:CYS86 2.3 28.4 1.0 SG D:CYS89 2.3 35.0 1.0 CE1 D:HIS56 3.1 28.5 1.0 CG D:HIS56 3.2 29.7 1.0 CB D:CYS86 3.3 27.6 1.0 CB D:CYS89 3.4 34.4 1.0 CB D:HIS56 3.6 31.1 1.0 N D:CYS86 3.7 28.6 1.0 N D:CYS89 4.0 30.9 1.0 NAA D:6AM201 4.0 71.5 1.0 CA D:CYS86 4.0 27.9 1.0 NAE D:6AM201 4.1 82.0 1.0 CE D:MET88 4.2 33.0 1.0 NE2 D:HIS56 4.2 28.8 1.0 OE1 D:GLU58 4.3 42.5 1.0 CAG D:6AM201 4.3 72.7 1.0 CA D:CYS89 4.3 32.8 1.0 CD2 D:HIS56 4.3 28.4 1.0 O D:CYS86 4.5 29.5 1.0 C D:CYS86 4.5 27.7 1.0 CB D:MET88 4.7 33.2 1.0 CD D:GLU58 4.7 43.9 1.0 C D:HIS85 4.9 29.6 1.0 NE1 C:TRP95 5.0 35.9 1.0 OE2 D:GLU58 5.0 56.1 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