Zinc in PDB 5xkp: Crystal Structure of MSMEG3575 in Complex with 5-Azacytosine

The structure of Crystal Structure of MSMEG3575 in Complex with 5-Azacytosine, PDB code: 5xkp 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)	62.08 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.621, 108.831, 62.076, 90.00, 89.95, 90.00
R / Rfree (%)	18 / 24.2

The binding sites of Zinc atom in the Crystal Structure of MSMEG3575 in Complex with 5-Azacytosine (pdb code 5xkp). 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 5-Azacytosine, PDB code: 5xkp:
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 5-Azacytosine


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 5-Azacytosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:43.0 occ:0.77 O A:HOH302 1.8 42.7 1.0 ND1 A:HIS56 2.2 57.2 1.0 SG A:CYS86 2.2 45.6 1.0 SG A:CYS89 2.3 44.9 1.0 CE1 A:HIS56 2.9 60.9 1.0 CB A:CYS89 3.2 50.7 1.0 CB A:CYS86 3.3 46.3 1.0 CG A:HIS56 3.3 58.8 1.0 N A:CYS86 3.7 45.9 1.0 CB A:HIS56 3.8 57.0 1.0 N A:CYS89 3.8 52.3 1.0 N2 A:5AZ201 3.9 0.8 1.0 C3 A:5AZ201 3.9 0.4 1.0 CA A:CYS86 3.9 48.4 1.0 CE A:MET88 4.1 50.8 1.0 CA A:CYS89 4.1 52.1 1.0 O A:CYS86 4.1 48.2 1.0 N7 A:5AZ201 4.1 93.5 1.0 NE2 A:HIS56 4.1 63.2 1.0 C A:CYS86 4.3 50.0 1.0 OE2 A:GLU58 4.3 73.0 1.0 C1 A:5AZ201 4.3 0.6 1.0 N4 A:5AZ201 4.3 0.9 1.0 CD2 A:HIS56 4.3 62.0 1.0 CB A:MET88 4.4 50.1 1.0 OE1 A:GLU58 4.6 67.2 1.0 CD A:GLU58 4.6 60.9 1.0 N6 A:5AZ201 4.7 0.2 1.0 C5 A:5AZ201 4.7 0.1 1.0 NE1 B:TRP95 4.8 63.3 1.0 O8 A:5AZ201 4.8 88.0 1.0 C A:MET88 4.8 47.2 1.0 C A:HIS85 4.9 47.2 1.0 N A:MET88 5.0 45.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of MSMEG3575 in Complex with 5-Azacytosine


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 5-Azacytosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:44.2 occ:0.80 O B:HOH301 1.6 27.6 1.0 ND1 B:HIS56 2.0 53.5 1.0 SG B:CYS86 2.3 47.1 1.0 SG B:CYS89 2.3 42.7 1.0 CE1 B:HIS56 2.8 54.8 1.0 CG B:HIS56 3.2 52.3 1.0 CB B:CYS89 3.3 45.3 1.0 CB B:CYS86 3.4 48.7 1.0 N7 B:5AZ201 3.4 78.7 1.0 C3 B:5AZ201 3.5 83.2 1.0 N2 B:5AZ201 3.6 87.3 1.0 CB B:HIS56 3.6 53.5 1.0 N B:CYS86 3.8 49.9 1.0 N B:CYS89 3.9 48.5 1.0 CE B:MET88 4.0 47.6 1.0 NE2 B:HIS56 4.0 54.2 1.0 CA B:CYS86 4.1 50.2 1.0 N4 B:5AZ201 4.1 81.8 1.0 CD2 B:HIS56 4.2 52.8 1.0 CA B:CYS89 4.2 48.1 1.0 OE2 B:GLU58 4.3 58.8 1.0 O B:CYS86 4.3 54.3 1.0 C1 B:5AZ201 4.3 89.9 1.0 OE1 B:GLU58 4.5 62.0 1.0 CB B:MET88 4.5 50.0 1.0 C B:CYS86 4.5 50.8 1.0 NE1 A:TRP95 4.5 47.0 1.0 CD B:GLU58 4.6 56.7 1.0 C5 B:5AZ201 4.8 82.2 1.0 N6 B:5AZ201 4.8 92.0 1.0 O8 B:5AZ201 4.9 74.7 1.0 C B:MET88 4.9 51.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of MSMEG3575 in Complex with 5-Azacytosine


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 5-Azacytosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:43.1 occ:0.77 O C:HOH302 1.9 36.2 1.0 ND1 C:HIS56 2.1 59.2 1.0 SG C:CYS86 2.2 51.1 1.0 SG C:CYS89 2.3 48.4 1.0 CE1 C:HIS56 2.9 59.2 1.0 CG C:HIS56 3.2 61.9 1.0 CB C:CYS89 3.2 50.7 1.0 CB C:CYS86 3.4 49.7 1.0 CB C:HIS56 3.7 60.8 1.0 N C:CYS89 3.8 54.1 1.0 N C:CYS86 3.8 49.5 1.0 CE C:MET88 3.9 47.4 1.0 C3 C:5AZ201 4.0 0.2 1.0 NE2 C:HIS56 4.1 61.3 1.0 CA C:CYS86 4.1 51.0 1.0 N2 C:5AZ201 4.1 0.8 1.0 CA C:CYS89 4.1 52.2 1.0 O C:CYS86 4.2 47.0 1.0 CD2 C:HIS56 4.2 63.3 1.0 OE1 C:GLU58 4.2 67.9 1.0 N7 C:5AZ201 4.3 0.7 1.0 N4 C:5AZ201 4.3 0.5 1.0 CB C:MET88 4.4 48.1 1.0 C C:CYS86 4.4 49.8 1.0 C1 C:5AZ201 4.5 0.8 1.0 C5 C:5AZ201 4.7 0.4 1.0 NE1 D:TRP95 4.8 61.1 1.0 N6 C:5AZ201 4.8 0.2 1.0 C C:MET88 4.8 49.5 1.0 CD C:GLU58 4.8 61.6 1.0 CA C:MET88 5.0 46.9 1.0 N C:MET88 5.0 45.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of MSMEG3575 in Complex with 5-Azacytosine


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 5-Azacytosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:46.9 occ:0.80 O D:HOH301 1.4 25.0 1.0 ND1 D:HIS56 2.1 50.3 1.0 SG D:CYS89 2.2 43.1 1.0 SG D:CYS86 2.3 44.5 1.0 CE1 D:HIS56 2.9 50.3 1.0 CB D:CYS89 3.1 45.4 1.0 CG D:HIS56 3.2 51.4 1.0 CB D:CYS86 3.5 46.1 1.0 N7 D:5AZ201 3.5 63.7 1.0 CB D:HIS56 3.6 52.7 1.0 C3 D:5AZ201 3.7 72.6 1.0 N2 D:5AZ201 3.8 78.6 1.0 N D:CYS86 3.8 46.7 1.0 N D:CYS89 3.8 46.8 1.0 CE D:MET88 4.0 46.3 1.0 CA D:CYS89 4.1 46.5 1.0 NE2 D:HIS56 4.1 49.9 1.0 CA D:CYS86 4.1 46.7 1.0 OE2 D:GLU58 4.2 57.2 1.0 CD2 D:HIS56 4.2 49.8 1.0 O D:CYS86 4.3 51.7 1.0 N4 D:5AZ201 4.3 70.8 1.0 OE1 D:GLU58 4.4 56.7 1.0 CD D:GLU58 4.5 53.3 1.0 C D:CYS86 4.5 46.0 1.0 CB D:MET88 4.5 49.4 1.0 C1 D:5AZ201 4.5 81.3 1.0 NE1 C:TRP95 4.7 47.3 1.0 C D:MET88 4.9 49.0 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