Zinc in PDB 7zob: Metagenomic Cytidine Deaminase Cdd

The structure of Metagenomic Cytidine Deaminase Cdd, PDB code: 7zob was solved by G.Tamulaitiene, N.Urbeliene, R.Meskys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.72 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.484, 128.899, 97.259, 90, 90.02, 90
R / Rfree (%)	14.6 / 16.1

The binding sites of Zinc atom in the Metagenomic Cytidine Deaminase Cdd (pdb code 7zob). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Metagenomic Cytidine Deaminase Cdd, PDB code: 7zob:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:12.1 occ:1.00 O A:HOH306 2.0 12.7 1.0 SG A:CYS53 2.3 12.3 1.0 SG A:CYS91 2.3 12.1 1.0 SG A:CYS88 2.3 11.5 1.0 CB A:CYS53 3.1 11.7 1.0 CB A:CYS91 3.3 11.0 1.0 CB A:CYS88 3.4 11.6 1.0 N A:CYS88 3.7 11.4 1.0 OE2 A:GLU55 3.9 16.5 1.0 N A:CYS91 3.9 10.5 1.0 O2 A:MPD202 4.0 13.5 1.0 CA A:CYS88 4.0 11.6 1.0 CD A:GLU55 4.2 14.9 1.0 CA A:CYS91 4.2 10.9 1.0 OG D:SER47 4.3 12.8 1.0 NH2 A:ARG56 4.3 14.4 1.0 OE1 A:GLU55 4.4 13.7 1.0 O A:HOH312 4.5 14.3 1.0 NE A:ARG56 4.5 14.3 1.0 C A:CYS88 4.5 11.0 1.0 O A:CYS88 4.5 11.2 1.0 O A:HOH333 4.6 13.8 1.0 CA A:CYS53 4.6 11.2 1.0 O D:HOH348 4.8 16.7 1.0 CB A:ILE90 4.8 10.5 1.0 C A:PRO87 4.8 11.5 1.0 CZ A:ARG56 4.9 13.3 1.0 CG A:GLU55 5.0 16.1 1.0

Zinc binding site 2 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:11.3 occ:1.00 O B:HOH306 2.0 12.1 1.0 SG B:CYS91 2.3 11.2 1.0 SG B:CYS53 2.3 11.5 1.0 SG B:CYS88 2.3 11.3 1.0 CB B:CYS53 3.1 10.3 1.0 CB B:CYS91 3.3 10.9 1.0 CB B:CYS88 3.3 11.5 1.0 N B:CYS88 3.7 10.5 1.0 OE2 B:GLU55 3.8 14.8 1.0 N B:CYS91 3.9 10.0 1.0 O2 B:MPD201 4.0 12.8 1.0 CA B:CYS88 4.0 11.0 1.0 CD B:GLU55 4.2 12.9 1.0 CA B:CYS91 4.2 10.5 1.0 OG C:SER47 4.3 10.8 0.8 NH2 B:ARG56 4.3 13.8 1.0 OE1 B:GLU55 4.4 12.6 1.0 O B:HOH314 4.4 13.9 1.0 NE B:ARG56 4.5 12.8 1.0 C B:CYS88 4.5 10.1 1.0 O B:CYS88 4.5 10.9 1.0 CA B:CYS53 4.5 10.1 1.0 O B:HOH340 4.6 12.9 1.0 CB B:ILE90 4.8 10.9 1.0 C B:PRO87 4.8 11.0 1.0 O C:HOH332 4.8 17.3 1.0 CZ B:ARG56 4.9 12.8 1.0

Zinc binding site 3 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn200 b:11.8 occ:1.00 O C:HOH318 2.0 13.1 1.0 SG C:CYS53 2.3 12.2 1.0 SG C:CYS91 2.3 12.2 1.0 SG C:CYS88 2.3 11.6 1.0 CB C:CYS53 3.1 11.9 1.0 CB C:CYS91 3.3 11.3 1.0 CB C:CYS88 3.4 11.7 1.0 N C:CYS88 3.7 11.4 1.0 N C:CYS91 3.9 10.4 1.0 O2 C:MPD202 4.0 13.5 1.0 CA C:CYS88 4.0 11.2 1.0 OE2 C:GLU55 4.1 16.2 1.0 CA C:CYS91 4.2 10.9 1.0 CD C:GLU55 4.3 15.4 1.0 OG B:SER47 4.3 12.8 1.0 NH2 C:ARG56 4.3 14.5 1.0 OE1 C:GLU55 4.4 13.7 1.0 NE C:ARG56 4.5 14.2 1.0 O C:HOH307 4.5 14.6 1.0 C C:CYS88 4.5 10.7 1.0 O C:CYS88 4.5 11.3 1.0 CA C:CYS53 4.6 10.9 1.0 O C:HOH335 4.6 13.9 1.0 CB C:ILE90 4.8 10.4 1.0 O B:HOH347 4.8 17.3 1.0 C C:PRO87 4.8 11.8 1.0 CZ C:ARG56 4.9 13.3 1.0 CG C:GLU55 4.9 15.9 1.0

Zinc binding site 4 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn200 b:11.1 occ:1.00 O D:HOH307 2.0 11.9 1.0 SG D:CYS53 2.3 11.4 1.0 SG D:CYS91 2.3 11.3 1.0 SG D:CYS88 2.3 11.3 1.0 CB D:CYS53 3.1 10.5 1.0 CB D:CYS91 3.3 10.8 1.0 CB D:CYS88 3.3 11.7 1.0 N D:CYS88 3.7 10.5 1.0 OE2 D:GLU55 3.8 14.3 1.0 N D:CYS91 3.9 9.9 1.0 O2 D:MPD202 4.0 12.4 1.0 CA D:CYS88 4.0 10.9 1.0 CD D:GLU55 4.2 12.1 1.0 CA D:CYS91 4.2 10.3 1.0 OG A:SER47 4.3 11.1 0.8 NH2 D:ARG56 4.3 13.7 1.0 OE1 D:GLU55 4.4 12.5 1.0 O D:HOH312 4.4 14.2 1.0 NE D:ARG56 4.5 12.5 1.0 C D:CYS88 4.5 10.2 1.0 O D:CYS88 4.5 10.7 1.0 CA D:CYS53 4.6 10.1 1.0 O D:HOH331 4.6 13.0 1.0 CB D:ILE90 4.8 10.8 1.0 O A:HOH335 4.8 17.3 1.0 C D:PRO87 4.8 10.9 1.0 CZ D:ARG56 4.9 12.9 1.0

Zinc binding site 5 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:12.1 occ:1.00 O E:HOH307 2.0 11.9 1.0 SG E:CYS91 2.3 12.2 1.0 SG E:CYS53 2.3 12.1 1.0 SG E:CYS88 2.3 11.4 1.0 CB E:CYS53 3.1 11.2 1.0 CB E:CYS91 3.3 11.5 1.0 CB E:CYS88 3.4 11.5 1.0 N E:CYS88 3.7 11.2 1.0 OE2 E:GLU55 3.8 15.9 1.0 N E:CYS91 3.9 10.9 1.0 O2 E:MPD202 4.0 13.3 1.0 CA E:CYS88 4.0 11.1 1.0 CD E:GLU55 4.2 14.7 1.0 CA E:CYS91 4.2 11.1 1.0 NH2 E:ARG56 4.3 14.9 1.0 OE1 E:GLU55 4.4 13.8 1.0 O E:HOH312 4.4 14.6 1.0 NE E:ARG56 4.4 13.6 1.0 C E:CYS88 4.5 10.7 1.0 O E:CYS88 4.5 11.1 1.0 CA E:CYS53 4.6 11.0 1.0 O E:HOH337 4.6 13.6 1.0 CB E:ILE90 4.8 11.6 1.0 C E:PRO87 4.8 11.6 1.0 CZ E:ARG56 4.9 13.9 1.0

Zinc binding site 6 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn200 b:12.5 occ:1.00 O F:HOH305 2.0 12.1 1.0 SG F:CYS53 2.3 12.4 1.0 SG F:CYS91 2.3 12.4 1.0 SG F:CYS88 2.3 12.2 1.0 CB F:CYS53 3.1 11.3 1.0 CB F:CYS91 3.3 11.4 1.0 CB F:CYS88 3.4 11.5 1.0 N F:CYS88 3.7 11.7 1.0 OE2 F:GLU55 3.8 16.0 1.0 N F:CYS91 3.9 10.6 1.0 O2 F:MPD202 4.0 13.5 1.0 CA F:CYS88 4.0 11.5 1.0 CD F:GLU55 4.2 14.7 1.0 CA F:CYS91 4.2 11.0 1.0 NH2 F:ARG56 4.3 13.9 1.0 OE1 F:GLU55 4.4 13.8 1.0 NE F:ARG56 4.5 14.0 1.0 O F:HOH311 4.5 14.4 1.0 C F:CYS88 4.5 10.9 1.0 O F:CYS88 4.5 11.2 1.0 CA F:CYS53 4.6 11.5 1.0 O F:HOH344 4.6 14.0 1.0 CB F:ILE90 4.8 11.2 1.0 C F:PRO87 4.8 11.9 1.0 CZ F:ARG56 4.9 13.5 1.0 CG F:GLU55 5.0 15.5 1.0

Zinc binding site 7 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn200 b:12.1 occ:1.00 O G:HOH310 2.0 11.8 1.0 SG G:CYS91 2.3 12.2 1.0 SG G:CYS53 2.3 11.9 1.0 SG G:CYS88 2.3 11.6 1.0 CB G:CYS53 3.1 11.4 1.0 CB G:CYS91 3.3 11.4 1.0 CB G:CYS88 3.4 11.8 1.0 N G:CYS88 3.7 11.4 1.0 OE2 G:GLU55 3.8 15.6 1.0 N G:CYS91 3.9 10.6 1.0 O2 G:MPD201 4.0 13.3 1.0 CA G:CYS88 4.0 11.5 1.0 CD G:GLU55 4.2 14.0 1.0 CA G:CYS91 4.2 10.9 1.0 NH2 G:ARG56 4.3 14.5 1.0 OE1 G:GLU55 4.4 13.8 1.0 O G:HOH312 4.4 14.5 1.0 NE G:ARG56 4.5 13.5 1.0 C G:CYS88 4.5 10.8 1.0 O G:CYS88 4.5 11.2 1.0 CA G:CYS53 4.6 10.9 1.0 O G:HOH348 4.6 13.7 1.0 CB G:ILE90 4.8 11.5 1.0 C G:PRO87 4.8 11.6 1.0 CZ G:ARG56 4.9 13.5 1.0

Zinc binding site 8 out of 8 in the Metagenomic Cytidine Deaminase Cdd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Metagenomic Cytidine Deaminase Cdd within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn200 b:11.6 occ:0.91 O H:HOH306 2.0 12.5 1.0 SG H:CYS53 2.3 12.4 1.0 SG H:CYS91 2.3 12.4 1.0 SG H:CYS88 2.3 12.2 1.0 CB H:CYS53 3.1 11.6 1.0 CB H:CYS91 3.3 11.8 1.0 CB H:CYS88 3.4 11.8 1.0 N H:CYS88 3.7 11.4 1.0 OE2 H:GLU55 3.8 15.7 1.0 N H:CYS91 3.9 10.9 1.0 O2 H:MPD202 4.0 13.8 1.0 CA H:CYS88 4.0 11.7 1.0 CD H:GLU55 4.2 14.5 1.0 CA H:CYS91 4.2 11.0 1.0 NH2 H:ARG56 4.3 14.3 1.0 OE1 H:GLU55 4.4 13.9 1.0 NE H:ARG56 4.4 13.8 1.0 O H:HOH312 4.5 14.2 1.0 C H:CYS88 4.5 10.5 1.0 O H:CYS88 4.5 11.4 1.0 CA H:CYS53 4.5 11.4 1.0 O H:HOH348 4.6 13.8 1.0 CB H:ILE90 4.8 11.5 1.0 C H:PRO87 4.8 11.5 1.0 CZ H:ARG56 4.9 13.5 1.0 CG H:GLU55 5.0 15.1 1.0

N.Urbeliene, M.Tiskus, G.Tamulaitiene, R.Gasparaviciute, R.Lapinskaite, V.Jauniskis, J.Sudzius, R.Meskiene, D.Tauraite, G.Urbelis, R.Meskys. Cytidine Deaminases Catalyze the Conversion of N(S,O)4-Substituted Pyrimidine Nucleosides. To Be Published 2023.