Zinc in PDB 8qc0: Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated

The structure of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated, PDB code: 8qc0 was solved by P.Tang, C.J.Harding, C.M.Czekster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.27 / 2.02
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	135.24, 135.24, 87.22, 90, 90, 120
R / Rfree (%)	21.4 / 24.1

The binding sites of Zinc atom in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated (pdb code 8qc0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated, PDB code: 8qc0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:67.5 occ:1.00 OE2 A:GLU83 2.1 49.9 1.0 SG D:CYS109 2.4 54.7 1.0 CD A:GLU83 3.1 47.7 1.0 O D:CYS109 3.3 53.2 1.0 OE1 A:GLU83 3.4 46.4 1.0 C D:CYS109 3.5 55.4 1.0 CB D:CYS109 3.7 50.8 1.0 CA D:CYS109 4.0 57.0 1.0 N D:SER110 4.1 54.9 1.0 OG1 B:THR79 4.1 48.2 1.0 CG2 B:THR79 4.2 45.8 1.0 CB D:PRO80 4.2 45.2 1.0 CB B:THR79 4.3 46.6 1.0 CG A:GLU83 4.5 41.3 1.0 CA D:SER110 4.6 50.8 1.0 CD B:ARG107 4.7 45.5 1.0 CA D:PRO80 4.8 42.7 1.0 CB D:ASN118 4.9 43.8 1.0

Zinc binding site 2 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:58.6 occ:1.00 OE2 B:GLU83 2.1 46.3 1.0 SG C:CYS109 2.4 50.9 1.0 CD B:GLU83 3.1 43.8 1.0 O C:CYS109 3.4 44.7 1.0 OE1 B:GLU83 3.5 42.5 1.0 O B:HOH306 3.6 38.7 1.0 O B:HOH330 3.6 42.2 1.0 C C:CYS109 3.7 46.2 1.0 CB C:CYS109 3.7 47.5 1.0 OG1 A:THR79 4.0 47.3 1.0 CB A:THR79 4.2 40.5 1.0 CG2 A:THR79 4.2 41.3 1.0 CA C:CYS109 4.2 44.8 1.0 CB C:PRO80 4.2 37.6 1.0 N C:SER110 4.2 39.9 1.0 CG B:GLU83 4.4 39.2 1.0 CD A:ARG107 4.7 39.8 1.0 CB C:ASN118 4.7 42.0 1.0 CA C:PRO80 4.8 37.5 1.0 CA C:SER110 4.8 43.5 1.0 N C:ASN118 5.0 39.2 1.0

Zinc binding site 3 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:66.8 occ:1.00 OE2 C:GLU83 2.2 51.1 1.0 SG B:CYS109 2.4 55.0 1.0 CD C:GLU83 3.2 46.6 1.0 O B:CYS109 3.4 52.5 1.0 OE1 C:GLU83 3.4 46.1 1.0 O C:HOH304 3.6 45.1 1.0 C B:CYS109 3.7 50.7 1.0 CB B:CYS109 3.7 52.0 1.0 OG1 D:THR79 4.0 49.0 1.0 CB B:PRO80 4.1 45.4 1.0 CB D:THR79 4.1 46.8 1.0 CA B:CYS109 4.1 55.7 1.0 CG2 D:THR79 4.2 48.1 1.0 N B:SER110 4.3 50.1 1.0 CG C:GLU83 4.5 39.6 1.0 NH1 D:ARG107 4.7 51.3 1.0 CA B:PRO80 4.8 44.6 1.0 CD D:ARG107 4.8 47.2 1.0 CA B:SER110 4.8 51.5 1.0 CB B:ASN118 4.8 47.5 1.0 CD B:PRO81 5.0 43.0 1.0

Zinc binding site 4 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 Wt Ribosylated within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:68.0 occ:1.00 OE2 D:GLU83 2.2 48.4 1.0 SG A:CYS109 2.4 50.7 1.0 CD D:GLU83 3.2 44.0 1.0 O A:CYS109 3.2 48.8 1.0 OE1 D:GLU83 3.5 42.8 1.0 C A:CYS109 3.5 45.7 1.0 CB A:CYS109 3.6 45.4 1.0 O D:HOH305 3.7 42.0 1.0 CA A:CYS109 4.0 41.1 1.0 OG1 C:THR79 4.1 45.8 1.0 CG2 C:THR79 4.1 44.8 1.0 N A:SER110 4.2 41.5 1.0 CB A:PRO80 4.2 35.0 1.0 CB C:THR79 4.2 44.2 1.0 CG D:GLU83 4.5 43.4 1.0 CA A:SER110 4.7 46.4 1.0 CB A:ASN118 4.8 42.1 1.0 CA A:PRO80 4.8 38.5 1.0 N A:ASN118 4.9 42.4 1.0 CD C:ARG107 4.9 41.4 1.0 NH1 C:ARG107 4.9 45.2 1.0 CD A:PRO81 5.0 33.9 1.0

P.Tang, C.J.Harding, A.L.Dickson, R.G.Da Silva, D.J.Harrison, C.M.Czekster. Snapshots of the Reaction Coordinate of A Thermophilic 2'-Deoxyribonucleoside/Ribonucleoside Transferase Acs Catalysis 3090 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C06260