Zinc in PDB 6xtx: Cryoem Structure of Human Cmg Bound to Atpgammas and Dna

All present enzymatic activity of Cryoem Structure of Human Cmg Bound to Atpgammas and Dna:
3.6.4.12;

The structure of Cryoem Structure of Human Cmg Bound to Atpgammas and Dna also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Cryoem Structure of Human Cmg Bound to Atpgammas and Dna (pdb code 6xtx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryoem Structure of Human Cmg Bound to Atpgammas and Dna, PDB code: 6xtx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Cryoem Structure of Human Cmg Bound to Atpgammas and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of Human Cmg Bound to Atpgammas and Dna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Zn1000 b:0.9 occ:1.00 SG 2:CYS332 2.2 0.9 1.0 SG 2:CYS352 2.2 0.3 1.0 SG 2:CYS355 2.3 0.8 1.0 SG 2:CYS329 2.3 0.4 1.0 CB 2:CYS329 2.8 0.4 1.0 CB 2:CYS352 3.1 0.3 1.0 CB 2:CYS332 3.1 0.9 1.0 CB 2:CYS355 3.9 0.8 1.0 N 2:CYS332 4.0 0.9 1.0 OG 2:SER357 4.1 0.0 1.0 N 2:CYS355 4.1 0.8 1.0 CA 2:CYS332 4.2 0.9 1.0 CA 2:CYS329 4.3 0.4 1.0 CB 2:SER357 4.3 0.0 1.0 CA 2:CYS355 4.5 0.8 1.0 CA 2:CYS352 4.6 0.3 1.0 C 2:LYS331 4.7 0.3 1.0 CB 2:GLU354 4.8 0.4 1.0 N 2:LYS331 4.8 0.3 1.0 C 2:CYS329 4.8 0.4 1.0 C 2:GLU354 4.9 0.4 1.0 C 2:CYS355 5.0 0.8 1.0 N 2:SER357 5.0 0.0 1.0

Zinc binding site 2 out of 5 in the Cryoem Structure of Human Cmg Bound to Atpgammas and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of Human Cmg Bound to Atpgammas and Dna within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn901 b:0.7 occ:1.00 SG 4:CYS306 2.1 0.3 1.0 SG 4:CYS328 2.1 0.8 1.0 SG 4:CYS309 2.2 0.7 1.0 SG 4:CYS331 2.3 0.3 1.0 CB 4:CYS328 2.5 0.8 1.0 CB 4:CYS306 2.8 0.3 1.0 CB 4:CYS309 3.1 0.7 1.0 N 4:CYS309 3.2 0.7 1.0 OG 4:SER336 3.4 0.6 1.0 CA 4:CYS309 3.7 0.7 1.0 CB 4:CYS331 3.8 0.3 1.0 CA 4:CYS328 3.9 0.8 1.0 CB 4:VAL308 4.2 0.4 1.0 CA 4:CYS306 4.2 0.3 1.0 C 4:VAL308 4.3 0.4 1.0 N 4:VAL308 4.4 0.4 1.0 N 4:CYS331 4.5 0.3 1.0 CA 4:VAL308 4.5 0.4 1.0 SD 4:MET337 4.6 0.7 1.0 C 4:CYS309 4.6 0.7 1.0 CB 4:SER336 4.6 0.6 1.0 CA 4:CYS331 4.7 0.3 1.0 N 4:ALA310 4.7 0.8 1.0 N 4:CYS328 4.7 0.8 1.0 N 4:HIS332 4.8 0.8 1.0 C 4:CYS306 4.8 0.3 1.0 C 4:CYS328 4.8 0.8 1.0 CG1 4:VAL308 4.9 0.4 1.0 N 4:GLN307 5.0 0.6 1.0

Zinc binding site 3 out of 5 in the Cryoem Structure of Human Cmg Bound to Atpgammas and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of Human Cmg Bound to Atpgammas and Dna within 5.0Å range: probe atom residue distance (Å) B Occ 5:Zn1000 b:0.1 occ:1.00 SG 5:CYS175 2.2 0.7 1.0 SG 5:CYS197 2.2 0.7 1.0 SG 5:CYS207 2.3 0.3 1.0 SG 5:CYS172 2.3 0.1 1.0 CB 5:CYS175 3.1 0.7 1.0 CB 5:CYS172 3.4 0.1 1.0 CB 5:CYS207 3.4 0.3 1.0 CB 5:CYS197 3.5 0.7 1.0 N 5:CYS175 3.6 0.7 1.0 OG 5:SER174 3.7 0.2 1.0 CA 5:CYS175 3.9 0.7 1.0 C 5:CYS175 4.4 0.7 1.0 N 5:ARG176 4.5 0.3 1.0 CB 5:ASN177 4.7 0.8 1.0 C 5:SER174 4.7 0.2 1.0 N 5:ASN177 4.7 0.8 1.0 CA 5:CYS172 4.8 0.1 1.0 CA 5:CYS207 4.8 0.3 1.0 CA 5:CYS197 4.8 0.7 1.0 N 5:SER174 4.8 0.2 1.0 CG 5:PRO211 4.9 0.8 1.0 CB 5:PRO211 4.9 0.8 1.0 CB 5:SER174 5.0 0.2 1.0

Zinc binding site 4 out of 5 in the Cryoem Structure of Human Cmg Bound to Atpgammas and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryoem Structure of Human Cmg Bound to Atpgammas and Dna within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn901 b:0.5 occ:1.00 SG 6:CYS185 2.3 0.1 1.0 SG 6:CYS158 2.3 0.3 1.0 SG 6:CYS161 2.4 0.2 1.0 SG 6:CYS180 2.4 0.2 1.0 CB 6:CYS185 3.0 0.1 1.0 CB 6:CYS180 3.2 0.2 1.0 OD1 6:ASP160 3.3 0.1 1.0 CB 6:CYS161 3.4 0.2 1.0 CA 6:CYS185 3.8 0.1 1.0 CB 6:CYS158 3.8 0.3 1.0 OG1 6:THR163 4.0 0.2 1.0 CE1 6:PHE191 4.2 0.1 1.0 N 6:CYS161 4.3 0.2 1.0 CB 6:ASN182 4.3 0.1 1.0 CA 6:CYS161 4.5 0.2 1.0 CG 6:ASP160 4.5 0.1 1.0 CA 6:CYS180 4.7 0.2 1.0 O 6:VAL184 4.7 0.6 1.0 N 6:CYS185 4.8 0.1 1.0 ND2 6:ASN182 4.8 0.1 1.0 C 6:CYS185 4.8 0.1 1.0 CZ 6:PHE191 4.8 0.1 1.0 OD2 6:ASP160 4.9 0.1 1.0 OD1 6:ASN187 5.0 0.5 1.0

Zinc binding site 5 out of 5 in the Cryoem Structure of Human Cmg Bound to Atpgammas and Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryoem Structure of Human Cmg Bound to Atpgammas and Dna within 5.0Å range: probe atom residue distance (Å) B Occ 7:Zn1000 b:0.9 occ:1.00 SG 7:CYS184 2.2 0.8 1.0 SG 7:CYS206 2.3 0.2 1.0 SG 7:CYS187 2.3 0.0 1.0 SG 7:CYS211 2.4 0.5 1.0 CB 7:CYS184 2.9 0.8 1.0 CB 7:CYS211 3.0 0.5 1.0 CB 7:CYS187 3.0 0.0 1.0 CB 7:CYS206 3.6 0.2 1.0 N 7:CYS187 3.9 0.0 1.0 CA 7:CYS187 4.1 0.0 1.0 OG 7:SER208 4.1 0.4 1.0 CA 7:CYS184 4.4 0.8 1.0 CA 7:CYS211 4.5 0.5 1.0 O 7:CYS184 4.8 0.8 1.0 C 7:CYS184 4.9 0.8 1.0 C 7:CYS187 4.9 0.0 1.0 CA 7:CYS206 5.0 0.2 1.0

N.J.Rzechorzek, S.W.Hardwick, V.A.Jatikusumo, D.Y.Chirgadze, L.Pellegrini. Cryoem Structures of Human Cmg - Atpgammas - Dna and Cmg - and-1 Complexes Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAA429