Zinc in PDB 6mdw: Mechanism of Protease Dependent Dpc Repair

The structure of Mechanism of Protease Dependent Dpc Repair, PDB code: 6mdw was solved by F.Li, J.Raczynska, Z.Chen, H.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.58 / 1.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.422, 29.553, 50.242, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.3

The binding sites of Zinc atom in the Mechanism of Protease Dependent Dpc Repair (pdb code 6mdw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mechanism of Protease Dependent Dpc Repair, PDB code: 6mdw:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mechanism of Protease Dependent Dpc Repair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mechanism of Protease Dependent Dpc Repair within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:9.9 occ:0.50 ZN A:ZN804 0.0 9.9 0.5 ZN A:ZN804 1.2 8.7 0.5 NE2 A:HIS201 1.6 8.3 0.5 SG A:CYS173 2.0 8.8 0.5 NE2 A:HIS201 2.1 10.2 0.5 CD2 A:HIS201 2.1 8.1 0.5 SG A:CYS173 2.2 7.8 0.5 SG A:CYS205 2.3 11.7 0.5 SG A:CYS169 2.3 12.8 0.5 CB A:CYS173 2.8 8.2 0.5 CE1 A:HIS201 2.9 9.2 0.5 SG A:CYS205 2.9 10.3 0.5 CE1 A:HIS201 3.0 9.5 0.5 CD2 A:HIS201 3.1 11.1 0.5 CB A:CYS169 3.2 10.1 0.5 CB A:CYS205 3.3 16.1 0.5 SG A:CYS169 3.3 9.4 0.5 CB A:CYS173 3.3 10.9 0.5 CG A:HIS201 3.4 8.0 0.5 CB A:CYS205 3.4 11.0 0.5 O A:HOH1100 3.5 18.2 0.5 ND1 A:HIS201 3.7 9.2 0.5 CB A:CYS169 3.7 8.2 0.5 OH A:TYR209 4.0 14.7 0.5 N A:CYS173 4.1 9.2 0.5 ND1 A:HIS201 4.1 12.9 0.5 CA A:CYS173 4.1 10.5 0.5 CG A:HIS201 4.2 13.1 0.5 CA A:CYS173 4.2 9.5 0.5 N A:GLY207 4.3 13.8 0.5 CA A:GLY207 4.4 11.9 0.5 CZ A:TYR209 4.4 10.8 0.5 CE2 A:TYR209 4.4 10.4 0.5 CA A:GLY171 4.4 11.5 0.5 N A:CYS173 4.4 8.5 0.5 N A:GLY171 4.5 11.1 0.5 OH A:TYR209 4.5 14.2 0.5 C A:GLY171 4.6 13.2 0.5 CA A:CYS169 4.6 9.5 0.5 CA A:CYS205 4.7 16.8 0.5 CB A:HIS201 4.7 9.0 0.5 CZ A:TYR209 4.8 17.1 0.5 O A:GLY171 4.8 15.4 0.5 C A:CYS173 4.8 7.1 0.5 C A:GLY207 4.8 13.7 0.5 CA A:CYS205 4.9 10.9 0.5 C A:CYS173 4.9 9.9 0.5 O A:GLY207 5.0 16.5 0.5 O A:HOH975 5.0 29.6 1.0 C A:CYS205 5.0 15.1 0.5

Zinc binding site 2 out of 3 in the Mechanism of Protease Dependent Dpc Repair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mechanism of Protease Dependent Dpc Repair within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:8.7 occ:0.50 ZN A:ZN804 0.0 8.7 0.5 ZN A:ZN804 1.2 9.9 0.5 SG A:CYS169 1.5 12.8 0.5 NE2 A:HIS201 2.1 8.3 0.5 SG A:CYS173 2.2 8.8 0.5 SG A:CYS169 2.3 9.4 0.5 SG A:CYS205 2.3 10.3 0.5 SG A:CYS205 2.4 11.7 0.5 CB A:CYS169 2.7 10.1 0.5 SG A:CYS173 2.9 7.8 0.5 NE2 A:HIS201 3.0 10.2 0.5 CD2 A:HIS201 3.1 8.1 0.5 CE1 A:HIS201 3.1 9.2 0.5 CB A:CYS169 3.1 8.2 0.5 CB A:CYS173 3.2 8.2 0.5 N A:GLY171 3.3 11.1 0.5 CA A:GLY171 3.4 11.5 0.5 CB A:CYS205 3.4 11.0 0.5 CE1 A:HIS201 3.6 9.5 0.5 CA A:GLY207 3.7 11.9 0.5 C A:GLY171 3.8 13.2 0.5 CB A:CYS205 3.9 16.1 0.5 CB A:CYS173 3.9 10.9 0.5 CA A:CYS169 3.9 9.5 0.5 N A:GLY207 4.0 13.8 0.5 O A:GLY171 4.0 15.4 0.5 N A:CYS173 4.0 9.2 0.5 N A:CYS173 4.1 8.5 0.5 C A:CYS169 4.1 12.7 0.5 ND1 A:HIS201 4.2 9.2 0.5 CA A:CYS173 4.2 10.5 0.5 CD2 A:HIS201 4.2 11.1 0.5 CG A:HIS201 4.2 8.0 0.5 C A:GLY207 4.3 13.7 0.5 N A:ASN170 4.3 14.5 0.5 N A:GLY207 4.3 17.4 0.5 CA A:GLY171 4.4 11.9 0.5 CA A:GLY207 4.4 14.7 0.5 N A:PRO172 4.4 14.0 0.5 CA A:CYS173 4.5 9.5 0.5 N A:GLY171 4.5 9.4 0.5 C A:GLY171 4.6 11.2 0.5 O A:HOH1100 4.6 18.2 0.5 CA A:CYS169 4.6 9.9 0.5 C A:ASN170 4.6 13.4 0.5 O A:GLY207 4.7 16.5 0.5 O A:CYS169 4.7 14.4 0.5 CE2 A:TYR209 4.8 10.4 0.5 OH A:TYR209 4.8 14.7 0.5 C A:GLY207 4.8 15.0 0.5 O A:GLY171 4.8 11.1 0.5 CA A:CYS205 4.8 10.9 0.5 N A:THR208 4.8 11.5 0.5 O A:GLY207 4.8 13.8 0.5 C A:CYS173 4.8 7.1 0.5 CZ A:TYR209 4.8 10.8 0.5 ND1 A:HIS201 4.9 12.9 0.5 N A:GLN174 4.9 9.9 0.5 CD A:PRO172 4.9 17.2 0.5

Zinc binding site 3 out of 3 in the Mechanism of Protease Dependent Dpc Repair


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mechanism of Protease Dependent Dpc Repair within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:11.1 occ:1.00 NE2 A:HIS111 2.0 8.0 1.0 NE2 A:HIS130 2.1 12.1 1.0 NE2 A:HIS115 2.1 8.9 1.0 OHB A:FLC801 2.1 12.7 1.0 OB2 A:FLC801 2.1 13.4 1.0 OA2 A:FLC801 2.1 12.0 1.0 CBC A:FLC801 2.8 24.7 1.0 CB A:FLC801 2.8 23.9 1.0 CE1 A:HIS130 3.0 17.9 1.0 CE1 A:HIS111 3.0 8.0 1.0 CE1 A:HIS115 3.1 9.5 1.0 CD2 A:HIS111 3.1 9.5 1.0 CAC A:FLC801 3.1 18.4 1.0 CD2 A:HIS115 3.1 8.8 1.0 CD2 A:HIS130 3.2 10.8 1.0 CA A:FLC801 3.5 19.0 1.0 OB1 A:FLC801 4.0 25.5 1.0 CD2 A:HIS153 4.1 33.9 0.5 ND1 A:HIS130 4.1 19.2 1.0 ND1 A:HIS111 4.1 8.9 1.0 O A:HOH955 4.2 24.5 1.0 CG A:HIS111 4.2 7.5 1.0 CG A:FLC801 4.2 21.9 1.0 ND1 A:HIS115 4.2 8.6 1.0 OA1 A:FLC801 4.2 20.9 1.0 CG A:HIS130 4.2 12.5 1.0 CG A:HIS115 4.3 7.0 1.0 NE2 A:HIS153 4.4 26.7 0.5 CGC A:FLC801 4.5 41.0 1.0 CE2 A:PHE134 4.6 9.1 0.5 OG2 A:FLC801 4.7 47.4 1.0 CZ A:PHE134 4.8 9.5 0.5 CG A:HIS153 4.8 39.3 0.5 CE2 A:PHE134 4.8 8.0 0.5 O A:VAL151 4.9 22.0 0.5 O A:VAL151 5.0 13.0 0.5

F.Li, J.E.Raczynska, Z.Chen, H.Yu. Structural Insight Into Dna-Dependent Activation of Human Metalloprotease Spartan. Cell Rep V. 26 3336 2019.
ISSN: ESSN 2211-1247
PubMed: 30893605
DOI: 10.1016/J.CELREP.2019.02.082