Zinc in PDB 5lcm: Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna

The structure of Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna, PDB code: 5lcm was solved by S.Schneider, C.Ebert, N.Simon, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.20 / 1.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	53.041, 53.041, 131.345, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 26.9

The binding sites of Zinc atom in the Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna (pdb code 5lcm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna, PDB code: 5lcm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:23.7 occ:1.00 SG A:CYS216 2.3 26.6 1.0 SG A:CYS213 2.3 24.1 1.0 SG A:CYS194 2.4 21.2 1.0 SG A:CYS191 2.4 23.7 1.0 CB A:CYS194 3.1 25.7 1.0 CB A:CYS216 3.1 23.8 1.0 CB A:CYS191 3.2 25.0 1.0 CB A:CYS213 3.5 24.9 1.0 N A:CYS194 3.6 27.9 1.0 CA A:CYS194 4.0 27.7 1.0 N A:CYS213 4.1 24.1 1.0 CA A:CYS216 4.3 25.5 1.0 N A:CYS216 4.3 24.4 1.0 CA A:CYS213 4.3 23.4 1.0 CB A:ASN197 4.4 21.8 1.0 ND2 A:ASN197 4.5 21.7 1.0 CB A:GLU193 4.6 32.8 1.0 CA A:CYS191 4.6 26.0 1.0 C A:GLU193 4.7 30.8 1.0 O A:CYS213 4.8 21.9 1.0 C A:CYS213 4.9 23.1 1.0 C A:CYS194 4.9 28.9 1.0 N A:GLU193 4.9 29.1 1.0 C A:CYS191 5.0 27.5 1.0 CG A:ASN197 5.0 22.0 1.0

Zinc binding site 2 out of 2 in the Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the RAD14 Dna-Binding Domain in Complex with N2- Acetylaminonaphtyl- Guanine Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:22.2 occ:1.00 SG B:CYS216 2.3 25.4 1.0 SG B:CYS194 2.3 22.4 1.0 SG B:CYS191 2.3 23.2 1.0 SG B:CYS213 2.4 22.7 1.0 CB B:CYS191 3.1 23.5 1.0 CB B:CYS194 3.1 27.0 1.0 CB B:CYS216 3.2 24.3 1.0 CB B:CYS213 3.5 21.5 1.0 N B:CYS194 3.7 28.4 1.0 CA B:CYS194 4.0 29.1 1.0 N B:CYS213 4.1 21.2 1.0 CA B:CYS213 4.3 21.0 1.0 CA B:CYS216 4.4 26.0 1.0 N B:CYS216 4.4 24.1 1.0 ND2 B:ASN197 4.4 21.3 1.0 CB B:GLU193 4.4 32.2 1.0 CB B:ASN197 4.5 21.3 1.0 CA B:CYS191 4.6 24.3 1.0 C B:GLU193 4.7 31.1 1.0 O B:CYS213 4.8 21.8 1.0 C B:CYS213 4.9 20.8 1.0 N B:GLU193 4.9 29.4 1.0 C B:CYS194 4.9 30.2 1.0 CA B:GLU193 4.9 31.5 1.0 N B:ASN197 5.0 21.7 1.0 C B:CYS191 5.0 26.0 1.0 CG B:ASN197 5.0 21.4 1.0

C.Ebert, N.Simon, S.Schneider, T.Carell. Structural Insights Into the Recognition of N(2) -Aryl- and C8-Aryl Dna Lesions By the Repair Protein Xpa/RAD14. Chembiochem V. 18 1379 2017.
ISSN: ESSN 1439-7633
PubMed: 28444956
DOI: 10.1002/CBIC.201700169