Zinc in PDB 8b4j: RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2

The structure of RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2, PDB code: 8b4j was solved by L.A.Yates, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.01 / 1.58
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	39.996, 39.996, 282.062, 90, 90, 120
R / Rfree (%)	19.1 / 22.9

The binding sites of Zinc atom in the RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2 (pdb code 8b4j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2, PDB code: 8b4j:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2 within 5.0Å range: probe atom residue distance (Å) B Occ O:Zn202 b:24.5 occ:1.00 NE2 O:HIS127 2.1 28.2 1.0 CD2 O:HIS127 3.0 27.0 1.0 CE1 O:HIS127 3.1 26.5 1.0 HD2 O:HIS127 3.2 32.3 1.0 HE1 O:HIS127 3.4 31.8 1.0 OH O:TYR123 3.7 23.7 1.0 HE1 O:TYR123 4.0 29.5 1.0 HH O:TYR123 4.0 28.3 1.0 CG O:HIS127 4.2 26.6 1.0 ND1 O:HIS127 4.2 25.1 1.0 CZ O:TYR123 4.4 22.4 1.0 CE1 O:TYR123 4.4 24.6 1.0 H11 O:EDO201 4.4 60.0 1.0 H21 O:EDO201 4.5 31.1 1.0 H22 O:EDO201 5.0 31.1 1.0

Zinc binding site 2 out of 3 in the RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2 within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:24.8 occ:0.62 O P:HOH202 1.6 36.5 1.0 O3P P:SEP11 1.9 49.4 1.0 OD1 P:ASP12 1.9 42.9 1.0 CG P:ASP12 2.7 43.9 1.0 OD2 P:ASP12 2.9 44.8 1.0 P P:SEP11 3.0 48.8 1.0 O2P P:SEP11 3.3 48.4 1.0 ZN P:ZN102 3.4 26.5 0.5 H P:ASP12 3.4 54.4 1.0 OG P:SEP11 3.4 56.9 1.0 CB P:ASP12 4.2 44.0 1.0 N P:ASP12 4.2 45.4 1.0 OD1 P:ASP13 4.3 43.3 1.0 O1P P:SEP11 4.5 64.7 1.0 CA P:ASP12 4.6 45.3 1.0 HB3 P:ASP12 4.7 52.7 1.0 HB2 P:ASP12 4.7 52.7 1.0 CB P:SEP11 4.7 51.5 1.0 HB2 P:SEP11 4.7 61.9 1.0 CG P:ASP13 4.7 49.5 1.0 OD2 P:ASP13 4.8 47.0 1.0 H P:ASP13 4.8 56.7 1.0 C P:ASP12 4.8 41.4 1.0 N P:ASP13 4.8 47.2 1.0

Zinc binding site 3 out of 3 in the RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RFA1-N-Terminal Domain in Complex with Phosphorylated DDC2 within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn102 b:26.5 occ:0.45 O2P P:SEP11 1.9 48.4 1.0 OD1 P:ASP13 2.0 43.3 1.0 O P:HOH202 2.0 36.5 1.0 O P:HOH203 2.1 42.9 1.0 OD2 P:ASP13 2.5 47.0 1.0 CG P:ASP13 2.6 49.5 1.0 P P:SEP11 3.3 48.8 1.0 ZN P:ZN101 3.4 24.8 0.6 HB2 P:SEP11 3.5 61.9 1.0 O3P P:SEP11 3.7 49.4 1.0 OG P:SEP11 3.8 56.9 1.0 OD1 P:ASP12 4.0 42.9 1.0 CB P:ASP13 4.1 43.0 1.0 H P:ASP13 4.1 56.7 1.0 CB P:SEP11 4.1 51.5 1.0 H P:ASP12 4.2 54.4 1.0 HB2 P:ASP13 4.4 51.6 1.0 HB3 P:SEP11 4.4 61.9 1.0 N P:ASP13 4.5 47.2 1.0 HB3 P:ASP13 4.6 51.6 1.0 O1P P:SEP11 4.6 64.7 1.0 CA P:ASP13 4.7 40.6 1.0 HA P:ASP13 4.7 48.8 1.0 N P:ASP12 4.9 45.4 1.0

L.A.Yates, E.A.Tannous, R.M.Morgan, P.M.Burgers, X.Zhang. A Dna Damage-Induced Phosphorylation Circuit Enhances MEC1 Atr DDC2 Atrip Recruitment to Replication Protein A. Proc.Natl.Acad.Sci.Usa V. 120 50120 2023.
ISSN: ESSN 1091-6490
PubMed: 36996117
DOI: 10.1073/PNAS.2300150120