Zinc in PDB 5ecg: Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX)

The structure of Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX), PDB code: 5ecg was solved by M.Day, A.W.Oliver, L.H.Pearl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.06 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.264, 94.498, 131.742, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.4

The binding sites of Zinc atom in the Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX) (pdb code 5ecg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX), PDB code: 5ecg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:80.0 occ:1.00 ND1 A:HIS179 2.1 94.1 1.0 SG A:CYS176 2.2 56.3 1.0 SG A:CYS238 2.2 89.7 1.0 SG A:CYS242 2.4 91.2 1.0 CE1 A:HIS179 2.9 91.5 1.0 CG A:HIS179 3.1 77.7 1.0 CB A:CYS242 3.3 75.3 1.0 CB A:CYS238 3.4 89.3 1.0 CA A:CYS238 3.4 78.4 1.0 CB A:HIS179 3.5 74.8 1.0 CB A:CYS176 3.7 70.5 1.0 N A:ASN239 3.9 56.6 1.0 NE2 A:HIS179 4.1 86.8 1.0 O A:MET237 4.1 78.3 1.0 CD2 A:HIS179 4.2 81.7 1.0 C A:CYS238 4.2 70.9 1.0 N A:CYS176 4.3 60.5 1.0 CA A:CYS176 4.6 60.0 1.0 N A:CYS238 4.6 81.5 1.0 N A:HIS179 4.7 96.0 1.0 CA A:CYS242 4.8 73.1 1.0 CA A:HIS179 4.8 95.4 1.0 CG A:ARG175 4.8 72.9 1.0 C A:MET237 4.8 77.2 1.0 O A:CYS176 4.9 68.2 1.0 O A:ASN239 5.0 64.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Brct Domains of 53BP1 in Complex with P53 and H2AX-PSER139 (GAMMAH2AX) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.2 occ:1.00 ND1 B:HIS179 2.0 0.5 1.0 SG B:CYS176 2.3 93.1 1.0 SG B:CYS238 2.3 0.5 1.0 SG B:CYS242 2.3 0.9 1.0 CE1 B:HIS179 2.6 0.4 1.0 CB B:CYS242 2.8 0.7 1.0 CB B:CYS176 3.1 98.9 1.0 CG B:HIS179 3.2 0.8 1.0 CB B:CYS238 3.3 93.0 1.0 NE2 B:HIS179 3.7 0.8 1.0 CB B:HIS179 3.8 0.7 1.0 CA B:CYS238 4.0 91.0 1.0 CD2 B:HIS179 4.0 0.8 1.0 N B:CYS176 4.1 82.1 1.0 CA B:CYS242 4.1 98.8 1.0 CA B:CYS176 4.2 87.7 1.0 N B:ASN239 4.3 81.0 1.0 C B:CYS238 4.7 86.4 1.0 N B:HIS179 4.7 0.9 1.0 O B:ASN239 4.7 79.9 1.0 O B:CYS176 4.8 0.0 1.0 C B:CYS242 4.8 91.3 1.0 O B:MET237 4.8 87.5 1.0 C B:CYS176 4.9 88.4 1.0 CA B:HIS179 4.9 0.0 1.0

R.A.Baldock, M.Day, O.J.Wilkinson, R.Cloney, P.A.Jeggo, A.W.Oliver, F.Z.Watts, L.H.Pearl. Atm Localization and Heterochromatin Repair Depend on Direct Interaction of the 53BP1-BRCT2 Domain with Gamma H2AX. Cell Rep V. 13 2081 2015.
ISSN: ESSN 2211-1247
PubMed: 26628370
DOI: 10.1016/J.CELREP.2015.10.074