Bromine in PDB 6npi: Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments

The structure of Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments, PDB code: 6npi was solved by T.E.Messick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.34 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.704, 67.452, 69.498, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 16.3

The binding sites of Bromine atom in the Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments (pdb code 6npi). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments, PDB code: 6npi:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Br702 b:17.8 occ:0.46 BR B:KW1702 0.0 17.8 0.5 BR B:KW1702 0.6 19.6 0.5 C06 B:KW1702 1.6 13.6 0.5 C06 B:KW1702 2.0 15.7 0.5 C02 B:KW1702 2.5 20.3 0.5 C05 B:KW1702 2.8 14.6 0.5 H013 B:KW1702 2.8 26.4 0.5 C02 B:KW1702 3.0 20.9 0.5 C01 B:KW1702 3.0 22.0 0.5 C05 B:KW1702 3.0 11.3 0.5 H011 B:KW1702 3.1 26.4 0.5 H013 B:KW1702 3.2 19.3 0.5 O B:LEU536 3.2 9.6 1.0 H011 B:KW1702 3.4 19.3 0.5 C01 B:KW1702 3.4 16.1 0.5 N08 B:KW1702 3.4 13.3 0.5 N08 B:KW1702 3.4 18.1 0.5 O03 B:KW1702 3.7 18.6 0.5 HB2 B:PRO535 3.7 13.1 1.0 C09 B:KW1702 3.7 17.2 0.5 O A:HOH763 3.7 15.1 1.0 N04 B:KW1702 3.8 13.7 0.5 O10 B:KW1702 3.8 12.2 0.5 O10 B:KW1702 3.8 15.7 0.5 H081 B:KW1702 3.8 16.0 0.5 C09 B:KW1702 3.9 18.8 0.5 HB3 B:PRO535 3.9 13.1 1.0 H081 B:KW1702 3.9 21.8 0.5 HB2 B:LEU536 4.0 11.2 1.0 H012 B:KW1702 4.0 26.4 0.5 O15 B:KW1702 4.0 13.3 0.5 O15 B:KW1702 4.0 12.5 0.5 C14 B:KW1702 4.0 13.2 0.5 H131 B:KW1702 4.0 20.0 0.5 O03 B:KW1702 4.1 25.4 0.5 C14 B:KW1702 4.1 13.8 0.5 N04 B:KW1702 4.1 23.8 0.5 S12 B:KW1702 4.2 22.9 0.5 O16 B:KW1702 4.2 13.5 0.5 C B:LEU536 4.2 8.5 1.0 O16 B:KW1702 4.2 13.8 0.5 CB B:PRO535 4.3 10.9 1.0 H012 B:KW1702 4.3 19.3 0.5 N B:LEU536 4.4 8.5 1.0 C13 B:KW1702 4.6 16.7 0.5 CB B:LEU536 4.6 9.3 1.0 CA B:LEU536 4.7 9.0 1.0 HB3 B:LEU536 4.7 11.2 1.0 C11 B:KW1702 4.7 10.3 0.5 O A:HOH769 4.7 36.3 1.0 C13 B:KW1702 4.8 15.7 0.5 O A:HOH836 4.8 45.2 1.0 O B:HOH853 4.9 36.9 1.0 HA B:SER537 4.9 10.3 1.0 O B:HOH967 4.9 41.8 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, Bound to Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Br702 b:19.6 occ:0.54 BR B:KW1702 0.0 19.6 0.5 BR B:KW1702 0.6 17.8 0.5 C06 B:KW1702 1.9 13.6 0.5 C06 B:KW1702 2.4 15.7 0.5 C05 B:KW1702 3.0 14.6 0.5 C02 B:KW1702 3.0 20.3 0.5 C05 B:KW1702 3.2 11.3 0.5 N08 B:KW1702 3.3 13.3 0.5 N08 B:KW1702 3.3 18.1 0.5 H013 B:KW1702 3.4 26.4 0.5 C02 B:KW1702 3.5 20.9 0.5 HB2 B:PRO535 3.5 13.1 1.0 H131 B:KW1702 3.5 20.0 0.5 O B:LEU536 3.6 9.6 1.0 C09 B:KW1702 3.6 17.2 0.5 HB3 B:PRO535 3.6 13.1 1.0 C01 B:KW1702 3.6 22.0 0.5 C14 B:KW1702 3.7 13.2 0.5 H011 B:KW1702 3.7 26.4 0.5 S12 B:KW1702 3.7 22.9 0.5 C14 B:KW1702 3.7 13.8 0.5 C09 B:KW1702 3.7 18.8 0.5 H081 B:KW1702 3.7 16.0 0.5 O10 B:KW1702 3.7 15.7 0.5 O15 B:KW1702 3.7 13.3 0.5 O10 B:KW1702 3.7 12.2 0.5 H013 B:KW1702 3.8 19.3 0.5 O A:HOH763 3.8 15.1 1.0 O15 B:KW1702 3.8 12.5 0.5 H081 B:KW1702 3.8 21.8 0.5 O16 B:KW1702 3.8 13.5 0.5 O16 B:KW1702 3.9 13.8 0.5 H011 B:KW1702 3.9 19.3 0.5 C01 B:KW1702 4.0 16.1 0.5 CB B:PRO535 4.0 10.9 1.0 C13 B:KW1702 4.1 16.7 0.5 N04 B:KW1702 4.1 13.7 0.5 O03 B:KW1702 4.1 18.6 0.5 O A:HOH769 4.2 36.3 1.0 C13 B:KW1702 4.3 15.7 0.5 HB2 B:LEU536 4.3 11.2 1.0 C11 B:KW1702 4.4 10.3 0.5 N04 B:KW1702 4.4 23.8 0.5 O B:HOH853 4.4 36.9 1.0 O03 B:KW1702 4.5 25.4 0.5 O A:HOH836 4.5 45.2 1.0 N B:LEU536 4.6 8.5 1.0 H012 B:KW1702 4.6 26.4 0.5 C B:LEU536 4.6 8.5 1.0 C11 B:KW1702 4.7 21.9 0.5 H112 B:KW1702 4.8 26.4 0.5 H131 B:KW1702 4.8 18.9 0.5 H132 B:KW1702 4.9 20.0 0.5 H012 B:KW1702 4.9 19.3 0.5 CA B:LEU536 5.0 9.0 1.0 HG2 B:PRO535 5.0 16.5 1.0 H112 B:KW1702 5.0 12.3 0.5 S12 B:KW1702 5.0 16.4 0.5 CB B:LEU536 5.0 9.3 1.0

T.E.Messick, G.R.Smith, S.S.Soldan, M.E.Mcdonnell, J.S.Deakyne, K.A.Malecka, L.Tolvinski, A.P.J.Van Den Heuvel, B.W.Gu, J.A.Cassel, D.H.Tran, B.R.Wassermann, Y.Zhang, V.Velvadapu, E.R.Zartler, P.Busson, A.B.Reitz, P.M.Lieberman. Structure-Based Design of Small-Molecule Inhibitors of EBNA1 Dna Binding Blocks Epstein-Barr Virus Latent Infection and Tumor Growth. Sci Transl Med V. 11 2019.
ISSN: ESSN 1946-6242
PubMed: 30842315
DOI: 10.1126/SCITRANSLMED.AAU5612