Zinc in PDB 3lyr: Human Early B-Cell Factor 1 (EBF1) Dna-Binding Domain

The structure of Human Early B-Cell Factor 1 (EBF1) Dna-Binding Domain, PDB code: 3lyr was solved by M.I.Siponen, M.Wisniewska, C.H.Arrowsmith, C.Bountra, R.Collins, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, T.Karlberg, P.Kraulis, T.Kotenyova, N.Markova, M.Moche, P.Nordlund, T.Nyman, C.Persson, H.Schuler, P.Schutz, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, E.Wahlberg, J.Weigelt, M.Welin, H.Berglund, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.12 / 2.51
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	134.218, 134.218, 72.391, 90.00, 90.00, 120.00
R / Rfree (%)	23.3 / 27.4

The binding sites of Zinc atom in the Human Early B-Cell Factor 1 (EBF1) Dna-Binding Domain (pdb code 3lyr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human Early B-Cell Factor 1 (EBF1) Dna-Binding Domain, PDB code: 3lyr:

Zinc binding site 1 out of 1 in the Human Early B-Cell Factor 1 (EBF1) Dna-Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Early B-Cell Factor 1 (EBF1) Dna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:42.2 occ:1.00 SG A:CYS164 2.1 51.1 1.0 NE2 A:HIS157 2.2 36.8 1.0 SG A:CYS170 2.2 45.2 1.0 SG A:CYS161 2.3 43.9 1.0 CE1 A:HIS157 3.0 36.6 1.0 CB A:CYS170 3.1 48.8 1.0 CD2 A:HIS157 3.2 36.8 1.0 CB A:CYS161 3.3 49.4 1.0 CB A:CYS164 3.4 54.2 1.0 N A:CYS164 3.9 54.6 1.0 CA A:CYS164 4.1 54.6 1.0 ND1 A:HIS157 4.2 37.0 1.0 CB A:ARG173 4.2 48.8 1.0 CG A:HIS157 4.3 38.0 1.0 N A:ARG173 4.4 46.9 1.0 CA A:CYS170 4.5 49.2 1.0 CA A:ARG173 4.7 47.8 1.0 CA A:CYS161 4.7 49.5 1.0 CB A:ARG163 4.7 54.9 1.0 C A:ARG163 4.8 54.3 1.0

M.I.Siponen, M.Wisniewska, L.Lehtio, I.Johansson, L.Svensson, G.Raszewski, L.Nilsson, M.Sigvardsson, H.Berglund. Structural Determination of Functional Domains in Early B-Cell Factor (Ebf) Family of Transcription Factors Reveals Similarities to Rel Dna-Binding Proteins and A Novel Dimerization Motif. J.Biol.Chem. V. 285 25875 2010.
ISSN: ISSN 0021-9258
PubMed: 20592035
DOI: 10.1074/JBC.C110.150482