Zinc in PDB 3mln: Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II)

The structure of Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II), PDB code: 3mln was solved by N.Treiber, T.Treiber, G.Zocher, R.Grosschedl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.31 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.200, 100.700, 72.000, 90.00, 101.20, 90.00
R / Rfree (%)	17.1 / 21.9

The binding sites of Zinc atom in the Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II) (pdb code 3mln). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II), PDB code: 3mln:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:46.2 occ:1.00 NE2 A:HIS157 2.1 42.8 1.0 SG A:CYS170 2.2 45.6 1.0 SG A:CYS164 2.2 43.2 1.0 SG A:CYS161 2.3 49.4 1.0 CD2 A:HIS157 3.0 41.6 1.0 CE1 A:HIS157 3.1 43.4 1.0 CB A:CYS161 3.1 47.4 1.0 CB A:CYS170 3.1 49.9 1.0 CB A:CYS164 3.6 47.5 1.0 N A:CYS164 3.7 50.5 1.0 CG A:HIS157 4.2 42.5 1.0 ND1 A:HIS157 4.2 39.3 1.0 N A:ARG173 4.2 50.7 1.0 CA A:CYS164 4.2 50.3 1.0 CB A:ARG163 4.3 52.5 1.0 CB A:ASN172 4.4 47.6 1.0 CA A:CYS161 4.6 47.7 1.0 CA A:CYS170 4.6 51.9 1.0 CB A:ARG173 4.6 52.7 1.0 C A:ARG163 4.7 52.6 1.0 NE A:ARG163 4.7 51.5 1.0 CA A:ARG163 4.9 53.0 1.0 CA A:ARG173 4.9 51.2 1.0 C A:ASN172 4.9 49.1 1.0 N A:ARG163 4.9 51.5 1.0 NH2 A:ARG163 4.9 48.0 1.0 NH2 A:ARG173 4.9 60.5 1.0 C A:CYS161 5.0 49.0 1.0 OD1 A:ASN172 5.0 48.1 1.0

Zinc binding site 2 out of 2 in the Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:42.3 occ:1.00 NE2 B:HIS157 2.0 43.5 1.0 SG B:CYS170 2.2 40.0 1.0 SG B:CYS164 2.2 47.5 1.0 SG B:CYS161 2.3 43.5 1.0 CE1 B:HIS157 2.9 44.2 1.0 CD2 B:HIS157 3.0 43.5 1.0 CB B:CYS170 3.2 42.5 1.0 CB B:CYS161 3.2 44.9 1.0 CB B:CYS164 3.5 47.1 1.0 N B:CYS164 3.8 47.8 1.0 ND1 B:HIS157 4.0 41.7 1.0 CG B:HIS157 4.1 42.8 1.0 N B:ARG173 4.1 46.8 1.0 CA B:CYS164 4.2 48.8 1.0 CB B:ARG173 4.4 49.5 1.0 CB B:ARG163 4.4 46.5 1.0 CB B:ASN172 4.4 44.4 1.0 CA B:CYS170 4.7 43.6 1.0 CA B:CYS161 4.7 45.8 1.0 CA B:ARG173 4.7 48.0 1.0 C B:ARG163 4.8 48.1 1.0 NE B:ARG163 4.9 42.0 1.0 C B:ASN172 4.9 45.6 1.0 CA B:ARG163 5.0 47.7 1.0 O B:HIS157 5.0 43.9 1.0

N.Treiber, T.Treiber, G.Zocher, R.Grosschedl. Structure of An EBF1:Dna Complex Reveals Unusual Dna Recognition and Structural Homology with Rel Proteins Genes Dev. V. 24 2270 2010.
ISSN: ISSN 0890-9369
PubMed: 20876732
DOI: 10.1101/GAD.1976610