Zinc in PDB 3mlp: Early B-Cell Factor 1 (EBF1) Bound to Dna

The structure of Early B-Cell Factor 1 (EBF1) Bound to Dna, PDB code: 3mlp 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)	38.75 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.490, 78.690, 103.570, 88.99, 90.00, 77.81
R / Rfree (%)	20.4 / 26.4

The binding sites of Zinc atom in the Early B-Cell Factor 1 (EBF1) Bound to Dna (pdb code 3mlp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Early B-Cell Factor 1 (EBF1) Bound to Dna, PDB code: 3mlp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Early B-Cell Factor 1 (EBF1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Early B-Cell Factor 1 (EBF1) Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:43.4 occ:1.00 SG A:CYS161 1.9 44.5 1.0 NE2 A:HIS157 2.2 39.0 1.0 SG A:CYS164 2.3 47.5 1.0 SG A:CYS170 2.3 45.8 1.0 CB A:CYS161 2.6 43.9 1.0 CE1 A:HIS157 3.0 37.6 1.0 CB A:CYS170 3.1 49.1 1.0 CD2 A:HIS157 3.2 37.4 1.0 CB A:CYS164 3.4 47.1 1.0 N A:CYS164 3.8 50.5 1.0 CA A:CYS161 4.1 44.4 1.0 ND1 A:HIS157 4.1 35.3 1.0 CA A:CYS164 4.2 50.9 1.0 CG A:HIS157 4.3 35.1 1.0 CB A:ARG163 4.4 53.3 1.0 N A:ARG173 4.6 48.4 1.0 CA A:CYS170 4.6 51.7 1.0 CB A:ASN172 4.6 44.4 1.0 NE A:ARG163 4.7 50.9 1.0 C A:ARG163 4.7 54.0 1.0 CB A:ARG173 4.7 52.5 1.0 C A:CYS161 4.8 47.5 1.0 N A:ARG163 4.9 52.0 1.0 CA A:ARG163 4.9 54.0 1.0

Zinc binding site 2 out of 4 in the Early B-Cell Factor 1 (EBF1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Early B-Cell Factor 1 (EBF1) Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:38.4 occ:1.00 NE2 B:HIS157 2.0 33.5 1.0 SG B:CYS170 2.0 36.6 1.0 SG B:CYS161 2.2 37.3 1.0 SG B:CYS164 2.3 42.3 1.0 CB B:CYS161 2.9 36.4 1.0 CD2 B:HIS157 3.0 32.3 1.0 CE1 B:HIS157 3.0 32.8 1.0 CB B:CYS170 3.1 38.3 1.0 CB B:CYS164 3.4 40.2 1.0 N B:CYS164 3.8 42.6 1.0 ND1 B:HIS157 4.1 31.7 1.0 CG B:HIS157 4.1 31.3 1.0 CA B:CYS164 4.2 42.4 1.0 N B:ARG173 4.3 43.0 1.0 CA B:CYS161 4.3 37.2 1.0 CB B:ASN172 4.4 38.2 1.0 CB B:ARG163 4.5 42.4 1.0 CA B:CYS170 4.5 39.5 1.0 NE B:ARG163 4.7 40.7 1.0 C B:ARG163 4.8 43.1 1.0 C B:CYS161 4.9 39.2 1.0 CB B:ARG173 4.9 46.1 1.0 C B:ASN172 4.9 39.6 1.0 N B:ARG163 5.0 42.6 1.0 CA B:ARG173 5.0 43.9 1.0

Zinc binding site 3 out of 4 in the Early B-Cell Factor 1 (EBF1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Early B-Cell Factor 1 (EBF1) Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:38.3 occ:1.00 SG E:CYS161 2.0 38.8 1.0 NE2 E:HIS157 2.1 34.1 1.0 SG E:CYS170 2.1 42.6 1.0 SG E:CYS164 2.2 38.1 1.0 CB E:CYS161 3.0 39.0 1.0 CE1 E:HIS157 3.0 36.2 1.0 CD2 E:HIS157 3.0 33.0 1.0 CB E:CYS170 3.3 42.0 1.0 CB E:CYS164 3.3 39.3 1.0 N E:CYS164 3.8 43.6 1.0 ND1 E:HIS157 4.1 31.8 1.0 CA E:CYS164 4.1 42.7 1.0 CG E:HIS157 4.1 32.0 1.0 N E:ARG173 4.2 39.2 1.0 CB E:ASN172 4.3 39.0 1.0 CA E:CYS161 4.4 39.6 1.0 CB E:ARG173 4.5 41.2 1.0 CB E:ARG163 4.6 47.1 1.0 CA E:CYS170 4.7 43.9 1.0 C E:ARG163 4.8 46.7 1.0 CA E:ARG173 4.8 39.2 1.0 C E:ASN172 4.9 38.1 1.0 NE E:ARG163 4.9 45.5 1.0 CA E:GLU158 5.0 37.8 1.0

Zinc binding site 4 out of 4 in the Early B-Cell Factor 1 (EBF1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Early B-Cell Factor 1 (EBF1) Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:32.4 occ:1.00 NE2 F:HIS157 2.0 27.1 1.0 SG F:CYS161 2.0 30.6 1.0 SG F:CYS170 2.0 30.7 1.0 SG F:CYS164 2.3 35.2 1.0 CE1 F:HIS157 2.9 26.6 1.0 CD2 F:HIS157 3.0 26.9 1.0 CB F:CYS161 3.1 29.1 1.0 CB F:CYS170 3.2 32.6 1.0 CB F:CYS164 3.4 33.2 1.0 N F:CYS164 4.0 35.6 1.0 ND1 F:HIS157 4.1 25.3 1.0 CG F:HIS157 4.1 27.9 1.0 CA F:CYS164 4.3 35.4 1.0 N F:ARG173 4.3 35.8 1.0 CB F:ASN172 4.4 32.0 1.0 CB F:ARG163 4.5 36.5 1.0 CA F:CYS161 4.5 30.1 1.0 CA F:CYS170 4.6 34.0 1.0 NE F:ARG163 4.6 34.9 1.0 CB F:ARG173 4.8 40.6 1.0 C F:ASN172 4.9 34.1 1.0 C F:CYS161 4.9 32.2 1.0 CA F:ARG173 4.9 37.1 1.0 C F:ARG163 4.9 37.5 1.0 NH2 F:ARG163 5.0 32.9 1.0 CA F:ASN172 5.0 32.9 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