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

Protein crystallography data

The structure of Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form I), PDB code: 3mlo 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) 29.71 / 3.01
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.750, 70.750, 601.560, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 27.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form I) (pdb code 3mlo). 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 I), PDB code: 3mlo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3mlo

Go back to Zinc Binding Sites List in 3mlo
Zinc binding site 1 out of 2 in the Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form I)


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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:47.4
occ:1.00
NE2 A:HIS157 2.0 49.0 1.0
SG A:CYS161 2.1 50.2 1.0
SG A:CYS164 2.2 50.0 1.0
SG A:CYS170 2.4 47.2 1.0
CE1 A:HIS157 2.8 49.5 1.0
CB A:CYS161 2.8 50.1 1.0
CD2 A:HIS157 3.1 48.7 1.0
CB A:CYS170 3.5 52.6 1.0
CB A:CYS164 3.6 50.7 1.0
ND1 A:HIS157 3.9 48.2 1.0
N A:CYS164 4.0 54.6 1.0
CB A:ASN172 4.1 51.6 1.0
CG A:HIS157 4.1 47.2 1.0
CA A:CYS161 4.3 51.4 1.0
N A:ARG173 4.4 52.9 1.0
CA A:CYS164 4.4 53.5 1.0
CB A:ARG163 4.5 57.1 1.0
C A:ASN172 4.6 51.1 1.0
CA A:ASN172 4.7 51.8 1.0
CB A:ARG173 4.8 54.6 1.0
N A:ASN172 4.8 53.4 1.0
C A:CYS161 4.9 53.8 1.0
CA A:CYS170 5.0 54.6 1.0

Zinc binding site 2 out of 2 in 3mlo

Go back to Zinc Binding Sites List in 3mlo
Zinc binding site 2 out of 2 in the Dna Binding Domain of Early B-Cell Factor 1 (EBF1) Bound to Dna (Crystal Form I)


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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:51.7
occ:1.00
NE2 B:HIS157 2.0 45.9 1.0
SG B:CYS161 2.1 51.1 1.0
SG B:CYS170 2.2 49.3 1.0
SG B:CYS164 2.3 53.0 1.0
CD2 B:HIS157 2.9 44.6 1.0
CB B:CYS161 2.9 49.6 1.0
CE1 B:HIS157 3.1 44.7 1.0
CB B:CYS170 3.2 53.2 1.0
CB B:CYS164 3.4 53.4 1.0
N B:CYS164 3.9 56.9 1.0
CG B:HIS157 4.0 43.2 1.0
ND1 B:HIS157 4.1 42.4 1.0
CA B:CYS164 4.2 56.7 1.0
CA B:CYS161 4.4 50.7 1.0
N B:ARG173 4.5 53.6 1.0
CB B:ARG163 4.5 58.5 1.0
CA B:CYS170 4.6 55.6 1.0
CB B:ARG173 4.7 55.2 1.0
O B:CYS161 4.7 54.3 1.0
C B:CYS161 4.8 53.5 1.0
CB B:ASN172 4.8 51.1 1.0
NE B:ARG163 4.8 53.8 1.0
C B:ARG163 4.9 59.4 1.0
NH2 B:ARG163 4.9 47.1 1.0
CA B:ARG173 4.9 53.3 1.0
O B:HIS157 4.9 44.9 1.0

Reference:

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
Page generated: Wed Dec 16 04:35:34 2020

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