Zinc in PDB 5ju7: Dna Binding Domain of E.Coli Cadc

The structure of Dna Binding Domain of E.Coli Cadc, PDB code: 5ju7 was solved by R.Janowski, A.Schlundt, M.Sattler, D.Niessing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.00 / 2.05
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	104.140, 104.140, 44.000, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.3

The binding sites of Zinc atom in the Dna Binding Domain of E.Coli Cadc (pdb code 5ju7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Dna Binding Domain of E.Coli Cadc, PDB code: 5ju7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Dna Binding Domain of E.Coli Cadc


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 E.Coli Cadc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:90.9 occ:0.70 OE1 A:GLU74 2.4 89.1 1.0 O A:HOH314 2.4 70.2 1.0 OE2 A:GLU30 2.4 94.7 1.0 CD A:GLU74 3.1 86.3 1.0 CD A:GLU30 3.4 87.4 1.0 OE2 A:GLU74 3.4 92.4 1.0 OE1 A:GLU30 3.6 95.5 1.0 ZN A:ZN202 3.7 75.7 0.7 CD2 A:LEU33 4.0 72.0 1.0 CG A:LEU33 4.1 73.8 1.0 ZN A:ZN205 4.3 0.7 1.0 CG A:GLU74 4.4 84.1 1.0 CD1 A:LEU33 4.4 73.1 1.0 OG A:SER71 4.5 72.8 1.0 CB A:GLU74 4.6 70.6 1.0 CG A:GLU30 4.7 81.5 1.0 CB A:GLU30 4.8 68.5 1.0 CA A:SER71 4.9 64.8 1.0

Zinc binding site 2 out of 5 in the Dna Binding Domain of E.Coli Cadc


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 E.Coli Cadc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:75.7 occ:0.70 OE1 A:GLU30 2.3 95.5 1.0 OE2 A:GLU74 2.3 92.4 1.0 CD A:GLU74 3.2 86.3 1.0 CD A:GLU30 3.3 87.4 1.0 OE1 A:GLU74 3.5 89.1 1.0 ZN A:ZN201 3.7 90.9 0.7 OE2 A:GLU30 3.7 94.7 1.0 CG A:GLU30 4.6 81.5 1.0 CG A:GLU74 4.6 84.1 1.0

Zinc binding site 3 out of 5 in the Dna Binding Domain of E.Coli Cadc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Binding Domain of E.Coli Cadc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:94.7 occ:1.00 OE2 A:GLU46 2.7 0.5 1.0 ND1 A:HIS43 3.2 86.8 1.0 O A:GLN42 3.2 88.3 1.0 CD A:GLU46 3.4 0.8 1.0 CA A:HIS43 3.5 78.5 1.0 ZN A:ZN204 3.5 86.5 1.0 OE1 A:GLU46 3.9 0.6 1.0 CG A:HIS43 3.9 86.0 1.0 CB A:HIS43 4.0 79.0 1.0 CE1 A:HIS43 4.0 82.6 1.0 C A:GLN42 4.1 86.3 1.0 N A:HIS43 4.3 80.3 1.0 CG A:GLU46 4.3 1.0 1.0 C A:HIS43 4.4 87.7 1.0 CD2 A:HIS43 5.0 82.3 1.0 N A:SER44 5.0 89.6 1.0

Zinc binding site 4 out of 5 in the Dna Binding Domain of E.Coli Cadc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dna Binding Domain of E.Coli Cadc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:86.5 occ:1.00 OE1 A:GLU46 2.2 0.6 1.0 ND1 A:HIS43 2.4 86.8 1.0 CD A:GLU46 3.1 0.8 1.0 CG A:HIS43 3.2 86.0 1.0 OE2 A:GLU46 3.3 0.5 1.0 CE1 A:HIS43 3.3 82.6 1.0 ZN A:ZN203 3.5 94.7 1.0 CB A:HIS43 3.6 79.0 1.0 NE2 A:HIS43 4.2 82.7 1.0 CD2 A:HIS43 4.3 82.3 1.0 CD2 A:LEU48 4.4 88.2 1.0 CG A:GLU46 4.4 1.0 1.0 CA A:HIS43 4.5 78.5 1.0 CB A:GLU46 4.8 0.2 1.0 OE1 A:GLU52 4.9 0.5 1.0

Zinc binding site 5 out of 5 in the Dna Binding Domain of E.Coli Cadc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Dna Binding Domain of E.Coli Cadc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:0.7 occ:1.00 OG A:SER71 3.7 72.8 1.0 CB A:GLN70 3.8 88.3 1.0 O A:VAL67 3.8 73.4 1.0 N A:SER71 3.9 66.2 1.0 C A:GLN70 4.0 69.7 1.0 CG1 A:VAL67 4.2 84.9 1.0 ZN A:ZN201 4.3 90.9 0.7 CA A:GLN70 4.4 75.6 1.0 CA A:SER71 4.4 64.8 1.0 O A:HOH314 4.5 70.2 1.0 O A:GLN70 4.5 69.2 1.0 CA A:VAL67 4.5 87.8 1.0 C A:VAL67 4.6 76.2 1.0 OE1 A:GLU74 4.6 89.1 1.0 CB A:SER71 4.7 67.0 1.0 CB A:VAL67 4.8 86.7 1.0

A.Schlundt, S.Buchner, R.Janowski, T.Heydenreich, R.Heermann, J.Lassak, A.Geerlof, R.Stehle, D.Niessing, K.Jung, M.Sattler. Structure-Function Analysis of the Dna-Binding Domain of A Transmembrane Transcriptional Activator. Sci Rep V. 7 1051 2017.
ISSN: ESSN 2045-2322
PubMed: 28432336
DOI: 10.1038/S41598-017-01031-9