Zinc in PDB 7rcj: Crystal Structure of Znua From Citrobacter Koseri

The structure of Crystal Structure of Znua From Citrobacter Koseri, PDB code: 7rcj was solved by E.T.Yukl, E.L.Yekwa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.47 / 3.15
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.246, 81.667, 126.555, 90, 112.99, 90
R / Rfree (%)	21.7 / 25.4

The structure of Crystal Structure of Znua From Citrobacter Koseri also contains other interesting chemical elements:

Tellurium	(Te)	3 atoms
Tungsten	(W)	18 atoms

The binding sites of Zinc atom in the Crystal Structure of Znua From Citrobacter Koseri (pdb code 7rcj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Znua From Citrobacter Koseri, PDB code: 7rcj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Znua From Citrobacter Koseri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Znua From Citrobacter Koseri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:84.7 occ:1.00 OE1 A:GLU59 1.7 112.3 1.0 CE1 A:HIS211 2.1 89.7 1.0 NE2 A:HIS147 2.1 93.2 1.0 NE2 A:HIS211 2.3 81.9 1.0 NE2 A:HIS60 2.4 72.3 1.0 CD2 A:HIS147 2.8 98.1 1.0 CD A:GLU59 2.8 94.8 1.0 CE1 A:HIS60 3.1 75.1 1.0 CE1 A:HIS147 3.2 89.6 1.0 ND1 A:HIS211 3.4 99.0 1.0 CG A:GLU59 3.4 81.5 1.0 CD2 A:HIS60 3.4 69.4 1.0 CD2 A:HIS211 3.7 78.0 1.0 OE2 A:GLU59 3.8 89.2 1.0 CG A:HIS147 4.0 88.1 1.0 CG A:HIS211 4.2 81.7 1.0 ND1 A:HIS147 4.2 79.0 1.0 CB A:ALA213 4.2 77.8 1.0 ND1 A:HIS60 4.3 79.4 1.0 CG A:HIS60 4.5 74.5 1.0 CA A:ALA213 4.8 77.8 1.0 CB A:GLU59 4.9 82.3 1.0 CH2 A:TRP149 4.9 87.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Znua From Citrobacter Koseri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Znua From Citrobacter Koseri within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:89.0 occ:1.00 OE1 B:GLU59 1.9 91.1 1.0 NE2 B:HIS147 2.0 83.7 1.0 NE2 B:HIS60 2.0 106.6 1.0 NE2 B:HIS211 2.1 85.2 1.0 CE1 B:HIS60 2.7 106.2 1.0 CE1 B:HIS211 2.8 85.5 1.0 CD2 B:HIS147 2.9 78.3 1.0 CD B:GLU59 2.9 76.6 1.0 CE1 B:HIS147 3.1 97.3 1.0 CD2 B:HIS60 3.2 105.0 1.0 CD2 B:HIS211 3.3 97.2 1.0 CG B:GLU59 3.4 77.5 1.0 ND1 B:HIS60 3.9 102.9 1.0 ND1 B:HIS211 4.0 82.1 1.0 OE2 B:GLU59 4.0 80.5 1.0 CG B:HIS147 4.1 81.6 1.0 ND1 B:HIS147 4.1 91.4 1.0 CG B:HIS60 4.2 101.7 1.0 CG B:HIS211 4.2 89.4 1.0 CB B:ALA213 4.5 81.6 1.0 CE B:MET85 4.8 114.0 1.0 CB B:GLU59 4.9 79.8 1.0 O B:VAL231 5.0 132.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Znua From Citrobacter Koseri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Znua From Citrobacter Koseri within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:80.8 occ:1.00 OE1 C:GLU59 1.7 96.4 1.0 NE2 C:HIS60 2.0 98.2 1.0 NE2 C:HIS147 2.1 110.3 1.0 NE2 C:HIS211 2.2 97.6 1.0 CE1 C:HIS60 2.7 96.9 1.0 CD C:GLU59 2.8 71.4 1.0 CE1 C:HIS211 2.8 96.5 1.0 CD2 C:HIS147 2.9 109.6 1.0 CD2 C:HIS60 3.2 102.0 1.0 CG C:GLU59 3.2 66.7 1.0 CE1 C:HIS147 3.2 106.3 1.0 CD2 C:HIS211 3.4 92.9 1.0 OE2 C:GLU59 3.9 79.3 1.0 ND1 C:HIS60 3.9 92.1 1.0 ND1 C:HIS211 4.0 87.1 1.0 CG C:HIS147 4.1 114.0 1.0 CG C:HIS60 4.1 93.8 1.0 ND1 C:HIS147 4.2 105.8 1.0 CG C:HIS211 4.3 75.0 1.0 CB C:ALA213 4.6 115.1 1.0 CB C:GLU59 4.7 72.5 1.0 CE C:MET85 4.8 87.0 1.0 CH2 C:TRP149 4.9 96.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Znua From Citrobacter Koseri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Znua From Citrobacter Koseri within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:96.7 occ:1.00 NE2 D:HIS147 2.0 110.2 1.0 OE1 D:GLU59 2.0 73.8 1.0 NE2 D:HIS211 2.0 105.9 1.0 NE2 D:HIS60 2.1 92.1 1.0 CD D:GLU59 2.6 84.0 1.0 OE2 D:GLU59 2.7 87.2 1.0 CE1 D:HIS211 2.8 101.5 1.0 CE1 D:HIS60 2.8 80.3 1.0 CD2 D:HIS147 2.9 113.0 1.0 CE1 D:HIS147 3.0 112.9 1.0 CD2 D:HIS211 3.2 111.8 1.0 CD2 D:HIS60 3.3 108.3 1.0 CG D:GLU59 3.9 80.7 1.0 ND1 D:HIS211 3.9 99.2 1.0 ND1 D:HIS60 4.0 76.3 1.0 CG D:HIS147 4.0 101.8 1.0 ND1 D:HIS147 4.1 99.3 1.0 CG D:HIS211 4.2 100.0 1.0 CG D:HIS60 4.3 87.5 1.0 CB D:ALA213 4.4 105.4 1.0 O D:ASP212 4.9 94.8 1.0 CA D:ALA213 4.9 97.4 1.0 CB D:GLU59 4.9 83.8 1.0 O D:VAL231 5.0 175.1 1.0 CE D:MET85 5.0 93.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Znua From Citrobacter Koseri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Znua From Citrobacter Koseri within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:93.3 occ:1.00 OE1 E:GLU59 1.8 82.3 1.0 NE2 E:HIS147 2.0 104.5 1.0 NE2 E:HIS60 2.1 89.3 1.0 CE1 E:HIS211 2.3 79.2 1.0 CE1 E:HIS60 2.7 79.5 1.0 NE2 E:HIS211 2.7 67.2 1.0 CD2 E:HIS147 2.8 99.0 1.0 CE1 E:HIS147 3.1 118.2 1.0 CD E:GLU59 3.1 94.8 1.0 CD2 E:HIS60 3.2 95.0 1.0 ND1 E:HIS211 3.6 90.1 1.0 ND1 E:HIS60 3.9 89.5 1.0 OE2 E:GLU59 3.9 108.9 1.0 CG E:HIS147 4.0 98.6 1.0 CD2 E:HIS211 4.1 81.8 1.0 ND1 E:HIS147 4.1 115.3 1.0 CG E:GLU59 4.1 105.5 1.0 CG E:HIS60 4.2 93.2 1.0 CG E:HIS211 4.5 94.7 1.0 CB E:ALA213 4.6 89.9 1.0 CB E:GLU59 4.6 97.7 1.0 CE E:MET85 4.7 92.0 1.0 CH2 E:TRP149 4.9 81.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Znua From Citrobacter Koseri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Znua From Citrobacter Koseri within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:91.9 occ:1.00 OE1 F:GLU59 1.7 128.8 1.0 CE1 F:HIS211 2.1 129.4 1.0 NE2 F:HIS147 2.1 100.8 1.0 NE2 F:HIS60 2.2 73.9 1.0 NE2 F:HIS211 2.4 120.9 1.0 CD F:GLU59 2.4 109.4 1.0 OE2 F:GLU59 2.6 148.4 1.0 CD2 F:HIS147 2.8 97.6 1.0 CE1 F:HIS60 3.0 89.2 1.0 CE1 F:HIS147 3.2 107.5 1.0 ND1 F:HIS211 3.3 123.9 1.0 CD2 F:HIS60 3.4 70.6 1.0 CD2 F:HIS211 3.7 98.8 1.0 CG F:GLU59 3.8 91.6 1.0 CG F:HIS147 4.1 95.8 1.0 ND1 F:HIS60 4.2 91.9 1.0 CG F:HIS211 4.2 100.8 1.0 ND1 F:HIS147 4.2 110.2 1.0 CB F:ALA213 4.3 86.0 1.0 CG F:HIS60 4.4 85.4 1.0 CB F:GLU59 4.8 76.9 1.0 CA F:ALA213 4.9 92.0 1.0 CH2 F:TRP149 5.0 82.6 1.0

E.L.Yekwa, F.A.Serrano, E.Yukl. Conformational Flexibility in the Zinc Solute-Binding Protein Znua. Acta Crystallogr.,Sect.F V. 78 128 2022.
ISSN: ESSN 2053-230X
PubMed: 35234138
DOI: 10.1107/S2053230X22001662