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Zinc in PDB 5kay: Structure of Spelter Bound to ZN2+

Protein crystallography data

The structure of Structure of Spelter Bound to ZN2+, PDB code: 5kay was solved by S.L.Guffy, B.S.Der, B.Kuhlman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.78 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.714, 41.496, 61.506, 87.27, 83.09, 79.46
R / Rfree (%) 19.3 / 23.3

Other elements in 5kay:

The structure of Structure of Spelter Bound to ZN2+ also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Spelter Bound to ZN2+ (pdb code 5kay). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Spelter Bound to ZN2+, PDB code: 5kay:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5kay

Go back to Zinc Binding Sites List in 5kay
Zinc binding site 1 out of 2 in the Structure of Spelter Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Spelter Bound to ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:31.9
occ:1.00
NE2 A:HIS125 2.0 22.1 1.0
OE1 A:GLU200 2.0 29.5 1.0
O A:HOH466 2.1 27.5 1.0
OE1 A:GLU122 2.3 34.5 1.0
CD A:GLU200 2.8 27.2 1.0
CE1 A:HIS125 2.9 22.1 1.0
CD2 A:HIS125 3.0 21.1 1.0
OE2 A:GLU200 3.1 30.9 1.0
CD A:GLU122 3.2 28.9 1.0
OE2 A:GLU122 4.0 32.6 1.0
CG A:GLU122 4.0 32.4 1.0
ND1 A:HIS125 4.0 19.9 1.0
CG A:HIS125 4.1 19.9 1.0
CG A:GLU200 4.2 21.3 1.0
CB A:GLU122 4.3 23.1 1.0
CB A:GLU200 4.6 17.8 1.0
O A:GLU122 4.8 33.5 1.0
NE2 A:GLN129 4.8 28.9 1.0

Zinc binding site 2 out of 2 in 5kay

Go back to Zinc Binding Sites List in 5kay
Zinc binding site 2 out of 2 in the Structure of Spelter Bound to ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Spelter Bound to ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:38.1
occ:1.00
OE2 B:GLU200 1.9 32.2 1.0
NE2 B:HIS125 2.0 20.0 1.0
OE1 B:GLU122 2.2 41.5 1.0
O B:HOH477 2.2 27.9 1.0
CD B:GLU200 2.9 34.4 1.0
CD2 B:HIS125 2.9 21.4 1.0
CE1 B:HIS125 3.1 22.2 1.0
OE1 B:GLU200 3.2 41.2 1.0
CD B:GLU122 3.3 38.4 1.0
OE2 B:GLU122 4.0 37.1 1.0
CG B:HIS125 4.1 18.9 1.0
CB B:GLU122 4.1 29.9 1.0
ND1 B:HIS125 4.2 21.3 1.0
CG B:GLU200 4.2 26.4 1.0
CG B:GLU122 4.4 36.2 1.0
CB B:GLU200 4.7 21.6 1.0
O B:GLU122 4.7 43.1 1.0
NE2 B:GLN129 4.8 24.7 1.0

Reference:

S.L.Guffy, B.S.Der, B.Kuhlman. Probing the Minimal Determinants of Zinc Binding with Computational Protein Design. Protein Eng.Des.Sel. V. 29 327 2016.
ISSN: ESSN 1741-0134
PubMed: 27358168
DOI: 10.1093/PROTEIN/GZW026
Page generated: Wed Dec 16 06:26:41 2020

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