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Sodium in PDB 3uz5: Designed Protein KE59 R13 3/11H

Protein crystallography data

The structure of Designed Protein KE59 R13 3/11H, PDB code: 3uz5 was solved by O.Khersonsky, G.Kiss, D.Roethlisberger, O.Dym, S.Albeck, K.N.Houk, D.Baker, D.S.Tawfik, Israel Structural Proteomics Center (Ispc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.476, 123.744, 45.702, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 25.1

Other elements in 3uz5:

The structure of Designed Protein KE59 R13 3/11H also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Designed Protein KE59 R13 3/11H (pdb code 3uz5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Designed Protein KE59 R13 3/11H, PDB code: 3uz5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3uz5

Go back to Sodium Binding Sites List in 3uz5
Sodium binding site 1 out of 2 in the Designed Protein KE59 R13 3/11H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Designed Protein KE59 R13 3/11H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:4.4
occ:1.00
N A:TYR4 3.7 13.0 1.0
CB A:ARG3 4.0 14.6 1.0
CD2 A:TYR4 4.0 11.9 1.0
CG A:ARG3 4.1 15.9 1.0
CA A:ARG3 4.2 14.4 1.0
C A:ARG3 4.5 14.6 1.0
CB A:TYR4 4.5 14.4 1.0
CA A:TYR4 4.6 14.9 1.0
NH1 A:ARG3 4.7 24.0 1.0
CD A:ARG3 4.8 15.5 1.0
CG A:TYR4 4.8 13.5 1.0
O A:TYR4 4.8 17.7 1.0
CE2 A:TYR4 5.0 13.5 1.0

Sodium binding site 2 out of 2 in 3uz5

Go back to Sodium Binding Sites List in 3uz5
Sodium binding site 2 out of 2 in the Designed Protein KE59 R13 3/11H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Designed Protein KE59 R13 3/11H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:2.9
occ:1.00
N B:TYR4 3.8 16.7 1.0
CB B:ARG3 4.0 18.2 1.0
CD2 B:TYR4 4.1 15.4 1.0
CA B:ARG3 4.3 17.6 1.0
CB B:TYR4 4.4 15.3 1.0
C B:ARG3 4.6 17.4 1.0
CG B:ARG3 4.6 18.3 1.0
O B:TYR4 4.6 15.9 1.0
CA B:TYR4 4.7 15.4 1.0
CG B:TYR4 4.8 14.6 1.0
CD B:ARG3 4.8 23.6 1.0

Reference:

O.Khersonsky, G.Kiss, D.Rothlisberger, O.Dym, S.Albeck, K.N.Houk, D.Baker, D.S.Tawfik. Bridging the Gaps in Design Methodologies By Evolutionary Optimization of the Stability and Proficiency of Designed Kemp Eliminase KE59. Proc.Natl.Acad.Sci.Usa V. 109 10358 2012.
ISSN: ISSN 0027-8424
PubMed: 22685214
DOI: 10.1073/PNAS.1121063109
Page generated: Tue Dec 15 06:28:03 2020

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