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Sodium in PDB 3uy7: Designed Protein KE59 R1 7/10H with G130S Mutation

Protein crystallography data

The structure of Designed Protein KE59 R1 7/10H with G130S Mutation, PDB code: 3uy7 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) 39.99 / 1.45
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 61.529, 61.529, 119.961, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 20.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Designed Protein KE59 R1 7/10H with G130S Mutation (pdb code 3uy7). 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 R1 7/10H with G130S Mutation, PDB code: 3uy7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3uy7

Go back to Sodium Binding Sites List in 3uy7
Sodium binding site 1 out of 2 in the Designed Protein KE59 R1 7/10H with G130S Mutation


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 R1 7/10H with G130S Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na256

b:34.2
occ:1.00
N A:TYR93 3.0 18.8 1.0
OE1 A:GLU86 3.1 38.7 1.0
NH2 A:ARG19 3.2 18.1 1.0
CB A:TYR93 3.6 17.0 1.0
CA A:SER92 3.7 19.6 1.0
CD2 A:TYR93 3.7 19.2 1.0
CG A:TYR93 3.7 17.8 1.0
CB A:SER92 3.8 22.8 1.0
C A:SER92 3.8 16.6 1.0
CD A:GLU86 3.8 33.0 1.0
CA A:TYR93 3.9 18.6 1.0
CZ A:ARG19 4.2 17.6 1.0
NE A:ARG19 4.3 18.8 1.0
OE2 A:GLU86 4.5 31.1 1.0
CG A:GLU86 4.6 27.0 1.0
CE2 A:TYR93 4.6 19.5 1.0
CD1 A:TYR93 4.7 18.6 1.0
N A:GLU94 4.7 20.3 1.0
C A:TYR93 4.8 18.7 1.0
N A:SER92 4.9 19.9 1.0
OG A:SER92 5.0 27.2 1.0
O A:GLY91 5.0 23.1 1.0

Sodium binding site 2 out of 2 in 3uy7

Go back to Sodium Binding Sites List in 3uy7
Sodium binding site 2 out of 2 in the Designed Protein KE59 R1 7/10H with G130S Mutation


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 R1 7/10H with G130S Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na257

b:35.6
occ:1.00
NZ A:LYS115 3.1 18.2 1.0
O A:ARG18 3.3 23.9 1.0
C A:ARG18 3.5 19.8 1.0
CA A:ARG18 3.6 20.0 1.0
O A:LEU17 3.8 18.9 1.0
O A:HOH275 3.8 21.1 1.0
O A:ARG19 3.8 19.0 1.0
N A:ARG19 4.2 20.0 1.0
C A:ARG19 4.2 19.3 1.0
CE A:LYS115 4.5 17.5 1.0
C A:LEU17 4.6 16.3 1.0
N A:ARG18 4.6 18.0 1.0
CB A:ARG18 4.6 22.4 1.0
N A:PRO20 4.8 18.9 1.0
CA A:PRO20 4.8 18.4 1.0
CA A:ARG19 4.9 20.4 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 06:28:02 2020

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