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Sodium in PDB 4m5p: OYE2.6 Y78W, I113C

Protein crystallography data

The structure of OYE2.6 Y78W, I113C, PDB code: 4m5p was solved by B.Sullivan, J.D.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.04 / 1.50
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 126.487, 126.487, 123.307, 90.00, 90.00, 120.00
R / Rfree (%) 14.1 / 17

Sodium Binding Sites:

The binding sites of Sodium atom in the OYE2.6 Y78W, I113C (pdb code 4m5p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the OYE2.6 Y78W, I113C, PDB code: 4m5p:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4m5p

Go back to Sodium Binding Sites List in 4m5p
Sodium binding site 1 out of 3 in the OYE2.6 Y78W, I113C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of OYE2.6 Y78W, I113C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:15.5
occ:1.00
O A:HOH671 2.3 15.2 1.0
O A:HOH822 2.4 25.0 1.0
OD1 A:ASN104 2.5 16.6 1.0
CG A:ASN104 3.4 16.0 1.0
O A:HOH684 3.9 18.7 1.0
CA A:ASN104 4.0 13.2 1.0
CB A:ASN104 4.0 13.8 1.0
O A:ASN104 4.3 13.7 1.0
O A:THR58 4.4 14.5 1.0
ND2 A:ASN104 4.4 17.7 1.0
C A:ASN104 4.6 12.3 1.0
O A:ALA103 4.9 13.6 1.0

Sodium binding site 2 out of 3 in 4m5p

Go back to Sodium Binding Sites List in 4m5p
Sodium binding site 2 out of 3 in the OYE2.6 Y78W, I113C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of OYE2.6 Y78W, I113C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:31.5
occ:1.00
O A:HOH858 2.4 23.6 1.0
O A:HOH682 2.4 19.0 1.0
O A:ASP335 2.5 15.3 1.0
OD2 A:ASP338 2.5 16.8 1.0
CG A:ASP338 3.1 15.4 1.0
OG1 A:THR341 3.1 13.4 1.0
C A:ASP335 3.4 14.1 1.0
OD1 A:ASP338 3.5 14.4 1.0
O A:HOH949 3.8 35.1 1.0
CA A:ASP335 3.9 14.9 1.0
CB A:THR341 4.0 12.4 1.0
CB A:ASP338 4.1 14.8 1.0
CG2 A:THR341 4.3 13.6 1.0
O A:HOH751 4.3 20.9 1.0
OG A:SER309 4.3 16.3 1.0
O A:GLU334 4.4 17.8 1.0
N A:ILE336 4.6 14.5 1.0
N A:ASP338 4.6 15.0 1.0
CB A:ASP335 4.7 14.9 1.0
CA A:ILE336 4.9 15.0 1.0
O A:HOH1088 4.9 35.0 1.0
NE A:ARG340 5.0 14.4 1.0
CA A:ASP338 5.0 14.6 1.0

Sodium binding site 3 out of 3 in 4m5p

Go back to Sodium Binding Sites List in 4m5p
Sodium binding site 3 out of 3 in the OYE2.6 Y78W, I113C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of OYE2.6 Y78W, I113C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:33.3
occ:0.08
O A:HOH1087 2.3 40.1 1.0
O A:HOH765 3.5 21.0 1.0
O A:HOH667 4.1 17.1 1.0
O A:HOH916 4.7 31.3 1.0
O A:HOH813 4.8 24.7 1.0

Reference:

A.Z.Walton, B.Sullivan, A.C.Patterson-Orazem, J.D.Stewart. Residues Controlling Facial Selectivity in An Alkene Reductase and Semirational Alterations to Create Stereocomplementary Variants. Acs Catalysis V. 4 2307 2014.
ISSN: ESSN 2155-5435
PubMed: 25068071
DOI: 10.1021/CS500429K
Page generated: Tue Dec 15 06:53:27 2020

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