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Sodium in PDB 5nof: Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis

Enzymatic activity of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis

All present enzymatic activity of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis:
2.4.2.18;

Protein crystallography data

The structure of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis, PDB code: 5nof was solved by S.Perveen, N.Rashid, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.19 / 2.42
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.605, 81.389, 179.392, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 25.5

Other elements in 5nof:

The structure of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis (pdb code 5nof). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis, PDB code: 5nof:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5nof

Go back to Sodium Binding Sites List in 5nof
Sodium binding site 1 out of 2 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:56.4
occ:1.00
OD1 A:ASP278 2.5 74.3 1.0
NH2 A:ARG274 3.0 85.2 1.0
CG A:ASP278 3.5 71.8 1.0
CZ A:ARG274 3.7 0.5 1.0
CG2 A:ILE246 3.8 60.3 1.0
OD2 A:ASP278 4.0 74.5 1.0
NH1 A:ARG274 4.1 0.5 1.0
CD1 A:LEU281 4.3 43.3 1.0
NE A:ARG274 4.4 0.4 1.0
CD A:ARG305 4.7 75.0 1.0
CB A:ASP278 4.7 58.5 1.0
CB A:ILE246 4.8 50.5 1.0
CD2 A:LEU301 4.8 52.5 1.0

Sodium binding site 2 out of 2 in 5nof

Go back to Sodium Binding Sites List in 5nof
Sodium binding site 2 out of 2 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:77.0
occ:1.00
CD B:PRO128 4.1 53.3 1.0
CG B:PRO128 4.2 55.2 1.0
CL B:CL403 4.8 51.4 0.7

Reference:

S.Perveen, N.Rashid, X.F.Tang, T.Imanaka, A.C.Papageorgiou. Anthranilate Phosphoribosyltransferase From the Hyperthermophilic Archaeon Thermococcus Kodakarensis Shows Maximum Activity with Zinc and Forms A Unique Dimeric Structure. Febs Open Bio V. 7 1217 2017.
ISSN: ESSN 2211-5463
PubMed: 28781961
DOI: 10.1002/2211-5463.12264
Page generated: Tue Dec 15 11:21:32 2020

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