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Sodium in PDB 3d54: Structure of Purlqs From Thermotoga Maritima

Enzymatic activity of Structure of Purlqs From Thermotoga Maritima

All present enzymatic activity of Structure of Purlqs From Thermotoga Maritima:
6.3.5.3;

Protein crystallography data

The structure of Structure of Purlqs From Thermotoga Maritima, PDB code: 3d54 was solved by S.E.Ealick, M.Morar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.70 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 256.851, 187.337, 159.177, 90.00, 99.12, 90.00
R / Rfree (%) 25.2 / 28.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Purlqs From Thermotoga Maritima (pdb code 3d54). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Purlqs From Thermotoga Maritima, PDB code: 3d54:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3d54

Go back to Sodium Binding Sites List in 3d54
Sodium binding site 1 out of 3 in the Structure of Purlqs From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Purlqs From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3003

b:0.0
occ:1.00
OD2 A:ASP94 2.8 1.0 1.0
OD1 A:ASP236 2.8 0.8 1.0
OD2 A:ASP236 3.2 0.9 1.0
CG A:ASP236 3.4 0.4 1.0
CG A:ASP94 3.5 1.0 1.0
OD1 A:ASP94 3.6 1.0 1.0
OE1 A:GLU70 4.3 0.6 1.0
NZ A:LYS68 4.6 0.3 1.0
CB A:ASP94 4.7 1.0 1.0
OE1 A:GLN235 4.8 0.6 1.0
CB A:ASP236 4.9 0.4 1.0

Sodium binding site 2 out of 3 in 3d54

Go back to Sodium Binding Sites List in 3d54
Sodium binding site 2 out of 3 in the Structure of Purlqs From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Purlqs From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na3001

b:0.0
occ:1.00
OD1 I:ASP236 2.8 0.1 1.0
OD2 I:ASP94 2.8 1.0 1.0
OD2 I:ASP236 3.2 0.3 1.0
CG I:ASP236 3.4 0.8 1.0
CG I:ASP94 3.4 1.0 1.0
OD1 I:ASP94 3.5 1.0 1.0
OE1 I:GLU70 4.3 0.1 1.0
NZ I:LYS68 4.6 0.7 1.0
CB I:ASP94 4.7 1.0 1.0
OE1 I:GLN235 4.8 0.4 1.0
CB I:ASP236 4.9 0.8 1.0

Sodium binding site 3 out of 3 in 3d54

Go back to Sodium Binding Sites List in 3d54
Sodium binding site 3 out of 3 in the Structure of Purlqs From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Purlqs From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na3002

b:0.0
occ:1.00
OD2 E:ASP94 2.8 1.0 1.0
OD1 E:ASP236 2.8 0.5 1.0
OD2 E:ASP236 3.2 1.0 1.0
CG E:ASP236 3.4 1.0 1.0
CG E:ASP94 3.4 1.0 1.0
OD1 E:ASP94 3.6 1.0 1.0
OE1 E:GLU70 4.2 0.5 1.0
NZ E:LYS68 4.5 0.0 1.0
CB E:ASP94 4.7 1.0 1.0
OE1 E:GLN235 4.8 0.8 1.0
CB E:ASP236 4.9 0.1 1.0

Reference:

M.Morar, A.A.Hoskins, J.Stubbe, S.E.Ealick. Formylglycinamide Ribonucleotide Amidotransferase From Thermotoga Maritima: Structural Insights Into Complex Formation. Biochemistry V. 47 7816 2008.
ISSN: ISSN 0006-2960
PubMed: 18597481
DOI: 10.1021/BI800329P
Page generated: Tue Dec 15 06:08:24 2020

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