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Sodium in PDB 6hk1: Crystal Structure of the Thiazole Synthase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4

Protein crystallography data

The structure of Crystal Structure of the Thiazole Synthase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4, PDB code: 6hk1 was solved by S.Engilberge, T.Wagner, G.Santoni, C.Breyton, S.Shima, B.Franzetti, F.Riobe, O.Maury, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.09 / 2.55
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 216.863, 216.863, 207.250, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.3

Other elements in 6hk1:

The structure of Crystal Structure of the Thiazole Synthase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4 also contains other interesting chemical elements:

Terbium (Tb) 49 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Thiazole Synthase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4 (pdb code 6hk1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Thiazole Synthase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4, PDB code: 6hk1:

Sodium binding site 1 out of 1 in 6hk1

Go back to Sodium Binding Sites List in 6hk1
Sodium binding site 1 out of 1 in the Crystal Structure of the Thiazole Synthase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Thiazole Synthase From Methanothermococcus Thermolithotrophicus Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na313

b:63.0
occ:1.00
OD1 E:ASN166 2.5 55.1 1.0
OG1 E:THR164 2.8 59.1 1.0
O E:THR164 2.9 42.4 1.0
C E:THR164 3.2 43.1 1.0
O E:ILE28 3.2 43.6 1.0
N E:ILE165 3.5 37.6 1.0
CB E:THR164 3.5 56.1 1.0
N E:ASN166 3.5 40.9 1.0
CA A:TYR10 3.6 39.7 1.0
CG E:ASN166 3.6 59.1 1.0
CA E:ILE165 3.7 36.8 1.0
N A:TYR10 3.9 40.9 1.0
C E:ILE165 3.9 42.4 1.0
CA E:THR164 3.9 43.5 1.0
CD1 A:TYR10 4.1 41.9 1.0
CB E:ILE28 4.1 42.9 1.0
C A:GLU9 4.2 44.5 1.0
CB A:TYR10 4.2 38.8 1.0
O A:GLU9 4.2 45.2 1.0
C E:ILE28 4.2 44.1 1.0
OG1 A:THR13 4.3 43.1 1.0
CB E:ASN166 4.4 37.1 1.0
CB A:THR13 4.4 43.2 1.0
CA E:ASN166 4.5 40.7 1.0
CA E:ILE28 4.6 40.0 1.0
ND2 E:ASN166 4.6 50.5 1.0
CG A:TYR10 4.6 39.7 1.0
CB A:GLU9 4.6 41.4 1.0
N E:THR164 4.6 43.6 1.0
C A:TYR10 4.7 43.7 1.0
CG2 A:THR13 4.7 37.1 1.0
O A:TYR10 4.7 41.7 1.0
CG2 E:ILE28 4.7 43.9 1.0
O E:ILE165 4.9 42.1 1.0
CG2 E:THR164 4.9 52.5 1.0

Reference:

S.Engilberge, T.Wagner, G.Santoni, C.Breyton, S.Shima, B.Franzetti, F.Riobe, O.Maury, E.Girard. Protein Crystal Structure Determination with the Crystallophore, A Nucleating and Phasing Agent. J.Appl.Crystallogr. V. 52 722 2019.
ISSN: ISSN 0021-8898
PubMed: 31396026
DOI: 10.1107/S1600576719006381
Page generated: Tue Dec 15 12:21:24 2020

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