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Sodium in PDB 7yq0: Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp

Enzymatic activity of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp

All present enzymatic activity of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp:
2.7.1.25;

Protein crystallography data

The structure of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp, PDB code: 7yq0 was solved by T.Kawakami, T.Teramoto, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.72 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.08, 74.32, 109.87, 90, 90, 90
R / Rfree (%) 18.7 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp (pdb code 7yq0). 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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp, PDB code: 7yq0:

Sodium binding site 1 out of 1 in 7yq0

Go back to Sodium Binding Sites List in 7yq0
Sodium binding site 1 out of 1 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp


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 Adenosine 5'-Phosphosulfate Kinase From Archaeoglobus Fulgidus in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:26.9
occ:1.00
 O B:ARG93 2.2 16.8 1.0
O B:ILE96 2.3 21.7 1.0
O B:HOH313 2.4 30.7 1.0
O B:HOH457 2.4 32.1 1.0
O B:HOH405 2.5 33.1 1.0
C B:ARG93 3.4 19.6 1.0
C B:ILE96 3.5 20.3 1.0
O B:GLU97 3.5 24.8 1.0
C B:GLU97 3.9 23.4 1.0
CA B:GLU97 4.1 22.8 1.0
CG B:ARG93 4.1 18.4 1.0
O B:HOH442 4.2 32.6 1.0
CB B:PHE99 4.3 18.0 1.0
N B:GLU97 4.3 19.8 1.0
CA B:ARG93 4.3 15.8 1.0
N B:LYS94 4.4 14.2 1.0
CA B:LYS94 4.4 16.0 0.8
CA B:LYS94 4.4 16.2 0.2
O B:LYS94 4.4 19.7 1.0
C B:LYS94 4.5 16.7 1.0
N B:ILE96 4.5 15.1 1.0
CA B:ILE96 4.6 17.1 0.4
CA B:ILE96 4.6 17.1 0.6
O B:HOH370 4.6 22.9 1.0
N B:LYS98 4.8 19.3 1.0
CB B:ARG93 4.8 15.8 1.0
N B:PHE99 4.8 16.7 1.0

Reference:

T.Kawakami, T.Teramoto, Y.Kakuta. Crystal Structure of Adenosine 5'-Phosphosulfate Kinase Isolated From Archaeoglobus Fulgidus. Biochem.Biophys.Res.Commun. V. 643 105 2022.
ISSN: ESSN 1090-2104
PubMed: 36592583
DOI: 10.1016/J.BBRC.2022.12.081
Page generated: Wed Oct 9 09:58:50 2024

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