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Sodium in PDB 1v47: Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps

Enzymatic activity of Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps

All present enzymatic activity of Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps:
2.7.7.4;

Protein crystallography data

The structure of Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps, PDB code: 1v47 was solved by Y.Taguchi, M.Sugishima, K.Fukuyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.858, 61.254, 128.665, 90.00, 95.43, 90.00
R / Rfree (%) 21.9 / 26.9

Other elements in 1v47:

The structure of Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps (pdb code 1v47). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps, PDB code: 1v47:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1v47

Go back to Sodium Binding Sites List in 1v47
Sodium binding site 1 out of 4 in the Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps


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 Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:30.4
occ:1.00
 OG1 A:THR109 3.2 21.7 1.0
N A:HIS110 4.0 16.1 1.0
CA A:HIS110 4.1 17.3 1.0
CB A:HIS110 4.2 17.9 1.0
C A:THR109 4.2 18.8 1.0
CB A:THR109 4.3 19.0 1.0
O A:THR109 4.4 20.3 1.0
CD2 A:PHE265 4.4 24.1 1.0
CG A:PHE265 4.8 24.2 1.0
CA A:THR109 4.9 18.9 1.0
CG A:HIS110 4.9 17.0 1.0
CE2 A:PHE265 4.9 24.0 1.0
OG A:SER107 4.9 24.7 1.0
CB A:PHE265 5.0 21.1 1.0

Sodium binding site 2 out of 4 in 1v47

Go back to Sodium Binding Sites List in 1v47
Sodium binding site 2 out of 4 in the Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:38.8
occ:1.00
 OE2 A:GLU96 2.7 37.0 1.0
CD A:GLU96 3.6 36.4 1.0
CG A:GLU96 3.7 33.7 1.0
O A:HOH733 4.4 34.4 1.0
CE1 A:TYR117 4.5 16.1 1.0
CD1 A:TYR117 4.5 18.2 1.0
CZ A:TYR117 4.7 18.2 1.0
O A:HOH670 4.7 43.8 1.0
CG A:TYR117 4.7 20.1 1.0
OE1 A:GLU96 4.8 39.0 1.0
CE2 A:TYR117 4.9 13.8 1.0
CD2 A:TYR117 4.9 14.3 1.0
CB A:GLU96 5.0 27.6 1.0

Sodium binding site 3 out of 4 in 1v47

Go back to Sodium Binding Sites List in 1v47
Sodium binding site 3 out of 4 in the Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:56.8
occ:1.00
 OE2 A:GLU219 2.8 42.7 1.0
CD A:GLU219 3.3 39.4 1.0
OE1 A:GLU219 3.7 35.3 1.0
CB B:GLU308 4.0 38.2 1.0
CG A:GLU219 4.1 39.2 1.0
CB A:GLU219 4.4 39.4 1.0
CG B:GLU308 4.5 44.3 1.0

Sodium binding site 4 out of 4 in 1v47

Go back to Sodium Binding Sites List in 1v47
Sodium binding site 4 out of 4 in the Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Atp Sulfurylase From Thermus Thermophillus HB8 in Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:65.2
occ:1.00
 OE2 B:GLU96 4.1 75.8 1.0
CG B:GLU96 4.1 74.4 1.0
CD1 B:TYR117 4.2 62.7 1.0
CG B:TYR117 4.3 62.7 1.0
CE1 B:TYR117 4.3 62.8 1.0
CD B:GLU96 4.4 75.5 1.0
CD2 B:TYR117 4.4 62.2 1.0
CZ B:TYR117 4.5 62.7 1.0
CE2 B:TYR117 4.6 61.9 1.0
CB B:TYR117 4.8 63.7 1.0
CB B:LEU95 4.9 69.5 1.0
CD1 B:LEU95 4.9 69.1 1.0

Reference:

Y.Taguchi, M.Sugishima, K.Fukuyama. Crystal Structure of A Novel Zinc-Binding Atp Sulfurylase From Thermus Thermophilus HB8 Biochemistry V. 43 4111 2004.
ISSN: ISSN 0006-2960
PubMed: 15065853
DOI: 10.1021/BI036052T
Page generated: Sun Oct 6 22:49:30 2024

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