Atomistry » Sodium » PDB 1v55-1w4n » 1v6s
Atomistry »
  Sodium »
    PDB 1v55-1w4n »
      1v6s »

Sodium in PDB 1v6s: Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8

All present enzymatic activity of Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8:
2.7.2.3;

Protein crystallography data

The structure of Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8, PDB code: 1v6s was solved by H.Mizutani, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 143.175, 143.175, 75.641, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8 (pdb code 1v6s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8, PDB code: 1v6s:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1v6s

Go back to Sodium Binding Sites List in 1v6s
Sodium binding site 1 out of 3 in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8


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 Phosphoglycerate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1405

b:24.8
occ:1.00
O A:HOH1755 2.3 31.4 1.0
O A:HOH1569 2.4 28.2 1.0
O A:GLU378 2.4 19.4 1.0
O A:HOH1757 2.4 36.5 1.0
O A:HOH1756 2.5 31.5 1.0
OG A:SER204 2.7 19.0 1.0
CB A:SER204 3.3 18.9 1.0
C A:GLU378 3.4 19.3 1.0
NH1 A:ARG208 3.8 27.1 1.0
CA A:SER204 4.1 16.9 1.0
O A:LEU377 4.1 17.9 1.0
N A:LYS379 4.2 19.3 1.0
CA A:LYS379 4.3 20.4 1.0
C A:LYS379 4.3 19.7 1.0
CA A:GLU378 4.3 18.4 1.0
O A:HOH1480 4.4 22.0 1.0
O A:LYS379 4.5 20.7 1.0
O A:HOH1606 4.6 32.0 1.0
O A:HOH1681 4.7 37.7 1.0
N A:GLY380 4.7 17.7 1.0
O A:SER204 4.8 17.4 1.0
CZ A:ARG208 4.8 26.5 1.0
C A:SER204 4.9 16.4 1.0
NH2 A:ARG208 4.9 28.1 1.0

Sodium binding site 2 out of 3 in 1v6s

Go back to Sodium Binding Sites List in 1v6s
Sodium binding site 2 out of 3 in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8


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 Phosphoglycerate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1406

b:27.0
occ:1.00
O B:GLU378 2.2 20.4 1.0
O B:HOH1717 2.3 36.5 1.0
O B:HOH1718 2.4 32.2 1.0
O B:HOH1748 2.5 40.9 1.0
O B:HOH1595 2.6 35.8 1.0
OG B:SER204 2.7 22.6 1.0
C B:GLU378 3.3 21.2 1.0
CB B:SER204 3.4 19.4 1.0
O B:LEU377 3.9 20.0 1.0
NH1 B:ARG208 4.1 27.4 1.0
CA B:GLU378 4.1 20.7 1.0
CA B:SER204 4.2 18.1 1.0
N B:LYS379 4.2 20.9 1.0
CA B:LYS379 4.4 21.7 1.0
O B:HOH1560 4.5 27.9 1.0
C B:LYS379 4.5 21.2 1.0
O B:HOH1617 4.8 38.9 1.0
C B:LEU377 4.8 18.6 1.0
N B:GLY380 4.8 19.9 1.0
NH2 B:ARG208 4.9 27.7 1.0
O B:HOH1664 4.9 29.1 1.0
O B:LYS379 4.9 22.0 1.0
N B:GLU378 5.0 19.4 1.0
CZ B:ARG208 5.0 25.9 1.0

Sodium binding site 3 out of 3 in 1v6s

Go back to Sodium Binding Sites List in 1v6s
Sodium binding site 3 out of 3 in the Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8


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 Phosphoglycerate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1407

b:43.3
occ:1.00
O B:HOH1545 2.5 34.0 1.0
O B:HOH1547 2.5 22.2 1.0
O B:HOH1668 2.6 37.0 1.0
O B:HOH1496 2.6 19.5 1.0
O B:HOH1746 2.6 43.1 1.0
O B:HOH1484 2.8 23.1 1.0
O B:ALA341 4.1 17.7 1.0
N B:GLY340 4.1 23.7 1.0
O B:LEU338 4.1 18.5 1.0
O B:HOH1733 4.2 40.3 1.0
O B:ARG362 4.3 17.9 1.0
O B:HOH1443 4.3 17.6 1.0
O B:HOH1428 4.3 15.5 1.0
O B:HOH1445 4.4 18.8 1.0
N B:ALA341 4.6 20.1 1.0
CA B:GLY340 4.8 23.7 1.0
CA B:GLU339 5.0 22.8 1.0
C B:GLU339 5.0 23.6 1.0

Reference:

H.Mizutani, N.Kunishima. Crystal Structure of Phosphoglycerate Kinase From Thermus Thermophilus HB8 To Be Published.
Page generated: Sun Oct 6 22:51:05 2024

Last articles

Ca in 5K89
Ca in 5K5S
Ca in 5K8D
Ca in 5K7T
Ca in 5K7S
Ca in 5K31
Ca in 5K7R
Ca in 5K5T
Ca in 5K39
Ca in 5JY7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy