Atomistry » Sodium » PDB 7b7h-7bov » 7bnh
Atomistry »
  Sodium »
    PDB 7b7h-7bov »
      7bnh »

Sodium in PDB 7bnh: Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid

Enzymatic activity of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid

All present enzymatic activity of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid:
3.4.24.75;

Protein crystallography data

The structure of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid, PDB code: 7bnh was solved by P.H.Malecki, I.Sabala, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.21 / 0.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 33.954, 54.781, 51.49, 90, 92.4, 90
R / Rfree (%) 8.5 / 10.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid (pdb code 7bnh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid, PDB code: 7bnh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7bnh

Go back to Sodium Binding Sites List in 7bnh
Sodium binding site 1 out of 2 in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:6.6
occ:0.60
OE1 A:GLN455 2.3 5.1 1.0
O A:HOH757 2.4 18.1 1.0
O A:HOH713 2.4 12.1 0.6
O A:HOH746 2.4 11.2 0.7
O A:HOH715 2.4 7.8 1.0
O A:HOH677 2.5 7.6 1.0
HE22 A:GLN455 3.2 5.5 1.0
HZ2 A:LYS480 3.3 38.9 0.3
HZ3 A:LYS480 3.3 48.3 0.7
CD A:GLN455 3.3 4.4 1.0
H A:ASP456 3.5 17.3 1.0
NE2 A:GLN455 3.6 4.9 1.0
O A:HOH731 3.8 7.0 0.3
HZ1 A:LYS480 3.9 16.7 0.7
NZ A:LYS480 4.0 8.9 0.7
NZ A:LYS480 4.1 9.1 0.3
HE2 A:PHE432 4.1 26.9 1.0
O A:HOH718 4.1 7.9 0.7
HZ1 A:LYS480 4.2 34.2 0.3
HZ3 A:LYS480 4.2 15.8 0.3
HZ2 A:LYS480 4.3 51.5 0.7
O A:HOH684 4.3 30.2 1.0
N A:ASP456 4.4 3.9 1.0
O A:HOH659 4.4 14.8 1.0
O A:HOH676 4.4 5.6 1.0
HA A:ASP456 4.5 3.8 1.0
HE21 A:GLN455 4.5 4.1 1.0
HA A:GLN455 4.5 4.0 1.0
O A:HOH731 4.5 6.0 0.7
O A:HOH795 4.5 22.2 0.7
CG A:GLN455 4.7 4.2 1.0
HG3 A:GLN455 4.7 4.3 1.0
O A:HOH612 4.9 27.3 1.0
O A:HOH823 4.9 35.3 1.0
O A:LYS407 4.9 6.3 1.0
HD2 A:LYS480 4.9 1.8 0.3
CE2 A:PHE432 4.9 8.4 1.0
CA A:ASP456 5.0 4.0 1.0

Sodium binding site 2 out of 2 in 7bnh

Go back to Sodium Binding Sites List in 7bnh
Sodium binding site 2 out of 2 in the Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex Structure at Atomic Resolution of SH3B Domain with Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:11.7
occ:0.45
O B:HOH734 2.3 28.7 1.0
OE1 B:GLN455 2.3 6.8 1.0
O B:HOH720 2.3 39.1 1.0
O B:HOH729 2.5 12.8 1.0
O B:HOH699 2.5 15.2 1.0
O B:HOH738 2.6 37.3 1.0
HE22 B:GLN455 3.1 16.1 1.0
CD B:GLN455 3.3 6.6 1.0
NE2 B:GLN455 3.6 7.1 1.0
H B:ASP456 3.6 4.7 1.0
O B:HOH681 4.0 12.2 1.0
O B:HOH676 4.2 7.8 1.0
HZ3 B:LYS480 4.3 92.8 0.8
HD3 B:LYS480 4.3 37.2 0.2
HE1 B:PHE432 4.4 52.1 1.0
HD3 B:LYS480 4.4 61.2 0.8
HE21 B:GLN455 4.4 6.5 1.0
HA B:GLN455 4.4 3.9 1.0
N B:ASP456 4.5 5.2 1.0
O B:HOH687 4.5 30.5 1.0
O B:HOH747 4.6 24.1 0.5
HD2 B:LYS480 4.7 81.1 0.8
CG B:GLN455 4.7 6.4 1.0
O B:HOH690 4.7 31.8 1.0
HA B:ASP456 4.7 7.9 1.0
HG3 B:GLN455 4.8 7.4 1.0
HD2 B:LYS480 4.9 26.0 0.2
HZ2 B:LYS480 4.9 90.7 0.8
NZ B:LYS480 5.0 25.7 0.8
CD B:LYS480 5.0 21.0 0.8

Reference:

P.H.Malecki, I.Sabala. Complex Structure of SH3B Domain with Benzoic Acid To Be Published.
Page generated: Tue Oct 8 16:14:43 2024

Last articles

Ca in 2XTT
Ca in 2XTJ
Ca in 2XT6
Ca in 2XSG
Ca in 2XRM
Ca in 2XR6
Ca in 2XRG
Ca in 2XR5
Ca in 2XR9
Ca in 2XQX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy