Atomistry » Sodium » PDB 2zgx-3a03 » 2zhq
Atomistry »
  Sodium »
    PDB 2zgx-3a03 »
      2zhq »

Sodium in PDB 2zhq: Thrombin Inhibition

Enzymatic activity of Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

Protein crystallography data

The structure of Thrombin Inhibition, PDB code: 2zhq was solved by B.Baum, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.100, 71.400, 72.900, 90.00, 100.80, 90.00
R / Rfree (%) 19.3 / 27.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Inhibition (pdb code 2zhq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin Inhibition, PDB code: 2zhq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zhq

Go back to Sodium Binding Sites List in 2zhq
Sodium binding site 1 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na601

b:1.2
occ:1.00
O H:ARG221A 2.5 13.8 1.0
O H:HOH1031 2.5 14.5 1.0
O H:HOH1153 2.5 22.8 1.0
O H:LYS224 2.5 14.9 1.0
O H:HOH1062 2.5 15.8 1.0
O H:HOH1083 2.5 22.0 1.0
C H:ARG221A 3.4 24.6 1.0
C H:LYS224 3.6 22.8 1.0
O H:HOH1050 3.7 24.1 1.0
N H:LYS224 3.8 19.0 1.0
O H:HOH1077 4.0 17.8 1.0
O H:TYR184A 4.0 23.7 1.0
CA H:ASP222 4.1 15.7 1.0
N H:ARG221A 4.1 21.3 1.0
N H:ASP222 4.1 13.3 1.0
C H:ASP221 4.2 26.4 1.0
N H:GLY223 4.2 23.0 1.0
CA H:LYS224 4.2 13.2 1.0
O H:HOH1066 4.2 11.5 1.0
CA H:ARG221A 4.4 23.2 1.0
C H:ASP222 4.4 15.4 1.0
CA H:ASP221 4.5 18.5 1.0
O H:ASP221 4.5 22.8 1.0
N H:TYR225 4.7 12.8 1.0
CB H:LYS224 4.7 14.1 1.0
C H:GLY223 4.8 19.7 1.0
OD1 H:ASP221 4.8 12.2 1.0
CA H:TYR225 4.9 10.7 1.0
CA H:GLY223 5.0 15.7 1.0

Sodium binding site 2 out of 2 in 2zhq

Go back to Sodium Binding Sites List in 2zhq
Sodium binding site 2 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibition within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na602

b:4.2
occ:1.00
O H:THR172 2.5 8.8 1.0
O H:LYS169 2.5 10.9 1.0
O H:HOH1059 2.5 17.0 1.0
O H:HOH1104 2.5 20.6 1.0
C H:LYS169 3.5 11.1 1.0
C H:THR172 3.7 9.8 1.0
CA H:ASP170 4.1 8.6 1.0
N H:ASP170 4.3 12.6 1.0
N H:THR172 4.3 7.7 1.0
C H:ASP170 4.5 14.1 1.0
CA H:ARG173 4.5 14.3 1.0
CA H:LYS169 4.6 13.6 1.0
N H:ARG173 4.6 6.8 1.0
CA H:THR172 4.6 12.2 1.0
OD1 H:ASP170 4.7 11.2 1.0
N H:SER171 4.9 16.6 1.0
O H:ASP170 4.9 9.4 1.0
CB H:LYS169 4.9 22.5 1.0
CG2 H:THR172 5.0 14.8 1.0
C H:ARG173 5.0 15.4 1.0

Reference:

B.Baum, L.Muley, M.Smolinski, A.Heine, D.Hangauer, G.Klebe. Non-Additivity of Functional Group Contributions in Protein-Ligand Binding: A Comprehensive Study By Crystallography and Isothermal Titration Calorimetry. J.Mol.Biol. V. 397 1042 2010.
ISSN: ISSN 0022-2836
PubMed: 20156458
DOI: 10.1016/J.JMB.2010.02.007
Page generated: Mon Oct 7 05:36:26 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy