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Sodium in PDB 2zfp: Thrombin Inibition

Enzymatic activity of Thrombin Inibition

All present enzymatic activity of Thrombin Inibition:
3.4.21.5;

Protein crystallography data

The structure of Thrombin Inibition, PDB code: 2zfp 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 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.500, 71.300, 72.900, 90.00, 100.60, 90.00
R / Rfree (%) 18 / 30.9

Other elements in 2zfp:

The structure of Thrombin Inibition also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Inibition (pdb code 2zfp). 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 Inibition, PDB code: 2zfp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zfp

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inibition within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na802

b:21.9
occ:1.00
O H:ARG221A 2.2 26.3 1.0
O H:LYS224 2.2 20.0 1.0
O H:HOH1090 2.6 19.1 1.0
O H:HOH1087 2.6 20.2 1.0
O H:HOH1045 2.7 37.4 1.0
C H:ARG221A 3.2 26.3 1.0
C H:LYS224 3.3 25.2 1.0
N H:LYS224 3.4 14.0 1.0
N H:ARG221A 3.8 25.4 1.0
O H:HOH1017 3.8 33.3 1.0
CA H:LYS224 3.9 19.1 1.0
C H:ASP221 4.1 16.8 1.0
N H:ASP222 4.1 30.0 1.0
CA H:ARG221A 4.1 29.7 1.0
N H:GLY223 4.1 25.0 1.0
CA H:ASP222 4.2 31.3 1.0
O H:HOH1051 4.2 21.8 1.0
O H:TYR184A 4.3 26.1 1.0
C H:ASP222 4.4 26.8 1.0
CB H:LYS224 4.4 30.7 1.0
N H:TYR225 4.4 19.0 1.0
CA H:ASP221 4.4 9.8 1.0
O H:HOH1043 4.5 14.9 1.0
C H:GLY223 4.5 21.6 1.0
O H:ASP221 4.6 29.1 1.0
OD1 H:ASP221 4.7 16.0 1.0
CA H:TYR225 4.7 21.6 1.0
CA H:GLY223 4.9 20.1 1.0
CB H:ARG221A 4.9 30.5 1.0

Sodium binding site 2 out of 2 in 2zfp

Go back to Sodium Binding Sites List in 2zfp
Sodium binding site 2 out of 2 in the Thrombin Inibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inibition within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na803

b:17.9
occ:1.00
O H:THR172 2.4 15.1 1.0
O H:LYS169 2.4 11.3 1.0
C H:LYS169 3.4 14.2 1.0
C H:THR172 3.6 11.0 1.0
CA H:ASP170 4.0 13.0 1.0
N H:ASP170 4.1 16.2 1.0
N H:THR172 4.3 8.1 1.0
C H:ASP170 4.4 13.1 1.0
CA H:LYS169 4.4 18.5 1.0
CA H:ARG173 4.4 19.8 1.0
N H:ARG173 4.4 9.7 1.0
CA H:THR172 4.6 10.7 1.0
O H:HOH1105 4.6 26.1 1.0
OD1 H:ASP170 4.6 10.6 1.0
CB H:LYS169 4.7 20.5 1.0
O H:ASP170 4.8 19.1 1.0
CG2 H:THR172 4.9 1.2 1.0
N H:SER171 4.9 10.8 1.0
C H:ARG173 4.9 20.7 1.0

Reference:

B.Baum, L.Muley, A.Heine, M.Smolinski, D.Hangauer, G.Klebe. Think Twice: Understanding the High Potency of Bis(Phenyl)Methane Inhibitors of Thrombin J.Mol.Biol. V. 391 552 2009.
ISSN: ISSN 0022-2836
PubMed: 19520086
DOI: 10.1016/J.JMB.2009.06.016
Page generated: Tue Dec 15 06:01:03 2020

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