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Sodium in PDB 4e7r: Thrombin in Complex with 3-Amidinophenylalanine Inhibitor

Enzymatic activity of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor

All present enzymatic activity of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor, PDB code: 4e7r was solved by E.Ruehmann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.26 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.242, 50.284, 71.837, 97.61, 96.61, 90.57
R / Rfree (%) 17.1 / 22.3

Other elements in 4e7r:

The structure of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor (pdb code 4e7r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor, PDB code: 4e7r:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4e7r

Go back to Sodium Binding Sites List in 4e7r
Sodium binding site 1 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:37.0
occ:1.00
 O H:HOH496 2.3 20.2 1.0
O H:LYS169 2.4 30.1 1.0
O H:HOH497 2.4 27.4 1.0
O H:THR172 2.4 23.5 1.0
O H:HOH475 2.6 34.6 1.0
C H:LYS169 3.4 30.5 1.0
C H:THR172 3.7 34.4 1.0
N H:ASP170 4.1 15.8 1.0
CA H:ASP170 4.2 29.6 1.0
CA H:LYS169 4.3 30.9 1.0
N H:THR172 4.4 26.2 1.0
CA H:ARG173 4.5 32.4 1.0
N H:ARG173 4.5 27.0 1.0
C H:ASP170 4.6 27.6 1.0
CA H:THR172 4.6 23.4 1.0
CB H:LYS169 4.6 27.2 1.0
O H:ILE174 4.8 24.9 1.0
CG2 H:THR172 4.8 18.9 1.0
OD1 H:ASP170 4.8 31.3 1.0
O H:HOH425 4.8 28.4 1.0
C H:ARG173 4.9 32.6 1.0
N H:SER171 4.9 23.9 1.0

Sodium binding site 2 out of 4 in 4e7r

Go back to Sodium Binding Sites List in 4e7r
Sodium binding site 2 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na304

b:29.4
occ:1.00
 O H:ARG221A 2.1 27.7 1.0
O H:HOH420 2.4 23.5 1.0
O H:LYS224 2.4 33.2 1.0
O H:HOH504 2.5 31.8 1.0
O H:HOH426 2.5 27.6 1.0
O H:HOH451 3.1 20.4 1.0
C H:ARG221A 3.1 35.9 1.0
C H:LYS224 3.4 26.3 1.0
N H:LYS224 3.5 38.8 1.0
N H:ARG221A 3.7 36.7 1.0
CA H:LYS224 3.9 27.5 1.0
O H:HOH428 3.9 27.4 1.0
N H:ASP222 3.9 31.2 1.0
C H:ASP221 4.0 34.1 1.0
CA H:ARG221A 4.0 43.9 1.0
CA H:ASP222 4.1 39.9 1.0
N H:GLY223 4.1 36.1 1.0
O H:HOH452 4.2 31.4 1.0
CB H:LYS224 4.2 26.6 1.0
C H:ASP222 4.2 33.8 1.0
O H:TYR184A 4.3 30.0 1.0
CA H:ASP221 4.3 37.3 1.0
N H:TYR225 4.4 20.5 1.0
O H:ASP221 4.5 30.3 1.0
O H:HOH467 4.5 23.1 1.0
C H:GLY223 4.6 35.6 1.0
OD1 H:ASP221 4.7 26.3 1.0
CA H:TYR225 4.8 26.2 1.0
O H:HOH439 4.9 27.0 1.0
O H:HOH453 4.9 29.1 1.0
CA H:GLY223 4.9 25.9 1.0
O H:ASP222 4.9 35.6 1.0
CB H:ARG221A 5.0 42.6 1.0

Sodium binding site 3 out of 4 in 4e7r

Go back to Sodium Binding Sites List in 4e7r
Sodium binding site 3 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1303

b:37.5
occ:1.00
 O G:THR1172 2.2 25.1 1.0
O G:HOH1505 2.4 35.6 1.0
O G:HOH1464 2.5 29.0 1.0
O G:LYS1169 2.7 29.7 1.0
O G:HOH1438 3.2 29.4 1.0
C G:THR1172 3.4 33.1 1.0
C G:LYS1169 3.7 31.8 1.0
O G:HOH1499 4.1 35.8 1.0
CA G:ARG1173 4.1 32.3 1.0
N G:ARG1173 4.2 25.8 1.0
N G:THR1172 4.4 29.2 1.0
O G:ILE1174 4.4 29.0 1.0
CA G:THR1172 4.4 25.9 1.0
C G:ARG1173 4.4 25.4 1.0
N G:ASP1170 4.6 18.8 1.0
CA G:ASP1170 4.6 31.8 1.0
CA G:LYS1169 4.6 30.7 1.0
CG2 G:THR1172 4.7 18.7 1.0
O G:ARG1173 4.7 35.2 1.0
O G:HOH1444 4.8 30.2 1.0
C G:ASP1170 4.9 27.0 1.0
N G:ILE1174 5.0 28.4 1.0

Sodium binding site 4 out of 4 in 4e7r

Go back to Sodium Binding Sites List in 4e7r
Sodium binding site 4 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1304

b:41.1
occ:1.00
 O G:HOH1503 2.3 40.2 1.0
O G:HOH1498 2.3 19.2 1.0
O G:HOH1449 2.4 30.0 1.0
O G:ARG1221A 2.5 35.2 1.0
O G:LYS1224 2.5 31.4 1.0
O G:HOH1420 2.6 30.3 1.0
C G:ARG1221A 3.4 40.7 1.0
C G:LYS1224 3.5 28.2 1.0
O G:HOH1506 3.6 39.8 1.0
N G:LYS1224 3.8 38.0 1.0
O G:TYR1184A 3.8 31.4 1.0
O G:HOH1413 4.0 23.9 1.0
N G:GLY1223 4.1 37.8 1.0
CA G:ASP1222 4.1 41.7 1.0
N G:ASP1222 4.1 35.6 1.0
CA G:LYS1224 4.1 31.4 1.0
N G:ARG1221A 4.2 38.9 1.0
O G:HOH1407 4.3 25.6 1.0
C G:ASP1221 4.3 39.7 1.0
C G:ASP1222 4.3 44.9 1.0
CA G:ARG1221A 4.5 41.5 1.0
N G:TYR1225 4.6 28.0 1.0
CA G:ASP1221 4.6 39.2 1.0
CB G:LYS1224 4.6 29.0 1.0
OD1 G:ASP1221 4.7 30.9 1.0
C G:GLY1223 4.7 40.8 1.0
O G:ASP1221 4.7 37.0 1.0
CA G:TYR1225 4.9 29.6 1.0
CA G:GLY1223 4.9 33.9 1.0
CD2 G:TYR1225 5.0 30.3 1.0

Reference:

M.Hammami, E.Ruehmann, M.Mauerer, A.Heine, M.Guetschow, G.Klebe, T.Steinmetzer. New 3-Amidinophenylalanine-Derived Inhibitors of Matriptase Medchemcomm V. 3 807 2012.
ISSN: ISSN 2040-2503
DOI: 10.1039/C2MD20074K
Page generated: Mon Oct 7 15:07:10 2024

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