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Sodium in PDB 2zg0: Exploring Thrombin S3 Pocket

Enzymatic activity of Exploring Thrombin S3 Pocket

All present enzymatic activity of Exploring Thrombin S3 Pocket:
3.4.21.5;

Protein crystallography data

The structure of Exploring Thrombin S3 Pocket, PDB code: 2zg0 was solved by T.Brandt, 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 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.700, 71.400, 72.800, 90.00, 100.60, 90.00
R / Rfree (%) 18.9 / 24.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Exploring Thrombin S3 Pocket (pdb code 2zg0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Exploring Thrombin S3 Pocket, PDB code: 2zg0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zg0

Go back to Sodium Binding Sites List in 2zg0
Sodium binding site 1 out of 2 in the Exploring Thrombin S3 Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Exploring Thrombin S3 Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na950

b:21.6
occ:1.00
O H:HOH1094 2.3 21.3 1.0
O H:HOH1159 2.3 24.2 1.0
O H:LYS224 2.3 22.0 1.0
O H:HOH1040 2.3 16.3 1.0
O H:ARG221A 2.4 25.9 1.0
O H:HOH1046 2.8 23.0 1.0
C H:ARG221A 3.4 27.4 1.0
C H:LYS224 3.5 18.4 1.0
O H:HOH1080 3.9 20.4 1.0
N H:LYS224 3.9 14.3 1.0
O H:HOH1020 3.9 19.9 1.0
N H:ARG221A 4.0 27.8 1.0
O H:TYR184A 4.1 18.7 1.0
O H:HOH1009 4.2 15.9 1.0
C H:ASP221 4.2 26.0 1.0
CA H:LYS224 4.2 13.3 1.0
N H:ASP222 4.2 26.5 1.0
CA H:ASP222 4.3 22.1 1.0
CA H:ARG221A 4.3 25.0 1.0
N H:GLY223 4.3 23.7 1.0
CA H:ASP221 4.4 16.1 1.0
N H:TYR225 4.5 21.2 1.0
C H:ASP222 4.5 28.6 1.0
OD1 H:ASP221 4.7 23.5 1.0
O H:ASP221 4.7 22.0 1.0
CA H:TYR225 4.8 18.7 1.0
CB H:LYS224 4.8 21.4 1.0
C H:GLY223 4.9 25.3 1.0
CD2 H:TYR225 4.9 16.9 1.0

Sodium binding site 2 out of 2 in 2zg0

Go back to Sodium Binding Sites List in 2zg0
Sodium binding site 2 out of 2 in the Exploring Thrombin S3 Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Exploring Thrombin S3 Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na951

b:16.9
occ:1.00
O H:THR172 2.2 15.6 1.0
O H:LYS169 2.4 16.8 1.0
O H:HOH1055 2.4 15.1 1.0
O H:HOH1039 2.6 20.5 1.0
O H:HOH1088 2.6 25.5 1.0
C H:THR172 3.4 12.4 1.0
C H:LYS169 3.5 18.2 1.0
CA H:ASP170 4.1 14.1 1.0
N H:ASP170 4.2 16.3 1.0
N H:THR172 4.2 16.0 1.0
N H:ARG173 4.3 14.4 1.0
CA H:THR172 4.4 16.4 1.0
CA H:ARG173 4.4 17.0 1.0
C H:ASP170 4.4 17.1 1.0
CA H:LYS169 4.5 11.7 1.0
CG2 H:THR172 4.5 16.9 1.0
OD1 H:ASP170 4.7 16.9 1.0
O H:ASP170 4.8 16.4 1.0
O H:ILE174 4.8 15.7 1.0
N H:SER171 4.9 15.1 1.0
CB H:LYS169 4.9 19.2 1.0
C H:ARG173 4.9 19.1 1.0
O H:HOH1023 4.9 31.4 1.0

Reference:

T.Brandt, B.Baum, D.Hangauer, A.Heine, G.Klebe. Exploring Thrombin S3 Pocket To Be Published.
Page generated: Tue Dec 15 06:01:05 2020

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