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Sodium in PDB 2zhf: 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: 2zhf 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 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.400, 71.200, 72.200, 90.00, 100.30, 90.00
R / Rfree (%) 17.5 / 26.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Exploring Thrombin S3 Pocket (pdb code 2zhf). 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: 2zhf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zhf

Go back to Sodium Binding Sites List in 2zhf
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:Na601

b:17.3
occ:1.00
O H:THR172 2.3 13.9 1.0
O H:LYS169 2.3 14.2 1.0
O H:HOH1034 2.4 19.0 1.0
O H:HOH1077 2.5 21.5 1.0
O H:HOH1033 2.8 27.2 1.0
C H:LYS169 3.4 20.0 1.0
C H:THR172 3.5 16.1 1.0
CA H:ASP170 4.0 16.4 1.0
N H:ASP170 4.1 15.9 1.0
N H:THR172 4.2 18.7 1.0
C H:ASP170 4.4 20.3 1.0
CA H:ARG173 4.4 14.5 1.0
N H:ARG173 4.4 13.9 1.0
CA H:THR172 4.5 14.4 1.0
O H:HOH1130 4.5 41.7 1.0
CA H:LYS169 4.5 18.4 1.0
OD1 H:ASP170 4.6 14.3 1.0
O H:ASP170 4.7 19.7 1.0
CG2 H:THR172 4.8 15.0 1.0
O H:ILE174 4.8 17.9 1.0
C H:ARG173 4.9 23.7 1.0
N H:SER171 4.9 16.9 1.0

Sodium binding site 2 out of 2 in 2zhf

Go back to Sodium Binding Sites List in 2zhf
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:Na602

b:22.9
occ:1.00
O H:LYS224 2.2 19.8 1.0
O H:HOH1143 2.2 20.8 1.0
O H:ARG221A 2.3 23.7 1.0
O H:HOH1090 2.6 17.1 1.0
O H:HOH1070 2.6 19.8 1.0
O H:HOH1042 2.7 23.9 1.0
C H:ARG221A 3.3 29.5 1.0
C H:LYS224 3.4 18.7 1.0
N H:LYS224 3.9 13.9 1.0
N H:ARG221A 4.0 23.1 1.0
O H:HOH1009 4.0 15.0 1.0
O H:HOH1071 4.0 21.0 1.0
CA H:LYS224 4.1 13.2 1.0
C H:ASP221 4.1 29.6 1.0
O H:TYR184A 4.1 22.7 1.0
N H:ASP222 4.2 20.7 1.0
CA H:ARG221A 4.3 30.5 1.0
N H:GLY223 4.3 22.6 1.0
CA H:ASP222 4.3 24.5 1.0
O H:HOH1048 4.3 18.3 1.0
CB H:LYS224 4.4 16.0 1.0
CA H:ASP221 4.4 13.9 1.0
N H:TYR225 4.4 18.2 1.0
C H:ASP222 4.5 28.2 1.0
O H:ASP221 4.5 28.2 1.0
CA H:TYR225 4.7 22.0 1.0
OD1 H:ASP221 4.8 20.8 1.0
O H:HOH1020 4.8 25.4 1.0
C H:GLY223 4.9 26.0 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 06:01:09 2020

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