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Sodium in PDB 2zff: Exploring Thrombin S1-Pocket

Enzymatic activity of Exploring Thrombin S1-Pocket

All present enzymatic activity of Exploring Thrombin S1-Pocket:
3.4.21.5;

Protein crystallography data

The structure of Exploring Thrombin S1-Pocket, PDB code: 2zff 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 / 1.47
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.100, 71.500, 72.500, 90.00, 100.30, 90.00
R / Rfree (%) 15.6 / 26

Sodium Binding Sites:

The binding sites of Sodium atom in the Exploring Thrombin S1-Pocket (pdb code 2zff). 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 S1-Pocket, PDB code: 2zff:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zff

Go back to Sodium Binding Sites List in 2zff
Sodium binding site 1 out of 2 in the Exploring Thrombin S1-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 S1-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na2002

b:22.3
occ:1.00
O H:HOH3143 2.3 20.9 1.0
O H:LYS224 2.3 19.1 1.0
O H:ARG221A 2.4 23.9 1.0
O H:HOH3057 2.4 22.3 1.0
O H:HOH3037 2.5 18.6 1.0
O H:HOH3068 2.8 23.8 1.0
C H:LYS224 3.4 16.2 1.0
C H:ARG221A 3.4 23.8 1.0
O H:HOH3032 3.8 19.5 1.0
N H:LYS224 3.9 21.0 1.0
N H:ARG221A 3.9 22.4 1.0
O H:HOH3044 4.0 24.9 1.0
C H:ASP221 4.1 23.1 1.0
CA H:LYS224 4.1 17.9 1.0
O H:TYR184A 4.2 21.2 1.0
N H:GLY223 4.2 24.4 1.0
O H:HOH3024 4.3 18.9 1.0
CA H:ASP221 4.3 23.2 1.0
N H:ASP222 4.3 24.8 1.0
CA H:ASP222 4.3 26.6 1.0
CA H:ARG221A 4.3 25.8 1.0
N H:TYR225 4.3 15.8 1.0
C H:ASP222 4.5 27.0 1.0
CB H:LYS224 4.5 19.1 1.0
O H:ASP221 4.5 26.6 1.0
CA H:TYR225 4.6 15.7 1.0
OD1 H:ASP221 4.7 21.6 1.0
C H:GLY223 4.9 20.9 1.0
O H:HOH3043 4.9 21.0 1.0
N H:ASP221 5.0 21.3 1.0

Sodium binding site 2 out of 2 in 2zff

Go back to Sodium Binding Sites List in 2zff
Sodium binding site 2 out of 2 in the Exploring Thrombin S1-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 S1-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na2003

b:17.4
occ:1.00
O H:THR172 2.3 16.7 1.0
O H:LYS169 2.3 17.0 1.0
O H:HOH3026 2.4 18.1 1.0
O H:HOH3045 2.4 25.7 1.0
O H:HOH3035 2.7 23.4 1.0
C H:LYS169 3.4 15.6 1.0
C H:THR172 3.5 15.1 1.0
CA H:ASP170 4.0 15.2 1.0
N H:ASP170 4.2 14.6 1.0
N H:THR172 4.2 16.1 1.0
N H:ARG173 4.4 16.5 1.0
C H:ASP170 4.4 15.8 1.0
CA H:ARG173 4.4 16.7 1.0
CA H:LYS169 4.5 15.2 1.0
CA H:THR172 4.5 14.9 1.0
OD1 H:ASP170 4.7 19.7 1.0
O H:ASP170 4.8 17.6 1.0
CG2 H:THR172 4.8 19.5 1.0
N H:SER171 4.8 15.6 1.0
CB H:LYS169 4.9 17.9 1.0
C H:ARG173 5.0 17.1 1.0

Reference:

B.Baum, D.Hangauer, A.Heine, G.Klebe. Exploring Thrombin S1-Pocket To Be Published.
Page generated: Tue Dec 15 06:01:03 2020

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