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Sodium in PDB 3pma: 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate

Enzymatic activity of 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate

All present enzymatic activity of 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate:
3.4.21.5;

Protein crystallography data

The structure of 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate, PDB code: 3pma was solved by H.T.Wright, J.N.Scarsdale, B.J.Desai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.80 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.562, 87.562, 191.990, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.5

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate (pdb code 3pma). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate, PDB code: 3pma:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3pma

Go back to Sodium Binding Sites List in 3pma
Sodium binding site 1 out of 2 in the 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1

b:32.5
occ:1.00
O B:HOH297 2.3 20.7 1.0
O B:HOH260 2.3 23.3 1.0
O B:LYS224 2.4 29.2 1.0
O B:HOH267 2.4 20.6 1.0
O B:ARG221A 2.5 30.9 1.0
O B:HOH264 2.9 26.5 1.0
C B:ARG221A 3.4 32.1 1.0
C B:LYS224 3.5 30.0 1.0
N B:ARG221A 3.8 31.9 1.0
O B:HOH2 3.8 23.5 1.0
O B:HOH265 3.8 22.1 1.0
O B:HOH258 4.0 24.2 1.0
O B:TYR184A 4.0 30.2 1.0
N B:LYS224 4.1 30.6 1.0
C B:ASP221 4.1 32.9 1.0
CA B:ARG221A 4.2 32.5 1.0
CA B:LYS224 4.2 30.6 1.0
N B:ASP222 4.3 32.1 1.0
CA B:ASP221 4.4 32.1 1.0
O B:HOH256 4.4 35.1 1.0
N B:TYR225 4.5 28.8 1.0
CA B:ASP222 4.5 32.6 1.0
N B:GLY223 4.5 31.8 1.0
OD1 B:ASP221 4.6 32.4 1.0
CB B:LYS224 4.6 31.9 1.0
CA B:TYR225 4.7 28.9 1.0
C B:ASP222 4.8 32.6 1.0
O B:ASP221 4.8 34.9 1.0
CD2 B:TYR225 5.0 25.0 1.0

Sodium binding site 2 out of 2 in 3pma

Go back to Sodium Binding Sites List in 3pma
Sodium binding site 2 out of 2 in the 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.2 Angstrom Crystal Structure of the Complex Between Bovine Thrombin and Sucrose Octasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2

b:34.8
occ:1.00
O D:ARG221A 2.3 32.9 1.0
O D:LYS224 2.4 33.3 1.0
O D:HOH262 2.4 25.6 1.0
O D:HOH3 2.4 17.5 1.0
O D:HOH255 2.5 24.1 1.0
O D:HOH7 2.9 22.2 1.0
C D:ARG221A 3.4 33.9 1.0
C D:LYS224 3.4 33.0 1.0
N D:ARG221A 3.8 32.3 1.0
O D:HOH9 3.8 22.4 1.0
N D:LYS224 3.9 33.1 1.0
O D:HOH5 4.0 30.0 1.0
C D:ASP221 4.0 33.2 1.0
CA D:LYS224 4.1 33.7 1.0
O D:TYR184A 4.1 33.1 1.0
O D:HOH13 4.2 23.8 1.0
CA D:ARG221A 4.2 34.0 1.0
N D:ASP222 4.3 34.5 1.0
CA D:ASP221 4.3 32.1 1.0
CA D:ASP222 4.4 34.9 1.0
N D:TYR225 4.4 32.9 1.0
N D:GLY223 4.4 34.5 1.0
CB D:LYS224 4.4 33.9 1.0
O D:ASP221 4.6 35.3 1.0
C D:ASP222 4.6 34.1 1.0
CA D:TYR225 4.6 32.5 1.0
OD1 D:ASP221 4.7 33.9 1.0
O D:HOH304 4.8 30.2 1.0
O D:HOH10 4.8 26.9 1.0
CD2 D:TYR225 4.9 30.3 1.0

Reference:

B.J.Desai, R.S.Boothello, A.Y.Mehta, J.N.Scarsdale, H.T.Wright, U.R.Desai. Interaction of Thrombin with Sucrose Octasulfate. Biochemistry V. 50 6973 2011.
ISSN: ISSN 0006-2960
PubMed: 21736375
DOI: 10.1021/BI2004526
Page generated: Tue Dec 15 06:21:48 2020

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