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Sodium in PDB 5mjt: Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide, PDB code: 5mjt was solved by A.Marca, A.Sandner, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.50 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.492, 71.613, 72.129, 90.00, 99.73, 90.00
R / Rfree (%) 14.8 / 17.2

Other elements in 5mjt:

The structure of Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide (pdb code 5mjt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide, PDB code: 5mjt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5mjt

Go back to Sodium Binding Sites List in 5mjt
Sodium binding site 1 out of 2 in the Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na308

b:14.5
occ:1.00
 O H:ARG221A 2.3 14.5 1.0
O H:HOH486 2.3 14.8 1.0
O H:HOH551 2.3 16.3 1.0
O H:LYS224 2.4 12.9 1.0
O H:HOH481 2.4 12.5 1.0
O H:HOH487 2.8 16.5 1.0
H H:LYS224 3.2 17.3 1.0
C H:ARG221A 3.3 16.8 1.0
C H:LYS224 3.4 12.5 1.0
HA H:ASP221 3.6 16.9 1.0
HA H:ASP222 3.7 19.0 1.0
O H:HOH521 3.8 14.8 1.0
HB2 H:LYS224 3.9 18.2 1.0
N H:LYS224 3.9 14.4 1.0
H H:GLY223 3.9 19.6 1.0
N H:ARG221A 3.9 14.9 1.0
H H:ARG221A 4.0 17.9 1.0
HA H:TYR225 4.0 13.4 1.0
O H:HOH484 4.0 18.7 1.0
C H:ASP221 4.1 15.5 1.0
O H:TYR184A 4.2 15.3 1.0
CA H:LYS224 4.2 13.0 1.0
N H:ASP222 4.2 17.7 1.0
CA H:ARG221A 4.2 15.5 1.0
O H:HOH482 4.2 13.0 1.0
N H:GLY223 4.3 16.3 1.0
CA H:ASP222 4.3 15.8 1.0
CA H:ASP221 4.3 14.1 1.0
N H:TYR225 4.4 12.5 1.0
C H:ASP222 4.5 16.2 1.0
CB H:LYS224 4.5 15.2 1.0
O H:ASP221 4.6 17.3 1.0
OD1 H:ASP221 4.6 15.1 1.0
CA H:TYR225 4.7 11.2 1.0
HB2 H:ARG221A 4.8 19.9 1.0
O H:HOH488 4.9 16.1 1.0
H H:ASP221 4.9 16.2 1.0
C H:GLY223 4.9 14.8 1.0
HA H:ARG221A 4.9 18.6 1.0
HA3 H:GLY184 5.0 12.4 1.0
HB2 H:ASP189 5.0 15.1 1.0
H H:ASP222 5.0 21.2 1.0

Sodium binding site 2 out of 2 in 5mjt

Go back to Sodium Binding Sites List in 5mjt
Sodium binding site 2 out of 2 in the Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3- Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na309

b:11.1
occ:1.00
 O H:THR172 2.3 11.8 1.0
O H:LYS169 2.3 13.0 1.0
O H:HOH491 2.6 21.4 1.0
HA H:ASP170 3.4 14.8 1.0
H H:THR172 3.4 14.3 1.0
C H:LYS169 3.5 13.2 1.0
HG2 H:LYS169 3.5 24.7 1.0
C H:THR172 3.5 11.9 1.0
HA H:ARG173 3.8 14.6 1.0
HG3 H:LYS169 3.9 24.7 1.0
HG23 H:THR172 4.0 15.3 1.0
CA H:ASP170 4.1 12.3 1.0
CG H:LYS169 4.1 20.6 1.0
N H:THR172 4.2 11.9 1.0
N H:ASP170 4.2 11.9 1.0
HG22 H:THR172 4.2 15.3 1.0
HA H:LYS169 4.4 14.3 1.0
CA H:THR172 4.4 10.8 1.0
C H:ASP170 4.4 12.3 1.0
N H:ARG173 4.5 11.7 1.0
CA H:LYS169 4.5 11.9 1.0
CA H:ARG173 4.5 12.2 1.0
CG2 H:THR172 4.5 12.7 1.0
HE2 H:LYS169 4.8 36.9 1.0
O H:ASP170 4.8 12.4 1.0
OD1 H:ASP170 4.8 18.4 1.0
N H:SER171 4.9 11.6 1.0
CB H:LYS169 4.9 14.4 1.0
H H:SER171 5.0 13.9 1.0

Reference:

A.Marca, K.Ngo, A.Sandner, A.Heine, G.Klebe. Thrombin Mutant A190S in Complex with (S) -1 - ((R) -2-Amino-3,3-Diphenylpropanoyl) -N- (3-Chlorobenzyl) Pyrrolidine-2-Carboxamide To Be Published.
Page generated: Tue Dec 15 11:18:46 2020

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