Sodium in PDB 5mls: Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(3- Chlorobenzyl)Pyrrolidine-2-Carboxamide

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

The structure of Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(3- Chlorobenzyl)Pyrrolidine-2-Carboxamide, PDB code: 5mls 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)	43.70 / 1.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.417, 71.597, 73.069, 90.00, 100.58, 90.00
R / Rfree (%)	16 / 18

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

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(3- Chlorobenzyl)Pyrrolidine-2-Carboxamide (pdb code 5mls). 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-(D-Phenylalanyl)-N-(3- Chlorobenzyl)Pyrrolidine-2-Carboxamide, PDB code: 5mls:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-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-(D-Phenylalanyl)-N-(3- Chlorobenzyl)Pyrrolidine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na310 b:13.4 occ:1.00 O H:THR172 2.3 13.9 1.0 O H:LYS169 2.4 13.3 1.0 O H:HOH472 2.6 23.9 1.0 O H:HOH478 2.9 24.7 1.0 HA H:ASP170 3.3 15.6 1.0 H H:THR172 3.5 16.2 1.0 HG2 H:LYS169 3.5 28.6 1.0 C H:LYS169 3.5 16.4 1.0 C H:THR172 3.6 14.0 1.0 HA H:ARG173 3.6 19.9 1.0 HZ3 H:LYS169 3.8 45.2 1.0 CA H:ASP170 4.0 13.0 1.0 N H:ASP170 4.2 14.2 1.0 N H:THR172 4.2 13.5 1.0 HG3 H:LYS169 4.3 28.6 1.0 CG H:LYS169 4.3 23.8 1.0 C H:ASP170 4.3 15.5 1.0 HG23 H:THR172 4.4 18.9 1.0 CA H:ARG173 4.4 16.5 1.0 N H:ARG173 4.4 14.5 1.0 HA H:LYS169 4.5 14.3 1.0 CA H:THR172 4.5 15.8 1.0 CA H:LYS169 4.5 11.9 1.0 NZ H:LYS169 4.7 37.6 1.0 O H:ASP170 4.7 15.6 1.0 OD1 H:ASP170 4.8 17.1 1.0 N H:SER171 4.8 14.6 1.0 HG22 H:THR172 4.8 18.9 1.0 H H:SER171 4.9 17.5 1.0 HZ2 H:LYS169 4.9 45.2 1.0 CB H:LYS169 5.0 12.4 1.0 H H:ASP170 5.0 17.0 1.0

Sodium binding site 2 out of 2 in the Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-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-(D-Phenylalanyl)-N-(3- Chlorobenzyl)Pyrrolidine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na311 b:17.6 occ:1.00 O H:ARG221A 2.3 16.8 1.0 O H:HOH538 2.3 18.1 1.0 O H:HOH470 2.3 17.8 1.0 O H:LYS224 2.4 15.3 1.0 O H:HOH479 2.4 15.6 1.0 O H:HOH483 2.8 21.2 1.0 H H:LYS224 3.3 19.7 1.0 C H:ARG221A 3.4 21.7 1.0 C H:LYS224 3.5 14.5 1.0 HA H:ASP221 3.6 22.1 1.0 HA H:ASP222 3.8 24.7 1.0 O H:HOH502 3.8 18.8 1.0 HB2 H:LYS224 3.9 20.7 1.0 N H:ARG221A 3.9 20.8 1.0 N H:LYS224 3.9 16.4 1.0 H H:ARG221A 3.9 24.9 1.0 O H:HOH461 4.0 22.6 1.0 H H:GLY223 4.0 26.0 1.0 HA H:TYR225 4.0 15.9 1.0 C H:ASP221 4.1 22.8 1.0 O H:TYR184A 4.2 19.2 1.0 CA H:LYS224 4.2 18.4 1.0 O H:HOH450 4.2 16.5 1.0 N H:ASP222 4.2 19.2 1.0 CA H:ARG221A 4.3 19.9 1.0 N H:GLY223 4.3 21.7 1.0 CA H:ASP222 4.3 20.6 1.0 CA H:ASP221 4.4 18.4 1.0 N H:TYR225 4.5 16.4 1.0 CB H:LYS224 4.5 17.2 1.0 C H:ASP222 4.6 19.1 1.0 O H:ASP221 4.6 22.2 1.0 OD1 H:ASP221 4.6 19.6 1.0 CA H:TYR225 4.8 13.3 1.0 HB2 H:ARG221A 4.8 20.5 1.0 C H:GLY223 4.9 16.2 1.0 HB2 H:ASP189 4.9 18.4 1.0 H H:ASP221 4.9 21.4 1.0 HA H:ARG221A 5.0 23.8 1.0 O H:HOH509 5.0 18.6 1.0 HB3 H:LYS224 5.0 20.7 1.0

A.Marca, A.Sandner, A.Heine, G.Klebe. Thrombin Mutante A190S in Complex with (S)-1-((R)-2-Amino-3,3-Diphenylpropanoyl) -N-(4-Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide To Be Published.