Sodium in PDB 5mm6: Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(4- Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(4- Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide:
3.4.21.5;

The structure of Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(4- Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide, PDB code: 5mm6 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)	43.58 / 1.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.344, 71.649, 72.538, 90.00, 100.48, 90.00
R / Rfree (%)	12.3 / 14.2

The binding sites of Sodium atom in the Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(4- Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide (pdb code 5mm6). 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-(4- Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide, PDB code: 5mm6:
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-(4- Carbamimidoylbenzyl)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-(4- Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na308 b:19.0 occ:1.00 O H:HOH564 2.3 23.4 1.0 O H:ARG221A 2.3 19.6 1.0 O H:HOH461 2.4 20.9 1.0 O H:LYS224 2.4 17.0 1.0 O H:HOH476 2.4 17.3 1.0 O H:HOH501 2.6 21.9 1.0 H H:LYS224 3.3 20.8 1.0 C H:ARG221A 3.4 19.1 1.0 C H:LYS224 3.5 15.8 1.0 HA H:ASP222 3.7 26.6 1.0 HA H:ASP221 3.7 23.4 1.0 H H:GLY223 3.8 24.4 1.0 N H:LYS224 3.9 17.4 1.0 O H:HOH511 3.9 21.0 1.0 HB2 H:LYS224 3.9 21.9 1.0 O H:HOH497 4.0 23.6 1.0 N H:ARG221A 4.0 19.4 1.0 O H:TYR184A 4.1 17.7 1.0 HA H:TYR225 4.1 16.6 1.0 H H:ARG221A 4.1 23.2 1.0 C H:ASP221 4.1 19.5 1.0 O H:HOH479 4.2 17.7 1.0 CA H:LYS224 4.2 16.8 1.0 N H:GLY223 4.2 20.3 1.0 N H:ASP222 4.2 21.8 1.0 CA H:ASP222 4.3 22.2 1.0 CA H:ARG221A 4.3 19.4 1.0 CA H:ASP221 4.4 19.5 1.0 C H:ASP222 4.5 20.8 1.0 O H:ASP221 4.5 21.2 1.0 N H:TYR225 4.5 14.3 1.0 CB H:LYS224 4.6 18.3 1.0 O H:HOH434 4.6 26.7 1.0 OD1 H:ASP221 4.6 20.4 1.0 CA H:TYR225 4.8 13.8 1.0 C H:GLY223 4.8 17.7 1.0 HB2 H:ARG221A 4.9 24.8 1.0 HA3 H:GLY184 5.0 16.5 1.0

Sodium binding site 2 out of 2 in the Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(4- Carbamimidoylbenzyl)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-(4- Carbamimidoylbenzyl)Pyrrolidine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na309 b:14.8 occ:1.00 O H:THR172 2.3 14.9 1.0 O H:LYS169 2.3 14.9 1.0 O H:HOH470 2.9 26.1 1.0 HA H:ASP170 3.3 18.4 1.0 C H:LYS169 3.5 14.6 1.0 HG2 H:LYS169 3.5 26.9 1.0 H H:THR172 3.5 17.3 1.0 C H:THR172 3.5 13.9 1.0 HA H:ARG173 3.6 18.0 1.0 HZ3 H:LYS169 3.7 43.8 1.0 CA H:ASP170 4.0 15.4 1.0 N H:ASP170 4.2 15.1 1.0 HG3 H:LYS169 4.2 26.9 1.0 N H:THR172 4.2 14.4 1.0 CG H:LYS169 4.3 22.4 1.0 HG23 H:THR172 4.3 19.7 1.0 C H:ASP170 4.4 15.2 1.0 CA H:ARG173 4.4 15.0 1.0 N H:ARG173 4.4 13.4 1.0 HA H:LYS169 4.5 16.5 1.0 O H:HOH439 4.5 44.1 1.0 CA H:THR172 4.5 14.5 1.0 CA H:LYS169 4.5 13.8 1.0 NZ H:LYS169 4.6 36.5 1.0 HZ2 H:LYS169 4.7 43.8 1.0 HG22 H:THR172 4.7 19.7 1.0 OD1 H:ASP170 4.7 22.3 1.0 O H:ASP170 4.8 16.1 1.0 N H:SER171 4.8 14.4 1.0 H H:SER171 4.8 17.2 1.0 CG2 H:THR172 4.9 16.4 1.0 CB H:LYS169 5.0 16.3 1.0 HZ1 H:LYS169 5.0 43.8 1.0 H H:ASP170 5.0 18.1 1.0

A.Marca, A.Sandner, A.Heine, G.Klebe. Thrombin Mutant A190S in Complex with (S)-1-(D-Phenylalanyl)-N-(4-Carbamimidoylbenzyl) Pyrrolidine-2-Carboxamide To Be Published.