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Sodium in PDB 6t8a: Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492)

Enzymatic activity of Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492)

All present enzymatic activity of Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492):
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492), PDB code: 6t8a was solved by S.A.Ngaha, A.Sandner, S.Huber, A.Heine, T.Steinmetzer, O.Pilgram, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.50 / 1.62
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.570, 71.302, 72.651, 90.00, 100.61, 90.00
R / Rfree (%) 16 / 18.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492) (pdb code 6t8a). 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 in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492), PDB code: 6t8a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6t8a

Go back to Sodium Binding Sites List in 6t8a
Sodium binding site 1 out of 2 in the Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:18.8
occ:1.00
 O H:THR172 2.3 18.8 1.0
O H:LYS169 2.4 19.2 1.0
O H:HOH471 2.6 26.3 1.0
C H:LYS169 3.5 18.8 1.0
C H:THR172 3.6 18.6 1.0
CA H:ASP170 4.1 19.4 1.0
N H:ASP170 4.2 20.6 1.0
O H:HOH482 4.2 43.4 1.0
N H:THR172 4.3 18.2 1.0
CA H:ARG173 4.4 19.7 1.0
C H:ASP170 4.4 18.1 1.0
N H:ARG173 4.4 18.9 1.0
CA H:LYS169 4.5 16.1 1.0
CA H:THR172 4.6 17.1 1.0
OD1 H:ASP170 4.8 22.9 1.0
O H:ASP170 4.8 18.9 1.0
O H:HOH614 4.8 49.5 1.0
CG2 H:THR172 4.8 20.8 1.0
CB H:LYS169 4.9 18.8 1.0
N H:SER171 4.9 17.6 1.0
C H:ARG173 5.0 20.3 1.0

Sodium binding site 2 out of 2 in 6t8a

Go back to Sodium Binding Sites List in 6t8a
Sodium binding site 2 out of 2 in the Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R)- 3-Cyclohexyl 2-((Phenylmethyl)Sulfonamido)Propanoyl)Pyrrolidine-2- Carboxamido)Methyl)Phosphonate (Mi-492) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na305

b:21.7
occ:1.00
 O H:ARG221A 2.3 24.0 1.0
O H:HOH562 2.3 21.5 1.0
O H:HOH496 2.4 22.9 1.0
O H:LYS224 2.4 21.6 1.0
O H:HOH470 2.5 20.8 1.0
O H:HOH472 2.6 22.8 1.0
C H:ARG221A 3.4 24.1 1.0
C H:LYS224 3.5 22.0 1.0
N H:LYS224 3.9 21.6 1.0
O H:HOH537 3.9 18.5 1.0
O H:HOH457 3.9 27.0 1.0
N H:ARG221A 3.9 23.6 1.0
O H:TYR184A 4.1 22.3 1.0
C H:ASP221 4.1 23.8 1.0
N H:GLY223 4.2 27.9 1.0
CA H:LYS224 4.2 20.7 1.0
N H:ASP222 4.2 27.0 1.0
O H:HOH495 4.3 21.1 1.0
CA H:ASP222 4.3 29.2 1.0
CA H:ARG221A 4.3 24.2 1.0
CA H:ASP221 4.4 24.7 1.0
C H:ASP222 4.5 25.7 1.0
N H:TYR225 4.5 19.2 1.0
O H:ASP221 4.6 27.1 1.0
CB H:LYS224 4.6 20.4 1.0
OD1 H:ASP221 4.6 24.9 1.0
CA H:TYR225 4.8 17.0 1.0
C H:GLY223 4.8 26.5 1.0
O H:HOH437 4.8 23.6 1.0

Reference:

S.A.Ngaha, A.Sandner, S.Huber, O.Pilgram, A.Heine, T.Steinmetzer. Thrombin in Complex with Diphenyl ((4-Carbamimidoylphenyl)((S)-1-((R) -3-Cyclohexyl-2-((Phenylmethyl)Sulfonamido)Propanoyl) Pyrrolidine-2-Carboxamido)Methyl)Phosphonate (Mi-492) To Be Published.
Page generated: Mon Aug 18 07:19:24 2025

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