Atomistry » Sodium » PDB 6syc-6tbn » 6t8a
Atomistry »
  Sodium »
    PDB 6syc-6tbn »
      6t8a »

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: Tue Oct 8 13:38:28 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy