Atomistry » Sodium » PDB 6syc-6tbn » 6t89
Atomistry »
  Sodium »
    PDB 6syc-6tbn »
      6t89 »

Sodium in PDB 6t89: Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498)

Enzymatic activity of Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498)

All present enzymatic activity of Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498):
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498), PDB code: 6t89 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) 35.42 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.914, 71.829, 72.158, 90.00, 100.95, 90.00
R / Rfree (%) 17.2 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498) (pdb code 6t89). 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 (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498), PDB code: 6t89:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6t89

Go back to Sodium Binding Sites List in 6t89
Sodium binding site 1 out of 2 in the Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498)


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 (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:24.1
occ:1.00
 O H:THR172 2.3 26.5 1.0
O H:HOH503 2.4 24.4 1.0
O H:LYS169 2.4 28.6 1.0
O H:HOH423 2.7 32.9 1.0
C H:LYS169 3.5 27.6 1.0
C H:THR172 3.6 31.2 1.0
CA H:ASP170 4.0 26.2 1.0
N H:ASP170 4.2 26.8 1.0
N H:THR172 4.3 24.5 1.0
CA H:ARG173 4.4 33.7 1.0
N H:ARG173 4.4 33.1 1.0
C H:ASP170 4.4 25.3 1.0
OD1 H:ASP170 4.5 32.6 1.0
CA H:LYS169 4.6 28.0 1.0
CA H:THR172 4.6 27.8 1.0
CG2 H:THR172 4.8 23.6 1.0
O H:ASP170 4.9 25.8 1.0
CB H:LYS169 4.9 30.3 1.0
N H:SER171 4.9 26.7 1.0
C H:ARG173 4.9 32.5 1.0

Sodium binding site 2 out of 2 in 6t89

Go back to Sodium Binding Sites List in 6t89
Sodium binding site 2 out of 2 in the Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498)


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 (S)-N-(Tert-Butyl)-4-(3-(3- Carbamimidoylphenyl)-2-((2',4'-Dimethoxy-[1,1'-Biphenyl])-3- Sulfonamido)Propanoyl)Piperazine-1-Carboxamide (Mi-498) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na304

b:32.4
occ:1.00
 O H:ARG221A 2.3 33.0 1.0
O H:HOH516 2.3 26.6 1.0
O H:HOH431 2.4 33.4 1.0
O H:LYS224 2.5 30.9 1.0
O H:HOH406 2.7 28.6 1.0
O H:HOH486 2.7 32.7 1.0
C H:ARG221A 3.3 36.7 1.0
C H:LYS224 3.5 29.8 1.0
N H:ARG221A 3.8 36.3 1.0
O H:HOH499 3.9 25.5 1.0
N H:LYS224 3.9 31.3 1.0
N H:ASP222 4.0 37.0 1.0
C H:ASP221 4.1 37.0 1.0
O H:TYR184A 4.1 33.6 1.0
O H:HOH472 4.2 34.5 1.0
CA H:ARG221A 4.2 37.2 1.0
CA H:ASP222 4.2 39.6 1.0
CA H:LYS224 4.2 31.6 1.0
N H:GLY223 4.3 39.4 1.0
O H:HOH444 4.3 31.1 1.0
CA H:ASP221 4.3 33.0 1.0
C H:ASP222 4.4 40.4 1.0
N H:TYR225 4.5 24.9 1.0
OD1 H:ASP221 4.6 37.4 1.0
CB H:LYS224 4.6 32.2 1.0
O H:ASP221 4.6 41.1 1.0
O H:HOH404 4.8 38.7 1.0
CA H:TYR225 4.8 25.0 1.0
O H:HOH497 4.9 35.1 1.0
C H:GLY223 4.9 35.6 1.0

Reference:

S.A.Ngaha, A.Sandner, S.Huber, O.Pilgram, A.Heine, T.Steinmetzer. Thrombin in Complex with (S)-N-(Tert-Butyl)-4-(3-(3-Carbamimidoylphenyl)-2-((2', 4'-Dimethoxy-[1,1'-Biphenyl])-3-Sulfonamido)Propanoyl) Piperazine-1-Carboxamide (Mi-498) To Be Published.
Page generated: Tue Oct 8 13:38:27 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy