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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

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