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Calcium in PDB 1ppc: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin

Enzymatic activity of Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin

All present enzymatic activity of Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin:
3.4.21.4;

Protein crystallography data

The structure of Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin, PDB code: 1ppc was solved by W.Bode, D.Turk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.510, 69.190, 63.810, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin (pdb code 1ppc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin, PDB code: 1ppc:

Calcium binding site 1 out of 1 in 1ppc

Go back to Calcium Binding Sites List in 1ppc
Calcium binding site 1 out of 1 in the Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl- Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4- Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap- Thrombin and Mqpa-Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca480

b:9.5
occ:1.00
O E:ASN72 2.3 6.1 1.0
O E:VAL75 2.3 8.6 1.0
OE1 E:GLU70 2.4 7.1 1.0
O E:HOH714 2.4 6.7 1.0
O E:HOH810 2.4 6.7 1.0
OE2 E:GLU80 2.6 7.9 1.0
CD E:GLU70 3.5 9.7 1.0
C E:VAL75 3.5 12.0 1.0
C E:ASN72 3.5 6.3 1.0
CD E:GLU80 3.6 8.9 1.0
OE2 E:GLU70 3.8 9.8 1.0
CG E:GLU80 3.8 6.8 1.0
CA E:VAL76 4.1 11.9 1.0
N E:VAL76 4.2 8.9 1.0
CA E:ILE73 4.3 6.9 1.0
N E:GLU77 4.3 12.3 1.0
N E:ILE73 4.3 6.1 1.0
N E:VAL75 4.4 9.4 1.0
CG E:GLU77 4.4 13.4 1.0
OE1 E:GLU77 4.4 12.2 1.0
O E:HOH706 4.4 5.6 1.0
N E:ASN72 4.5 7.2 1.0
CA E:VAL75 4.5 12.0 1.0
C E:ILE73 4.5 8.0 1.0
CA E:ASN72 4.5 7.3 1.0
N E:ASP71 4.6 6.8 1.0
C E:VAL76 4.6 14.0 1.0
OE1 E:GLU80 4.7 9.4 1.0
O E:HOH812 4.7 14.5 1.0
CG E:GLU70 4.7 7.3 1.0
O E:ILE73 4.8 8.3 1.0
CB E:ASN72 4.8 6.6 1.0
CA E:GLU70 4.9 5.6 1.0
CB E:GLU77 4.9 12.0 1.0
CD E:GLU77 4.9 14.0 1.0
N E:ASN74 4.9 9.2 1.0
CB E:GLU70 4.9 7.1 1.0

Reference:

W.Bode, D.Turk, J.Sturzebecher. Geometry of Binding of the Benzamidine- and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P- Amidinophenylalanyl-Pipe Ridine (Napap) and (2R,4R)-4-Methyl-1-[N Alpha-(3-Methyl-1,2,3,4-Tetrahydr Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin.X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin. Eur.J.Biochem. V. 193 175 1990.
ISSN: ISSN 0014-2956
PubMed: 2226434
DOI: 10.1111/J.1432-1033.1990.TB19320.X
Page generated: Sat Dec 12 03:14:27 2020

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