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Sodium in PDB 2a2q: Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+

Enzymatic activity of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+

All present enzymatic activity of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+:
3.4.21.21;

Protein crystallography data

The structure of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+, PDB code: 2a2q was solved by S.P.Bajaj, M.Bajaj, A.E.Schmidt, K.Padmanabhan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.720, 81.000, 126.120, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.9

Other elements in 2a2q:

The structure of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms
Calcium (Ca) 6 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ (pdb code 2a2q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+, PDB code: 2a2q:

Sodium binding site 1 out of 1 in 2a2q

Go back to Sodium Binding Sites List in 2a2q
Sodium binding site 1 out of 1 in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1010

b:20.0
occ:1.00
 O H:THR221 2.3 13.9 1.0
N H:GLY187 2.7 12.8 1.0
O H:HOH1101 2.8 53.4 1.0
O H:TYR184 2.9 11.4 1.0
O H:HOH1189 3.1 22.4 1.0
C H:THR221 3.1 13.1 1.0
CA H:GLY187 3.2 11.9 1.0
C H:SER185 3.2 12.5 1.0
O H:HIS224 3.3 10.8 1.0
O H:SER185 3.4 12.2 1.0
N H:THR221 3.4 12.7 1.0
C H:ALA221A 3.4 12.4 1.0
N H:ASP186 3.5 12.3 1.0
O H:ALA221A 3.6 13.4 1.0
CA H:SER185 3.6 12.1 1.0
N H:VAL222 3.7 12.0 1.0
CA H:ALA221A 3.8 12.1 1.0
C H:TYR184 3.8 11.5 1.0
C H:ASP186 3.8 13.2 1.0
CA H:THR221 3.9 13.1 1.0
CA H:VAL222 3.9 11.5 1.0
N H:SER185 4.2 11.5 1.0
CA H:ASP186 4.2 13.2 1.0
C H:GLY187 4.2 11.8 1.0
C H:HIS224 4.4 9.2 1.0
N H:HIS224 4.5 9.0 1.0
N H:SER188A 4.5 10.0 1.0
N H:GLY223 4.5 10.6 1.0
C H:VAL222 4.6 10.8 1.0
CB H:ALA221A 4.7 11.5 1.0
O H:HOH1098 4.8 16.2 1.0
N H:ALA221A 4.8 12.6 1.0
CA H:HIS224 4.9 8.2 1.0
O H:ASP186 4.9 14.0 1.0
OD1 H:ASP186 4.9 13.4 1.0
CB H:SER185 5.0 12.8 1.0

Reference:

S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, K.Padmanabhan. High Resolution Structures of P-Aminobenzamidine- and Benzamidine-Viia/Soluble Tissue Factor: Unpredicted Conformation of the 192-193 Peptide Bond and Mapping of CA2+, MG2+, Na+, and ZN2+ Sites in Factor Viia. J.Biol.Chem. V. 281 24873 2006.
ISSN: ISSN 0021-9258
PubMed: 16757484
DOI: 10.1074/JBC.M509971200
Page generated: Mon Oct 7 01:47:24 2024

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