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Zinc 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
Calcium (Ca) 6 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where 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:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2a2q

Go back to Zinc Binding Sites List in 2a2q
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn1011

b:41.1
occ:1.00
 O H:HOH1278 2.6 38.2 1.0
O H:HOH1252 2.6 25.6 1.0
OE1 H:GLU80 2.8 17.2 1.0
O H:HOH1204 2.8 30.5 1.0
ND1 H:HIS76 3.3 15.8 1.0
CE1 H:HIS76 3.5 17.7 1.0
OG H:SER82 3.7 14.7 1.0
O H:HOH1191 3.8 19.2 1.0
CB H:GLU80 3.8 10.8 1.0
CD H:GLU80 3.9 15.4 1.0
O H:HOH1230 4.1 24.6 1.0
CG1 H:VAL67 4.3 7.9 1.0
O H:HOH1296 4.4 42.3 1.0
CG H:GLU80 4.4 13.5 1.0
O H:HOH1132 4.4 29.6 1.0
CG H:HIS76 4.5 15.6 1.0
NE2 H:HIS76 4.7 18.9 1.0
O H:HOH1179 4.8 19.5 1.0
OE2 H:GLU80 4.9 14.6 1.0
OE1 H:GLU70 4.9 9.2 1.0
CB H:SER82 5.0 10.4 1.0

Zinc binding site 2 out of 2 in 2a2q

Go back to Zinc Binding Sites List in 2a2q
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn binding site number 2 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:Zn1012

b:44.5
occ:1.00
 NZ H:LYS24 2.8 12.7 1.0
O H:HOH1039 2.9 14.0 1.0
O H:GLY69 2.9 6.2 1.0
ND1 H:HIS117 3.2 10.4 1.0
CG H:LYS24 3.5 10.3 1.0
O H:HOH1042 3.6 12.8 1.0
CB H:HIS117 3.7 10.4 1.0
CG H:HIS117 3.7 9.3 1.0
C H:GLY69 3.8 5.6 1.0
CB H:ASP79 3.8 11.8 1.0
CE H:LYS24 3.8 11.3 1.0
OD2 H:ASP79 3.9 12.4 1.0
CA H:GLY69 4.2 5.8 1.0
CE1 H:HIS117 4.2 8.9 1.0
CD H:LYS24 4.2 11.1 1.0
N H:GLY25 4.3 8.3 1.0
CG H:ASP79 4.4 13.3 1.0
CB H:HIS71 4.5 8.9 1.0
O H:GLU70 4.5 8.6 1.0
O H:HIS117 4.7 9.9 1.0
C H:GLU70 4.7 8.3 1.0
CA H:GLY25 4.7 8.8 1.0
N H:GLU70 4.8 6.3 1.0
CA H:HIS117 4.8 10.0 1.0
CB H:LYS24 4.9 10.6 1.0
CD2 H:HIS117 4.9 9.3 1.0
C H:LYS24 4.9 9.4 1.0
OD1 H:ASP77 5.0 12.1 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: Wed Oct 16 21:29:23 2024

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