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Calcium 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
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2a2q

Go back to Calcium Binding Sites List in 2a2q
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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
L:Ca1002

b:55.5
occ:1.00
 O L:HOH1177 2.0 36.0 1.0
OE21 L:CGU26 2.3 29.2 1.0
O L:HOH1149 2.8 35.9 1.0
OE11 L:CGU29 2.9 25.2 1.0
OE12 L:CGU29 3.0 25.2 1.0
CD1 L:CGU29 3.4 24.3 1.0
O L:HOH1126 3.4 38.4 1.0
CD2 L:CGU26 3.4 27.1 1.0
O L:HOH1054 3.5 27.5 1.0
CA L:CA1003 3.8 53.5 1.0
OE22 L:CGU26 3.9 26.6 1.0
OE12 L:CGU25 4.4 30.9 1.0
CD1 L:CGU25 4.7 29.8 1.0
CG L:CGU26 4.7 26.8 1.0
CG L:CGU29 4.9 23.9 1.0
CG L:CGU25 4.9 28.0 1.0
MG L:MG1001 4.9 26.1 1.0

Calcium binding site 2 out of 6 in 2a2q

Go back to Calcium Binding Sites List in 2a2q
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
L:Ca1003

b:53.5
occ:1.00
 O L:HOH1149 2.1 35.9 1.0
OE12 L:CGU29 2.5 25.2 1.0
O L:HOH1073 2.6 47.3 1.0
OE22 L:CGU26 2.8 26.6 1.0
OE21 L:CGU26 3.3 29.2 1.0
CD2 L:CGU26 3.3 27.1 1.0
O L:HOH1106 3.4 48.2 1.0
OE21 L:CGU16 3.5 20.4 1.0
CD1 L:CGU29 3.7 24.3 1.0
CA L:CA1002 3.8 55.5 1.0
O L:HOH1095 3.8 21.2 1.0
MG L:MG1004 4.0 19.8 1.0
CD2 L:CGU16 4.4 22.1 1.0
CB L:CGU29 4.4 23.7 1.0
OE22 L:CGU16 4.5 21.4 1.0
OE11 L:CGU29 4.5 25.2 1.0
CA L:CGU26 4.6 24.1 1.0
CG L:CGU26 4.6 26.8 1.0
CG L:CGU29 4.7 23.9 1.0
CB L:CGU26 4.8 24.9 1.0
O L:CGU26 4.9 23.0 1.0

Calcium binding site 3 out of 6 in 2a2q

Go back to Calcium Binding Sites List in 2a2q
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca binding site number 3 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
L:Ca1005

b:51.9
occ:1.00
 OE11 L:CGU16 2.3 23.9 1.0
OE12 L:CGU16 2.4 24.7 1.0
O L:HOH1185 2.7 36.2 1.0
CD1 L:CGU16 2.7 23.5 1.0
O L:ALA1 3.0 52.8 1.0
OE21 L:CGU20 3.0 49.1 1.0
O L:HOH1079 3.1 25.0 1.0
OE12 L:CGU7 3.3 29.9 1.0
CD2 L:CGU20 3.3 46.7 1.0
CA L:CA1006 3.4 53.4 1.0
O L:HOH1053 3.6 31.8 1.0
OE22 L:CGU20 3.7 47.7 1.0
MG L:MG1004 4.0 19.8 1.0
CG L:CGU20 4.0 45.1 1.0
C L:ALA1 4.2 52.5 1.0
CG L:CGU16 4.2 23.2 1.0
OE11 L:CGU26 4.3 27.0 1.0
O L:HOH1095 4.4 21.2 1.0
CD1 L:CGU7 4.5 29.9 1.0
CB L:CGU20 4.5 41.2 1.0
CA L:CGU16 4.6 26.1 1.0
CB L:CGU16 4.6 24.1 1.0
O L:HOH1163 4.7 47.7 1.0
O L:HOH1105 5.0 42.6 1.0

Calcium binding site 4 out of 6 in 2a2q

Go back to Calcium Binding Sites List in 2a2q
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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
L:Ca1006

b:53.4
occ:1.00
 OE21 L:CGU6 2.2 37.7 1.0
OE22 L:CGU20 2.2 47.7 1.0
O L:HOH1185 2.3 36.2 1.0
CD2 L:CGU20 2.9 46.7 1.0
OE21 L:CGU20 2.9 49.1 1.0
CD2 L:CGU6 3.1 35.6 1.0
CA L:CA1005 3.4 51.9 1.0
CB L:CGU6 3.5 29.6 1.0
O L:HOH1105 3.5 42.6 1.0
OE22 L:CGU6 3.8 37.8 1.0
CG L:CGU6 3.9 33.9 1.0
O L:HOH1163 4.1 47.7 1.0
OE12 L:CGU16 4.3 24.7 1.0
CG L:CGU20 4.4 45.1 1.0
OE12 L:CGU7 4.5 29.9 1.0
O L:CGU6 4.8 24.1 1.0
CA L:CGU6 4.8 25.8 1.0
O L:HOH1108 4.9 61.1 1.0
CD1 L:CGU6 4.9 34.8 1.0
OE11 L:CGU6 4.9 34.7 1.0

Calcium binding site 5 out of 6 in 2a2q

Go back to Calcium Binding Sites List in 2a2q
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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
L:Ca1008

b:14.9
occ:1.00
 OD2 L:ASP63 2.2 20.1 1.0
OE1 L:GLN49 2.3 17.9 1.0
O L:GLN64 2.3 17.6 1.0
O L:GLY47 2.3 20.8 1.0
OD2 L:ASP46 2.3 20.1 1.0
O L:HOH1010 2.5 21.6 1.0
O T:HOH1136 2.5 26.2 1.0
OD1 L:ASP63 2.7 20.6 1.0
CG L:ASP63 2.8 20.4 1.0
CD L:GLN49 3.4 18.0 1.0
C L:GLN64 3.5 17.2 1.0
CG L:ASP46 3.5 20.1 1.0
C L:GLY47 3.6 21.5 1.0
NE2 L:GLN49 4.0 18.4 1.0
CB L:ASP46 4.1 19.8 1.0
N L:GLN64 4.1 17.6 1.0
N L:GLN49 4.2 20.4 1.0
N L:GLN66 4.2 19.0 1.0
CA L:LEU65 4.2 18.7 1.0
CB L:ASP63 4.2 19.2 1.0
N L:LEU65 4.2 17.9 1.0
CA L:ASP48 4.3 22.1 1.0
N L:ASP48 4.3 21.5 1.0
N L:GLY47 4.4 21.0 1.0
CA L:GLN64 4.4 17.7 1.0
C L:ASP46 4.5 20.6 1.0
OD1 L:ASP46 4.5 20.6 1.0
O L:ASP46 4.6 20.8 1.0
CA L:GLY47 4.6 21.3 1.0
O L:SER67 4.6 15.5 1.0
C L:LEU65 4.6 19.1 1.0
CG L:GLN49 4.7 18.2 1.0
C L:ASP48 4.8 21.6 1.0
C L:ASP63 4.8 17.9 1.0
CB L:GLN49 4.9 18.4 1.0
O L:HOH1101 4.9 42.2 1.0
CA L:ASP63 5.0 18.3 1.0
CA L:ASP46 5.0 20.4 1.0

Calcium binding site 6 out of 6 in 2a2q

Go back to Calcium Binding Sites List in 2a2q
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca1009

b:22.0
occ:1.00
 OE2 H:GLU80 2.0 14.6 1.0
O H:GLU75 2.0 14.2 1.0
O H:HOH1058 2.0 15.4 1.0
O H:HOH1037 2.1 5.9 1.0
O H:ASP72 2.2 10.5 1.0
OE2 H:GLU70 2.2 8.4 1.0
CD H:GLU80 3.1 15.4 1.0
CD H:GLU70 3.1 9.5 1.0
C H:GLU75 3.2 14.5 1.0
C H:ASP72 3.3 10.4 1.0
OE1 H:GLU70 3.4 9.2 1.0
OE1 H:GLU80 3.8 17.2 1.0
N H:ASP72 3.9 9.8 1.0
CA H:HIS76 3.9 14.1 1.0
N H:HIS76 4.0 14.2 1.0
CA H:ASP72 4.1 10.1 1.0
O H:HOH1042 4.1 12.8 1.0
CG H:GLU80 4.1 13.5 1.0
N H:LEU73 4.2 10.3 1.0
O H:HOH1081 4.2 17.8 1.0
N H:GLU75 4.3 12.4 1.0
CA H:GLU75 4.3 13.9 1.0
O H:HOH1262 4.3 26.8 1.0
CA H:LEU73 4.4 10.3 1.0
CB H:ASP72 4.4 10.6 1.0
N H:HIS71 4.4 8.2 1.0
CG H:GLU70 4.5 7.8 1.0
C H:LEU73 4.7 11.5 1.0
C H:HIS76 4.7 13.6 1.0
N H:ASP77 4.7 12.7 1.0
ND1 H:HIS76 4.7 15.8 1.0
CB H:GLU75 4.9 15.7 1.0
C H:HIS71 4.9 9.1 1.0
O H:LEU73 5.0 12.9 1.0
CA H:GLU70 5.0 7.4 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: Fri Jul 12 08:30:41 2024

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