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:
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
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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
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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
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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
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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
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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
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