Calcium in PDB 1kvo: Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
Enzymatic activity of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
All present enzymatic activity of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue:
3.1.1.4;
Protein crystallography data
The structure of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue, PDB code: 1kvo
was solved by
S.-S.Cha,
S.S.Abdel-Meguid,
B.-H.Oh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
8.00 /
2.00
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.620,
114.440,
64.710,
90.00,
119.90,
90.00
|
|
R / Rfree (%)
|
20.1 /
27.3
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
(pdb code 1kvo). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue, PDB code: 1kvo:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 1 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca191
b:14.2
occ:1.00
|
OD2
|
A:ASP48
|
2.2
|
10.9
|
1.0
|
|
O
|
A:GLY29
|
2.3
|
18.0
|
1.0
|
|
O32
|
A:OAP190
|
2.3
|
18.9
|
1.0
|
|
O
|
A:HIS27
|
2.4
|
18.0
|
1.0
|
|
OD1
|
A:ASP48
|
2.5
|
15.3
|
1.0
|
|
O21
|
A:OAP190
|
2.5
|
12.8
|
1.0
|
|
O
|
A:GLY31
|
2.6
|
18.6
|
1.0
|
|
CG
|
A:ASP48
|
2.7
|
12.1
|
1.0
|
|
C21
|
A:OAP190
|
3.5
|
10.7
|
1.0
|
|
C32
|
A:OAP190
|
3.5
|
14.2
|
1.0
|
|
C
|
A:GLY29
|
3.5
|
18.0
|
1.0
|
|
C
|
A:HIS27
|
3.6
|
14.9
|
1.0
|
|
C
|
A:GLY31
|
3.8
|
18.4
|
1.0
|
|
N
|
A:GLY29
|
3.9
|
16.6
|
1.0
|
|
N
|
A:GLY31
|
4.0
|
17.8
|
1.0
|
|
O
|
A:HOH1260
|
4.0
|
29.5
|
1.0
|
|
C2
|
A:OAP190
|
4.1
|
14.8
|
1.0
|
|
N21
|
A:OAP190
|
4.1
|
12.7
|
1.0
|
|
CB
|
A:ASP48
|
4.2
|
8.6
|
1.0
|
|
O31
|
A:OAP190
|
4.2
|
13.0
|
1.0
|
|
C3
|
A:OAP190
|
4.2
|
11.4
|
1.0
|
|
C
|
A:VAL30
|
4.3
|
20.1
|
1.0
|
|
C
|
A:CYS28
|
4.4
|
16.1
|
1.0
|
|
C22
|
A:OAP190
|
4.4
|
7.4
|
1.0
|
|
CA
|
A:HIS27
|
4.4
|
14.7
|
1.0
|
|
CA
|
A:GLY29
|
4.4
|
15.4
|
1.0
|
|
C31
|
A:OAP190
|
4.4
|
11.7
|
1.0
|
|
N
|
A:VAL30
|
4.5
|
19.0
|
1.0
|
|
CA
|
A:GLY31
|
4.5
|
17.3
|
1.0
|
|
CA
|
A:VAL30
|
4.5
|
21.0
|
1.0
|
|
N
|
A:CYS28
|
4.5
|
13.3
|
1.0
|
|
CA
|
A:CYS28
|
4.5
|
13.2
|
1.0
|
|
O
|
A:HOH1218
|
4.8
|
14.2
|
1.0
|
|
CB
|
A:HIS27
|
4.8
|
12.9
|
1.0
|
|
N
|
A:GLY32
|
4.9
|
19.4
|
1.0
|
|
O
|
A:CYS44
|
4.9
|
20.0
|
1.0
|
|
O
|
A:VAL30
|
5.0
|
20.3
|
1.0
|
|
CA
|
A:ASP48
|
5.0
|
10.0
|
1.0
|
|
Calcium binding site 2 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 2 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca192
b:26.1
occ:1.00
|
O
|
A:PHE23
|
2.3
|
18.9
|
1.0
|
|
O
|
A:HOH1209
|
2.4
|
27.9
|
1.0
|
|
O
|
A:GLY25
|
2.4
|
16.0
|
1.0
|
|
O
|
A:TYR112
|
2.5
|
24.0
|
1.0
|
|
OD1
|
A:ASN114
|
2.5
|
29.8
|
1.0
|
|
C
|
A:PHE23
|
3.4
|
16.2
|
1.0
|
|
O
|
A:HOH1245
|
3.5
|
47.0
|
1.0
|
|
C
|
A:GLY25
|
3.6
|
15.7
|
1.0
|
|
C
|
A:TYR112
|
3.7
|
25.8
|
1.0
|
|
CG
|
A:ASN114
|
3.7
|
29.2
|
1.0
|
|
CA
|
A:PHE23
|
4.0
|
15.2
|
1.0
|
|
C
|
A:TYR24
|
4.2
|
13.1
|
1.0
|
|
N
|
A:GLY25
|
4.2
|
14.1
|
1.0
|
|
CB
|
A:PHE23
|
4.2
|
16.4
|
1.0
|
|
O
|
A:TYR24
|
4.3
|
14.5
|
1.0
|
|
N
|
A:ASN114
|
4.3
|
26.6
|
1.0
|
|
CA
|
A:TYR112
|
4.4
|
23.1
|
1.0
|
|
CA
|
A:GLY25
|
4.4
|
12.1
|
1.0
|
|
CB
|
A:TYR112
|
4.4
|
26.3
|
1.0
|
|
N
|
A:TYR24
|
4.4
|
14.9
|
1.0
|
|
N
|
A:CYS26
|
4.5
|
15.7
|
1.0
|
|
N
|
A:TYR112
|
4.5
|
23.2
|
1.0
|
|
O
|
A:CYS28
|
4.5
|
16.3
|
1.0
|
|
ND2
|
A:ASN114
|
4.5
|
31.1
|
1.0
|
|
CA
|
A:CYS26
|
4.6
|
18.8
|
1.0
|
|
N
|
A:SER113
|
4.7
|
26.2
|
1.0
|
|
CB
|
A:ASN114
|
4.7
|
25.0
|
1.0
|
|
C
|
A:SER113
|
4.7
|
25.5
|
1.0
|
|
CA
|
A:ASN114
|
4.7
|
24.2
|
1.0
|
|
CA
|
A:TYR24
|
4.8
|
10.8
|
1.0
|
|
CA
|
A:SER113
|
4.9
|
27.1
|
1.0
|
|
CD2
|
A:TYR112
|
5.0
|
29.2
|
1.0
|
|
Calcium binding site 3 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 3 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca191
b:12.9
occ:1.00
|
O32
|
B:OAP190
|
2.0
|
19.1
|
1.0
|
|
O
|
B:GLY31
|
2.3
|
17.1
|
1.0
|
|
O21
|
B:OAP190
|
2.3
|
6.5
|
1.0
|
|
OD2
|
B:ASP48
|
2.4
|
12.0
|
1.0
|
|
O
|
B:GLY29
|
2.4
|
12.2
|
1.0
|
|
O
|
B:HIS27
|
2.5
|
22.2
|
1.0
|
|
OD1
|
B:ASP48
|
2.5
|
12.6
|
1.0
|
|
CG
|
B:ASP48
|
2.8
|
11.6
|
1.0
|
|
C32
|
B:OAP190
|
3.3
|
11.4
|
1.0
|
|
C21
|
B:OAP190
|
3.3
|
6.8
|
1.0
|
|
C
|
B:GLY31
|
3.5
|
17.9
|
1.0
|
|
C
|
B:GLY29
|
3.7
|
15.1
|
1.0
|
|
C
|
B:HIS27
|
3.7
|
18.4
|
1.0
|
|
N
|
B:GLY31
|
3.9
|
18.4
|
1.0
|
|
N
|
B:GLY29
|
4.0
|
15.3
|
1.0
|
|
O31
|
B:OAP190
|
4.0
|
17.1
|
1.0
|
|
N21
|
B:OAP190
|
4.1
|
15.0
|
1.0
|
|
C2
|
B:OAP190
|
4.1
|
14.5
|
1.0
|
|
C3
|
B:OAP190
|
4.1
|
9.9
|
1.0
|
|
CA
|
B:GLY31
|
4.2
|
16.2
|
1.0
|
|
CB
|
B:ASP48
|
4.2
|
7.8
|
1.0
|
|
C31
|
B:OAP190
|
4.3
|
7.4
|
1.0
|
|
C22
|
B:OAP190
|
4.3
|
8.8
|
1.0
|
|
C
|
B:CYS28
|
4.3
|
14.8
|
1.0
|
|
C
|
B:VAL30
|
4.4
|
16.4
|
1.0
|
|
CA
|
B:GLY29
|
4.5
|
11.9
|
1.0
|
|
CA
|
B:CYS28
|
4.5
|
15.3
|
1.0
|
|
N
|
B:CYS28
|
4.5
|
17.0
|
1.0
|
|
CA
|
B:HIS27
|
4.5
|
16.7
|
1.0
|
|
N
|
B:GLY32
|
4.6
|
21.1
|
1.0
|
|
N
|
B:VAL30
|
4.6
|
13.1
|
1.0
|
|
O
|
B:HOH1476
|
4.7
|
52.6
|
1.0
|
|
CA
|
B:VAL30
|
4.7
|
14.8
|
1.0
|
|
CA
|
B:GLY32
|
4.8
|
22.7
|
1.0
|
|
O
|
B:CYS28
|
4.9
|
14.4
|
1.0
|
|
O
|
B:VAL30
|
5.0
|
15.8
|
1.0
|
|
CA
|
B:ASP48
|
5.0
|
11.7
|
1.0
|
|
Calcium binding site 4 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 4 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca192
b:25.4
occ:1.00
|
O
|
B:TYR112
|
2.1
|
25.8
|
1.0
|
|
O
|
B:GLY25
|
2.3
|
14.7
|
1.0
|
|
O
|
B:PHE23
|
2.3
|
19.6
|
1.0
|
|
OD1
|
B:ASN114
|
2.4
|
36.3
|
1.0
|
|
O
|
B:HOH1242
|
2.4
|
17.4
|
1.0
|
|
C
|
B:TYR112
|
3.2
|
24.4
|
1.0
|
|
C
|
B:PHE23
|
3.4
|
15.9
|
1.0
|
|
C
|
B:GLY25
|
3.5
|
15.9
|
1.0
|
|
CG
|
B:ASN114
|
3.6
|
35.2
|
1.0
|
|
CA
|
B:PHE23
|
4.0
|
14.9
|
1.0
|
|
CA
|
B:TYR112
|
4.0
|
20.8
|
1.0
|
|
N
|
B:ASN114
|
4.0
|
28.1
|
1.0
|
|
N
|
B:GLY25
|
4.2
|
14.2
|
1.0
|
|
CB
|
B:TYR112
|
4.2
|
22.6
|
1.0
|
|
C
|
B:TYR24
|
4.2
|
15.7
|
1.0
|
|
N
|
B:TYR112
|
4.2
|
19.2
|
1.0
|
|
N
|
B:SER113
|
4.3
|
28.1
|
1.0
|
|
O
|
B:TYR24
|
4.3
|
13.9
|
1.0
|
|
CB
|
B:PHE23
|
4.3
|
19.0
|
1.0
|
|
CA
|
B:GLY25
|
4.3
|
16.3
|
1.0
|
|
C
|
B:SER113
|
4.4
|
26.8
|
1.0
|
|
ND2
|
B:ASN114
|
4.5
|
37.9
|
1.0
|
|
N
|
B:TYR24
|
4.5
|
14.3
|
1.0
|
|
N
|
B:CYS26
|
4.5
|
14.5
|
1.0
|
|
O
|
B:HOH1646
|
4.5
|
49.0
|
1.0
|
|
CA
|
B:SER113
|
4.5
|
27.4
|
1.0
|
|
CA
|
B:ASN114
|
4.5
|
28.2
|
1.0
|
|
CB
|
B:ASN114
|
4.6
|
30.4
|
1.0
|
|
O
|
B:CYS28
|
4.6
|
14.4
|
1.0
|
|
CA
|
B:CYS26
|
4.7
|
19.7
|
1.0
|
|
CD2
|
B:TYR112
|
4.8
|
24.1
|
1.0
|
|
CA
|
B:TYR24
|
4.8
|
13.7
|
1.0
|
|
C
|
B:TYR111
|
4.9
|
19.5
|
1.0
|
|
CG
|
B:TYR112
|
5.0
|
25.5
|
1.0
|
|
Calcium binding site 5 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 5 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca191
b:16.7
occ:1.00
|
O32
|
C:OAP190
|
2.2
|
11.0
|
1.0
|
|
OD2
|
C:ASP48
|
2.3
|
15.2
|
1.0
|
|
O
|
C:GLY31
|
2.4
|
22.6
|
1.0
|
|
O
|
C:GLY29
|
2.4
|
18.7
|
1.0
|
|
O
|
C:HIS27
|
2.5
|
13.5
|
1.0
|
|
O21
|
C:OAP190
|
2.7
|
19.9
|
1.0
|
|
OD1
|
C:ASP48
|
2.7
|
18.2
|
1.0
|
|
CG
|
C:ASP48
|
2.8
|
18.3
|
1.0
|
|
C32
|
C:OAP190
|
3.4
|
16.2
|
1.0
|
|
C21
|
C:OAP190
|
3.4
|
15.8
|
1.0
|
|
C
|
C:GLY31
|
3.5
|
18.3
|
1.0
|
|
C
|
C:HIS27
|
3.6
|
12.6
|
1.0
|
|
C
|
C:GLY29
|
3.6
|
17.7
|
1.0
|
|
N
|
C:GLY31
|
3.8
|
18.9
|
1.0
|
|
N
|
C:GLY29
|
4.0
|
14.3
|
1.0
|
|
N21
|
C:OAP190
|
4.1
|
17.2
|
1.0
|
|
CA
|
C:GLY31
|
4.1
|
18.7
|
1.0
|
|
O31
|
C:OAP190
|
4.1
|
13.9
|
1.0
|
|
C2
|
C:OAP190
|
4.1
|
17.6
|
1.0
|
|
C
|
C:VAL30
|
4.2
|
19.4
|
1.0
|
|
C3
|
C:OAP190
|
4.2
|
15.6
|
1.0
|
|
C22
|
C:OAP190
|
4.3
|
14.6
|
1.0
|
|
CB
|
C:ASP48
|
4.3
|
13.2
|
1.0
|
|
C31
|
C:OAP190
|
4.4
|
12.0
|
1.0
|
|
C
|
C:CYS28
|
4.4
|
13.7
|
1.0
|
|
CA
|
C:HIS27
|
4.4
|
13.0
|
1.0
|
|
N
|
C:GLY32
|
4.5
|
22.5
|
1.0
|
|
CA
|
C:GLY29
|
4.5
|
16.0
|
1.0
|
|
N
|
C:CYS28
|
4.5
|
10.4
|
1.0
|
|
CA
|
C:CYS28
|
4.5
|
14.6
|
1.0
|
|
N
|
C:VAL30
|
4.6
|
16.8
|
1.0
|
|
O
|
C:VAL30
|
4.6
|
17.3
|
1.0
|
|
CA
|
C:VAL30
|
4.6
|
16.0
|
1.0
|
|
CA
|
C:GLY32
|
4.7
|
22.2
|
1.0
|
|
CB
|
C:HIS27
|
4.8
|
9.7
|
1.0
|
|
O
|
C:CYS44
|
4.9
|
16.4
|
1.0
|
|
O
|
C:HOH1269
|
5.0
|
24.9
|
1.0
|
|
Calcium binding site 6 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 6 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca192
b:22.4
occ:1.00
|
O
|
C:GLY25
|
2.0
|
10.6
|
1.0
|
|
O
|
C:PHE23
|
2.3
|
18.2
|
1.0
|
|
O
|
C:TYR112
|
2.5
|
24.9
|
1.0
|
|
O
|
C:HOH1268
|
2.5
|
15.4
|
1.0
|
|
OD1
|
C:ASN114
|
2.5
|
23.2
|
1.0
|
|
C
|
C:GLY25
|
3.2
|
16.6
|
1.0
|
|
C
|
C:PHE23
|
3.4
|
17.9
|
1.0
|
|
O
|
C:TYR24
|
3.4
|
24.2
|
1.0
|
|
C
|
C:TYR112
|
3.7
|
23.8
|
1.0
|
|
CG
|
C:ASN114
|
3.7
|
27.2
|
1.0
|
|
C
|
C:TYR24
|
3.8
|
18.8
|
1.0
|
|
O
|
C:HOH1644
|
3.8
|
44.9
|
1.0
|
|
N
|
C:GLY25
|
4.0
|
17.9
|
1.0
|
|
N
|
C:CYS26
|
4.1
|
18.5
|
1.0
|
|
CA
|
C:GLY25
|
4.1
|
13.5
|
1.0
|
|
CA
|
C:PHE23
|
4.2
|
16.8
|
1.0
|
|
CA
|
C:CYS26
|
4.2
|
18.6
|
1.0
|
|
N
|
C:ASN114
|
4.3
|
22.0
|
1.0
|
|
ND2
|
C:ASN114
|
4.3
|
27.0
|
1.0
|
|
N
|
C:TYR24
|
4.3
|
19.0
|
1.0
|
|
O
|
C:CYS28
|
4.4
|
14.3
|
1.0
|
|
CB
|
C:PHE23
|
4.5
|
13.3
|
1.0
|
|
CB
|
C:TYR112
|
4.5
|
20.9
|
1.0
|
|
CA
|
C:TYR112
|
4.5
|
21.6
|
1.0
|
|
CA
|
C:TYR24
|
4.6
|
18.2
|
1.0
|
|
C
|
C:SER113
|
4.6
|
20.7
|
1.0
|
|
C
|
C:CYS26
|
4.6
|
16.6
|
1.0
|
|
N
|
C:SER113
|
4.6
|
20.8
|
1.0
|
|
CA
|
C:SER113
|
4.7
|
22.6
|
1.0
|
|
N
|
C:TYR112
|
4.7
|
16.6
|
1.0
|
|
CD2
|
C:TYR112
|
4.8
|
20.3
|
1.0
|
|
CA
|
C:ASN114
|
4.8
|
22.0
|
1.0
|
|
CB
|
C:ASN114
|
4.9
|
25.5
|
1.0
|
|
Calcium binding site 7 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 7 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca191
b:16.6
occ:1.00
|
O
|
D:GLY31
|
2.3
|
12.9
|
1.0
|
|
OD2
|
D:ASP48
|
2.3
|
14.1
|
1.0
|
|
O32
|
D:OAP190
|
2.4
|
13.7
|
1.0
|
|
O21
|
D:OAP190
|
2.4
|
21.7
|
1.0
|
|
O
|
D:HIS27
|
2.5
|
12.7
|
1.0
|
|
O
|
D:GLY29
|
2.5
|
13.9
|
1.0
|
|
OD1
|
D:ASP48
|
2.6
|
18.3
|
1.0
|
|
CG
|
D:ASP48
|
2.7
|
8.0
|
1.0
|
|
C
|
D:GLY31
|
3.3
|
14.3
|
1.0
|
|
C21
|
D:OAP190
|
3.4
|
16.6
|
1.0
|
|
C32
|
D:OAP190
|
3.4
|
12.4
|
1.0
|
|
C
|
D:HIS27
|
3.6
|
12.4
|
1.0
|
|
N
|
D:GLY31
|
3.7
|
15.1
|
1.0
|
|
C
|
D:GLY29
|
3.8
|
14.1
|
1.0
|
|
C3
|
D:OAP190
|
3.8
|
15.7
|
1.0
|
|
CA
|
D:GLY31
|
3.9
|
11.8
|
1.0
|
|
C2
|
D:OAP190
|
4.1
|
16.4
|
1.0
|
|
N
|
D:GLY29
|
4.1
|
15.7
|
1.0
|
|
N21
|
D:OAP190
|
4.1
|
21.8
|
1.0
|
|
C31
|
D:OAP190
|
4.2
|
12.2
|
1.0
|
|
CB
|
D:ASP48
|
4.2
|
11.4
|
1.0
|
|
O31
|
D:OAP190
|
4.2
|
8.2
|
1.0
|
|
C
|
D:VAL30
|
4.3
|
17.3
|
1.0
|
|
C22
|
D:OAP190
|
4.3
|
12.4
|
1.0
|
|
N
|
D:GLY32
|
4.4
|
15.0
|
1.0
|
|
CA
|
D:HIS27
|
4.4
|
6.5
|
1.0
|
|
N
|
D:CYS28
|
4.6
|
10.4
|
1.0
|
|
CA
|
D:GLY29
|
4.6
|
14.8
|
1.0
|
|
C
|
D:CYS28
|
4.6
|
11.6
|
1.0
|
|
N
|
D:VAL30
|
4.7
|
14.1
|
1.0
|
|
O
|
D:CYS44
|
4.7
|
9.8
|
1.0
|
|
CA
|
D:CYS28
|
4.7
|
10.6
|
1.0
|
|
CA
|
D:GLY32
|
4.7
|
16.8
|
1.0
|
|
O
|
D:VAL30
|
4.8
|
20.4
|
1.0
|
|
CA
|
D:VAL30
|
4.8
|
17.4
|
1.0
|
|
O
|
D:HOH1300
|
4.8
|
21.5
|
1.0
|
|
CB
|
D:HIS27
|
4.8
|
11.3
|
1.0
|
|
Calcium binding site 8 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 8 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca192
b:23.2
occ:1.00
|
O
|
D:TYR112
|
2.2
|
23.2
|
1.0
|
|
O
|
D:GLY25
|
2.3
|
14.1
|
1.0
|
|
OD1
|
D:ASN114
|
2.3
|
25.4
|
1.0
|
|
O
|
D:PHE23
|
2.4
|
20.4
|
1.0
|
|
CG
|
D:ASN114
|
3.4
|
24.4
|
1.0
|
|
C
|
D:TYR112
|
3.4
|
20.6
|
1.0
|
|
C
|
D:PHE23
|
3.5
|
17.8
|
1.0
|
|
C
|
D:GLY25
|
3.5
|
13.2
|
1.0
|
|
N
|
D:ASN114
|
3.9
|
23.8
|
1.0
|
|
O
|
D:TYR24
|
4.1
|
8.4
|
1.0
|
|
CA
|
D:PHE23
|
4.1
|
15.5
|
1.0
|
|
ND2
|
D:ASN114
|
4.1
|
23.8
|
1.0
|
|
C
|
D:TYR24
|
4.2
|
11.9
|
1.0
|
|
CB
|
D:PHE23
|
4.2
|
13.9
|
1.0
|
|
N
|
D:GLY25
|
4.3
|
12.9
|
1.0
|
|
CA
|
D:TYR112
|
4.3
|
18.9
|
1.0
|
|
N
|
D:SER113
|
4.4
|
20.1
|
1.0
|
|
CB
|
D:TYR112
|
4.4
|
20.2
|
1.0
|
|
C
|
D:SER113
|
4.4
|
22.5
|
1.0
|
|
CA
|
D:GLY25
|
4.4
|
13.9
|
1.0
|
|
N
|
D:CYS26
|
4.4
|
9.8
|
1.0
|
|
CA
|
D:SER113
|
4.4
|
20.6
|
1.0
|
|
CB
|
D:ASN114
|
4.5
|
25.6
|
1.0
|
|
CA
|
D:ASN114
|
4.5
|
24.1
|
1.0
|
|
CA
|
D:CYS26
|
4.5
|
13.0
|
1.0
|
|
N
|
D:TYR24
|
4.5
|
14.8
|
1.0
|
|
N
|
D:TYR112
|
4.5
|
19.9
|
1.0
|
|
O
|
D:CYS28
|
4.6
|
18.2
|
1.0
|
|
CA
|
D:TYR24
|
4.8
|
13.3
|
1.0
|
|
CD2
|
D:TYR112
|
4.9
|
19.4
|
1.0
|
|
C
|
D:CYS26
|
4.9
|
11.3
|
1.0
|
|
Calcium binding site 9 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 9 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca191
b:15.3
occ:1.00
|
OD2
|
E:ASP48
|
2.2
|
10.9
|
1.0
|
|
O
|
E:GLY29
|
2.4
|
10.2
|
1.0
|
|
O
|
E:GLY31
|
2.4
|
17.2
|
1.0
|
|
O32
|
E:OAP190
|
2.4
|
15.6
|
1.0
|
|
O
|
E:HIS27
|
2.5
|
18.9
|
1.0
|
|
O21
|
E:OAP190
|
2.6
|
12.6
|
1.0
|
|
OD1
|
E:ASP48
|
2.8
|
15.4
|
1.0
|
|
CG
|
E:ASP48
|
2.8
|
12.4
|
1.0
|
|
C21
|
E:OAP190
|
3.4
|
14.1
|
1.0
|
|
C
|
E:GLY31
|
3.4
|
20.1
|
1.0
|
|
C32
|
E:OAP190
|
3.5
|
14.2
|
1.0
|
|
C
|
E:GLY29
|
3.6
|
12.8
|
1.0
|
|
C
|
E:HIS27
|
3.6
|
20.6
|
1.0
|
|
N
|
E:GLY31
|
3.7
|
18.9
|
1.0
|
|
N
|
E:GLY29
|
3.9
|
13.1
|
1.0
|
|
C3
|
E:OAP190
|
4.0
|
8.5
|
1.0
|
|
CA
|
E:GLY31
|
4.0
|
15.8
|
1.0
|
|
C2
|
E:OAP190
|
4.0
|
10.4
|
1.0
|
|
N21
|
E:OAP190
|
4.0
|
10.4
|
1.0
|
|
C
|
E:VAL30
|
4.2
|
20.1
|
1.0
|
|
CB
|
E:ASP48
|
4.3
|
14.7
|
1.0
|
|
O31
|
E:OAP190
|
4.3
|
21.4
|
1.0
|
|
C31
|
E:OAP190
|
4.3
|
8.9
|
1.0
|
|
C22
|
E:OAP190
|
4.4
|
6.0
|
1.0
|
|
CA
|
E:GLY29
|
4.4
|
11.7
|
1.0
|
|
CA
|
E:HIS27
|
4.4
|
15.4
|
1.0
|
|
N
|
E:VAL30
|
4.5
|
11.7
|
1.0
|
|
O
|
E:HOH1449
|
4.5
|
18.6
|
1.0
|
|
C
|
E:CYS28
|
4.6
|
14.1
|
1.0
|
|
N
|
E:GLY32
|
4.6
|
17.7
|
1.0
|
|
CA
|
E:VAL30
|
4.6
|
16.7
|
1.0
|
|
N
|
E:CYS28
|
4.6
|
17.7
|
1.0
|
|
O
|
E:HOH1325
|
4.7
|
26.7
|
1.0
|
|
O
|
E:VAL30
|
4.7
|
22.1
|
1.0
|
|
CA
|
E:CYS28
|
4.7
|
16.5
|
1.0
|
|
CB
|
E:HIS27
|
4.7
|
14.0
|
1.0
|
|
O
|
E:CYS44
|
4.9
|
8.5
|
1.0
|
|
CA
|
E:GLY32
|
4.9
|
18.2
|
1.0
|
|
Calcium binding site 10 out
of 12 in 1kvo
Go back to
Calcium Binding Sites List in 1kvo
Calcium binding site 10 out
of 12 in the Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Human Phospholipase A2 Complexed with A Highly Potent Substrate Anologue within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca192
b:23.5
occ:1.00
|
O
|
E:PHE23
|
2.3
|
17.1
|
1.0
|
|
O
|
E:GLY25
|
2.5
|
20.4
|
1.0
|
|
O
|
E:TYR112
|
2.5
|
19.9
|
1.0
|
|
O
|
E:HOH1334
|
2.6
|
22.4
|
1.0
|
|
OD1
|
E:ASN114
|
2.7
|
27.3
|
1.0
|
|
C
|
E:PHE23
|
3.3
|
15.2
|
1.0
|
|
C
|
E:GLY25
|
3.6
|
18.3
|
1.0
|
|
C
|
E:TYR112
|
3.7
|
19.6
|
1.0
|
|
CA
|
E:PHE23
|
3.9
|
13.3
|
1.0
|
|
CG
|
E:ASN114
|
3.9
|
33.2
|
1.0
|
|
O
|
E:TYR24
|
4.0
|
15.5
|
1.0
|
|
C
|
E:TYR24
|
4.0
|
14.8
|
1.0
|
|
N
|
E:GLY25
|
4.2
|
16.6
|
1.0
|
|
CB
|
E:PHE23
|
4.2
|
11.5
|
1.0
|
|
N
|
E:TYR24
|
4.3
|
15.1
|
1.0
|
|
O
|
E:CYS28
|
4.4
|
18.9
|
1.0
|
|
N
|
E:ASN114
|
4.4
|
25.9
|
1.0
|
|
CA
|
E:GLY25
|
4.4
|
17.8
|
1.0
|
|
O
|
E:HOH1449
|
4.5
|
18.6
|
1.0
|
|
N
|
E:TYR112
|
4.5
|
21.9
|
1.0
|
|
CA
|
E:TYR112
|
4.5
|
18.8
|
1.0
|
|
N
|
E:CYS26
|
4.6
|
17.6
|
1.0
|
|
CA
|
E:TYR24
|
4.6
|
16.1
|
1.0
|
|
N
|
E:SER113
|
4.6
|
21.9
|
1.0
|
|
CB
|
E:TYR112
|
4.7
|
15.4
|
1.0
|
|
CA
|
E:CYS26
|
4.7
|
20.6
|
1.0
|
|
C
|
E:SER113
|
4.7
|
23.5
|
1.0
|
|
CA
|
E:SER113
|
4.7
|
23.4
|
1.0
|
|
ND2
|
E:ASN114
|
4.7
|
34.8
|
1.0
|
|
CB
|
E:ASN114
|
4.9
|
30.1
|
1.0
|
|
C
|
E:CYS26
|
4.9
|
19.8
|
1.0
|
|
CA
|
E:ASN114
|
5.0
|
27.1
|
1.0
|
|
Reference:
S.S.Cha,
D.Lee,
J.Adams,
J.T.Kurdyla,
C.S.Jones,
L.A.Marshall,
B.Bolognese,
S.S.Abdel-Meguid,
B.H.Oh.
High-Resolution X-Ray Crystallography Reveals Precise Binding Interactions Between Human Nonpancreatic Secreted Phospholipase A2 and A Highly Potent Inhibitor (FPL67047XX). J.Med.Chem. V. 39 3878 1996.
ISSN: ISSN 0022-2623
PubMed: 8831753
DOI: 10.1021/JM960502G
Page generated: Thu Jul 11 11:30:15 2024
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