Calcium in PDB 1poe: Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate
Enzymatic activity of Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate
All present enzymatic activity of Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate:
3.1.1.4;
Protein crystallography data
The structure of Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate, PDB code: 1poe
was solved by
D.L.Scott,
S.P.White,
P.B.Sigler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
2.10
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.300,
76.300,
115.300,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
n/a
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate
(pdb code 1poe). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate, PDB code: 1poe:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1poe
Go back to
Calcium Binding Sites List in 1poe
Calcium binding site 1 out
of 4 in the Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:13.3
occ:1.00
|
O
|
A:GLY29
|
2.2
|
16.7
|
1.0
|
O
|
A:HIS27
|
2.3
|
16.4
|
1.0
|
O4P
|
A:GEL930
|
2.3
|
16.1
|
1.0
|
O
|
A:GLY31
|
2.4
|
18.0
|
1.0
|
O2P
|
A:GEL930
|
2.4
|
14.9
|
1.0
|
OD1
|
A:ASP48
|
2.6
|
14.1
|
1.0
|
OD2
|
A:ASP48
|
2.6
|
16.8
|
1.0
|
CG
|
A:ASP48
|
3.0
|
13.9
|
1.0
|
C
|
A:GLY29
|
3.4
|
16.6
|
1.0
|
C
|
A:HIS27
|
3.5
|
16.4
|
1.0
|
C
|
A:GLY31
|
3.5
|
18.1
|
1.0
|
N
|
A:GLY31
|
3.7
|
17.7
|
1.0
|
P3
|
A:GEL930
|
3.7
|
16.3
|
1.0
|
N
|
A:GLY29
|
3.8
|
16.2
|
1.0
|
P2
|
A:GEL930
|
3.8
|
14.8
|
1.0
|
C2
|
A:GEL930
|
3.9
|
16.4
|
1.0
|
C3
|
A:GEL930
|
3.9
|
16.3
|
1.0
|
O1P
|
A:GEL930
|
4.2
|
14.6
|
1.0
|
CA
|
A:GLY31
|
4.2
|
17.9
|
1.0
|
CA
|
A:GLY29
|
4.3
|
16.4
|
1.0
|
O5P
|
A:GEL930
|
4.3
|
16.5
|
1.0
|
O2
|
A:GEL930
|
4.3
|
15.7
|
1.0
|
O3
|
A:GEL930
|
4.3
|
16.3
|
1.0
|
N
|
A:VAL30
|
4.4
|
16.9
|
1.0
|
N
|
A:CYS28
|
4.4
|
16.2
|
1.0
|
C
|
A:CYS28
|
4.4
|
16.1
|
1.0
|
O
|
A:HOH523
|
4.4
|
15.4
|
1.0
|
CA
|
A:CYS28
|
4.4
|
16.1
|
1.0
|
C
|
A:VAL30
|
4.4
|
17.8
|
1.0
|
CA
|
A:HIS27
|
4.4
|
16.5
|
1.0
|
O
|
A:HOH667
|
4.5
|
24.8
|
1.0
|
CB
|
A:ASP48
|
4.5
|
12.4
|
1.0
|
CA
|
A:VAL30
|
4.5
|
17.4
|
1.0
|
N
|
A:GLY32
|
4.7
|
18.6
|
1.0
|
O
|
A:CYS44
|
4.7
|
11.4
|
1.0
|
O
|
A:HOH521
|
4.8
|
13.5
|
1.0
|
CB
|
A:HIS27
|
4.8
|
13.2
|
1.0
|
O3P
|
A:GEL930
|
4.8
|
16.0
|
1.0
|
CB
|
A:CYS44
|
4.9
|
13.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1poe
Go back to
Calcium Binding Sites List in 1poe
Calcium binding site 2 out
of 4 in the Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca803
b:18.9
occ:1.00
|
O
|
A:GLY25
|
2.2
|
17.2
|
1.0
|
OD1
|
A:ASN114
|
2.4
|
40.9
|
1.0
|
O
|
A:TYR112
|
2.4
|
33.0
|
1.0
|
O
|
A:PHE23
|
2.5
|
16.6
|
1.0
|
O
|
A:HOH669
|
2.5
|
20.1
|
1.0
|
O
|
A:HOH535
|
3.1
|
22.3
|
1.0
|
C
|
A:GLY25
|
3.4
|
17.0
|
1.0
|
C
|
A:PHE23
|
3.5
|
16.3
|
1.0
|
CG
|
A:ASN114
|
3.5
|
37.6
|
1.0
|
C
|
A:TYR112
|
3.6
|
32.9
|
1.0
|
N
|
A:ASN114
|
4.0
|
34.3
|
1.0
|
CA
|
A:PHE23
|
4.1
|
16.1
|
1.0
|
CB
|
A:ASN114
|
4.1
|
37.2
|
1.0
|
C
|
A:TYR24
|
4.2
|
16.5
|
1.0
|
N
|
A:GLY25
|
4.2
|
16.6
|
1.0
|
O
|
A:TYR24
|
4.2
|
16.4
|
1.0
|
N
|
A:CYS26
|
4.3
|
17.4
|
1.0
|
C
|
A:SER113
|
4.3
|
34.0
|
1.0
|
CA
|
A:GLY25
|
4.3
|
16.8
|
1.0
|
O
|
A:HOH666
|
4.4
|
35.6
|
1.0
|
CA
|
A:ASN114
|
4.4
|
35.0
|
1.0
|
CB
|
A:TYR112
|
4.4
|
32.8
|
1.0
|
CB
|
A:PHE23
|
4.4
|
21.0
|
1.0
|
CA
|
A:CYS26
|
4.4
|
17.4
|
1.0
|
CA
|
A:TYR112
|
4.4
|
32.3
|
1.0
|
N
|
A:TYR24
|
4.5
|
16.2
|
1.0
|
O
|
A:CYS28
|
4.5
|
16.1
|
1.0
|
N
|
A:SER113
|
4.5
|
33.5
|
1.0
|
ND2
|
A:ASN114
|
4.6
|
36.3
|
1.0
|
O
|
A:HOH622
|
4.6
|
48.2
|
1.0
|
CA
|
A:SER113
|
4.6
|
34.1
|
1.0
|
N
|
A:TYR112
|
4.6
|
31.6
|
1.0
|
CA
|
A:TYR24
|
4.8
|
16.4
|
1.0
|
O
|
A:SER113
|
4.8
|
34.5
|
1.0
|
C
|
A:CYS26
|
4.9
|
17.1
|
1.0
|
O
|
A:HOH667
|
4.9
|
24.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1poe
Go back to
Calcium Binding Sites List in 1poe
Calcium binding site 3 out
of 4 in the Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca802
b:20.8
occ:1.00
|
O
|
B:HIS27
|
2.2
|
18.2
|
1.0
|
O
|
B:GLY31
|
2.3
|
21.9
|
1.0
|
O4P
|
B:GEL935
|
2.4
|
19.6
|
1.0
|
O
|
B:GLY29
|
2.4
|
18.6
|
1.0
|
OD2
|
B:ASP48
|
2.5
|
11.9
|
1.0
|
O2P
|
B:GEL935
|
2.5
|
15.7
|
1.0
|
OD1
|
B:ASP48
|
2.6
|
12.4
|
1.0
|
CG
|
B:ASP48
|
3.0
|
13.3
|
1.0
|
C
|
B:HIS27
|
3.4
|
18.2
|
1.0
|
C
|
B:GLY31
|
3.5
|
21.7
|
1.0
|
C
|
B:GLY29
|
3.6
|
18.6
|
1.0
|
P3
|
B:GEL935
|
3.7
|
19.6
|
1.0
|
N
|
B:GLY31
|
3.8
|
20.7
|
1.0
|
N
|
B:GLY29
|
3.9
|
18.0
|
1.0
|
P2
|
B:GEL935
|
3.9
|
15.7
|
1.0
|
C3
|
B:GEL935
|
4.0
|
18.4
|
1.0
|
C2
|
B:GEL935
|
4.1
|
17.9
|
1.0
|
O5P
|
B:GEL935
|
4.1
|
20.0
|
1.0
|
CA
|
B:GLY31
|
4.2
|
21.2
|
1.0
|
O1P
|
B:GEL935
|
4.3
|
15.7
|
1.0
|
CA
|
B:HIS27
|
4.3
|
18.3
|
1.0
|
N
|
B:CYS28
|
4.3
|
17.9
|
1.0
|
O2
|
B:GEL935
|
4.4
|
16.9
|
1.0
|
C
|
B:VAL30
|
4.4
|
20.5
|
1.0
|
CA
|
B:CYS28
|
4.4
|
17.9
|
1.0
|
CA
|
B:GLY29
|
4.5
|
18.2
|
1.0
|
C
|
B:CYS28
|
4.5
|
17.9
|
1.0
|
CB
|
B:ASP48
|
4.5
|
15.4
|
1.0
|
O3
|
B:GEL935
|
4.5
|
19.0
|
1.0
|
N
|
B:VAL30
|
4.6
|
19.2
|
1.0
|
N
|
B:GLY32
|
4.6
|
22.2
|
1.0
|
CA
|
B:VAL30
|
4.6
|
19.9
|
1.0
|
O
|
B:HOH557
|
4.7
|
43.0
|
1.0
|
O
|
B:HOH491
|
4.7
|
22.1
|
1.0
|
O
|
B:HOH565
|
4.7
|
23.2
|
1.0
|
CB
|
B:HIS27
|
4.8
|
19.8
|
1.0
|
O
|
B:CYS44
|
4.8
|
16.1
|
1.0
|
O3P
|
B:GEL935
|
4.9
|
19.8
|
1.0
|
CA
|
B:GLY32
|
4.9
|
22.4
|
1.0
|
CB
|
B:CYS44
|
5.0
|
16.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1poe
Go back to
Calcium Binding Sites List in 1poe
Calcium binding site 4 out
of 4 in the Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca804
b:16.7
occ:1.00
|
OD1
|
B:ASN114
|
2.2
|
31.2
|
1.0
|
O
|
B:GLY25
|
2.2
|
18.4
|
1.0
|
O
|
B:TYR112
|
2.4
|
31.8
|
1.0
|
O
|
B:PHE23
|
2.5
|
18.4
|
1.0
|
O
|
B:HOH563
|
2.7
|
40.6
|
1.0
|
CG
|
B:ASN114
|
3.4
|
30.2
|
1.0
|
C
|
B:GLY25
|
3.4
|
18.7
|
1.0
|
O
|
B:HOH552
|
3.4
|
31.6
|
1.0
|
C
|
B:PHE23
|
3.5
|
18.0
|
1.0
|
C
|
B:TYR112
|
3.6
|
31.6
|
1.0
|
ND2
|
B:ASN114
|
4.1
|
30.2
|
1.0
|
N
|
B:ASN114
|
4.1
|
33.7
|
1.0
|
CA
|
B:PHE23
|
4.1
|
17.9
|
1.0
|
C
|
B:TYR24
|
4.2
|
18.4
|
1.0
|
N
|
B:GLY25
|
4.2
|
18.5
|
1.0
|
O
|
B:TYR24
|
4.2
|
18.4
|
1.0
|
CB
|
B:PHE23
|
4.3
|
19.6
|
1.0
|
N
|
B:CYS26
|
4.3
|
18.9
|
1.0
|
CA
|
B:GLY25
|
4.3
|
18.6
|
1.0
|
C
|
B:SER113
|
4.4
|
33.2
|
1.0
|
CB
|
B:TYR112
|
4.4
|
35.5
|
1.0
|
CA
|
B:CYS26
|
4.4
|
19.1
|
1.0
|
CA
|
B:TYR112
|
4.4
|
31.2
|
1.0
|
CB
|
B:ASN114
|
4.5
|
32.6
|
1.0
|
N
|
B:TYR24
|
4.5
|
18.0
|
1.0
|
CA
|
B:ASN114
|
4.5
|
34.6
|
1.0
|
N
|
B:SER113
|
4.5
|
32.1
|
1.0
|
O
|
B:HOH640
|
4.5
|
38.8
|
1.0
|
CA
|
B:SER113
|
4.6
|
32.8
|
1.0
|
O
|
B:HOH491
|
4.6
|
22.1
|
1.0
|
N
|
B:TYR112
|
4.6
|
30.7
|
1.0
|
O
|
B:CYS28
|
4.6
|
17.8
|
1.0
|
CA
|
B:TYR24
|
4.8
|
18.1
|
1.0
|
C
|
B:CYS26
|
4.9
|
18.9
|
1.0
|
CD1
|
B:TYR112
|
4.9
|
43.2
|
1.0
|
O
|
B:SER113
|
5.0
|
33.1
|
1.0
|
|
Reference:
D.L.Scott,
S.P.White,
J.L.Browning,
J.J.Rosa,
M.H.Gelb,
P.B.Sigler.
Structures of Free and Inhibited Human Secretory Phospholipase A2 From Inflammatory Exudate. Science V. 254 1007 1991.
ISSN: ISSN 0036-8075
PubMed: 1948070
Page generated: Thu Jul 11 13:50:37 2024
|