Calcium in PDB 1pob: Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue
Enzymatic activity of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue
All present enzymatic activity of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue:
3.1.1.4;
Protein crystallography data
The structure of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue, PDB code: 1pob
was solved by
S.P.White,
D.L.Scott,
Z.Otwinowski,
P.B.Sigler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
2.00
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
34.600,
73.500,
181.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue
(pdb code 1pob). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue, PDB code: 1pob:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1pob
Go back to
Calcium Binding Sites List in 1pob
Calcium binding site 1 out
of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:14.6
occ:1.00
|
O
|
A:TYR27
|
2.2
|
11.6
|
1.0
|
OD2
|
A:ASP48
|
2.3
|
12.0
|
1.0
|
O2P
|
A:GEL930
|
2.4
|
15.8
|
1.0
|
OD1
|
A:ASP48
|
2.5
|
11.3
|
1.0
|
O4P
|
A:GEL930
|
2.5
|
16.4
|
1.0
|
O
|
A:GLY31
|
2.5
|
15.9
|
1.0
|
O
|
A:GLY29
|
2.6
|
14.0
|
1.0
|
CG
|
A:ASP48
|
2.7
|
11.2
|
1.0
|
C
|
A:TYR27
|
3.4
|
11.7
|
1.0
|
C
|
A:GLY31
|
3.6
|
16.2
|
1.0
|
C
|
A:GLY29
|
3.8
|
13.9
|
1.0
|
P2
|
A:GEL930
|
3.8
|
15.8
|
1.0
|
P3
|
A:GEL930
|
3.8
|
16.4
|
1.0
|
C3
|
A:GEL930
|
3.9
|
16.8
|
1.0
|
N
|
A:GLY29
|
3.9
|
12.8
|
1.0
|
N
|
A:GLY31
|
4.0
|
15.5
|
1.0
|
C2
|
A:GEL930
|
4.0
|
17.0
|
1.0
|
CB
|
A:ASP48
|
4.3
|
9.8
|
1.0
|
CA
|
A:TYR27
|
4.3
|
11.6
|
1.0
|
O1P
|
A:GEL930
|
4.3
|
16.1
|
1.0
|
CA
|
A:GLY31
|
4.3
|
15.9
|
1.0
|
O3
|
A:GEL930
|
4.4
|
16.6
|
1.0
|
O
|
A:HOH709
|
4.4
|
34.9
|
1.0
|
O2
|
A:GEL930
|
4.4
|
16.6
|
1.0
|
N
|
A:CYS28
|
4.4
|
11.6
|
1.0
|
O5P
|
A:GEL930
|
4.4
|
16.8
|
1.0
|
CA
|
A:CYS28
|
4.4
|
11.9
|
1.0
|
C
|
A:ARG30
|
4.5
|
15.3
|
1.0
|
CA
|
A:GLY29
|
4.6
|
13.4
|
1.0
|
C
|
A:CYS28
|
4.6
|
12.3
|
1.0
|
O
|
A:CYS44
|
4.6
|
6.8
|
1.0
|
CB
|
A:TYR27
|
4.7
|
10.6
|
1.0
|
N
|
A:GLY32
|
4.7
|
16.5
|
1.0
|
N
|
A:ARG30
|
4.8
|
14.6
|
1.0
|
O
|
A:HOH402
|
4.8
|
23.7
|
1.0
|
CA
|
A:ARG30
|
4.8
|
15.2
|
1.0
|
CB
|
A:CYS44
|
4.9
|
8.8
|
1.0
|
CA
|
A:GLY32
|
5.0
|
17.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1pob
Go back to
Calcium Binding Sites List in 1pob
Calcium binding site 2 out
of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca803
b:28.3
occ:1.00
|
O
|
A:HOH429
|
2.5
|
24.4
|
1.0
|
O
|
A:CYS28
|
2.8
|
11.8
|
1.0
|
O
|
A:GLY25
|
2.9
|
11.4
|
1.0
|
O
|
A:HOH709
|
3.1
|
34.9
|
1.0
|
O
|
A:TYR24
|
3.3
|
10.6
|
1.0
|
O
|
A:HOH442
|
3.6
|
16.4
|
1.0
|
C
|
A:CYS28
|
3.6
|
12.3
|
1.0
|
C
|
A:GLY25
|
3.7
|
11.1
|
1.0
|
C
|
A:TYR24
|
3.8
|
10.8
|
1.0
|
N
|
A:TYR24
|
3.8
|
11.0
|
1.0
|
N
|
A:CYS28
|
3.9
|
11.6
|
1.0
|
N
|
A:TYR27
|
3.9
|
11.5
|
1.0
|
C
|
A:CYS26
|
3.9
|
11.6
|
1.0
|
OD1
|
A:ASP23
|
4.1
|
17.0
|
1.0
|
CA
|
A:CYS26
|
4.2
|
11.7
|
1.0
|
C
|
A:TYR27
|
4.3
|
11.7
|
1.0
|
N
|
A:CYS26
|
4.3
|
11.2
|
1.0
|
O
|
A:CYS26
|
4.3
|
11.4
|
1.0
|
N
|
A:GLY25
|
4.3
|
10.7
|
1.0
|
CD2
|
A:LEU114
|
4.4
|
20.5
|
1.0
|
CA
|
A:TYR24
|
4.4
|
10.8
|
1.0
|
CA
|
A:CYS28
|
4.4
|
11.9
|
1.0
|
C
|
A:ASP23
|
4.4
|
10.8
|
1.0
|
N
|
A:GLY29
|
4.5
|
12.8
|
1.0
|
CD1
|
A:LEU114
|
4.5
|
18.2
|
1.0
|
CA
|
A:TYR27
|
4.5
|
11.6
|
1.0
|
CA
|
A:ASP23
|
4.6
|
11.1
|
1.0
|
CA
|
A:GLY25
|
4.7
|
11.0
|
1.0
|
CA
|
A:GLY29
|
4.7
|
13.4
|
1.0
|
CG
|
A:LEU114
|
4.9
|
19.4
|
1.0
|
O
|
A:TYR27
|
4.9
|
11.6
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1pob
Go back to
Calcium Binding Sites List in 1pob
Calcium binding site 3 out
of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca802
b:13.1
occ:1.00
|
O
|
B:TYR27
|
2.3
|
13.5
|
1.0
|
OD2
|
B:ASP48
|
2.4
|
13.4
|
1.0
|
O2P
|
B:GEL935
|
2.4
|
17.3
|
1.0
|
O
|
B:GLY29
|
2.4
|
16.0
|
1.0
|
OD1
|
B:ASP48
|
2.4
|
9.6
|
1.0
|
O
|
B:GLY31
|
2.4
|
18.2
|
1.0
|
O4P
|
B:GEL935
|
2.4
|
20.4
|
1.0
|
CG
|
B:ASP48
|
2.8
|
12.8
|
1.0
|
C
|
B:TYR27
|
3.5
|
13.0
|
1.0
|
C
|
B:GLY31
|
3.6
|
18.2
|
1.0
|
C
|
B:GLY29
|
3.6
|
15.9
|
1.0
|
C2
|
B:GEL935
|
3.8
|
19.1
|
1.0
|
P2
|
B:GEL935
|
3.8
|
17.3
|
1.0
|
P3
|
B:GEL935
|
3.8
|
20.0
|
1.0
|
N
|
B:GLY29
|
3.8
|
14.4
|
1.0
|
N
|
B:GLY31
|
3.9
|
17.9
|
1.0
|
O1P
|
B:GEL935
|
4.2
|
17.4
|
1.0
|
C3
|
B:GEL935
|
4.3
|
19.2
|
1.0
|
O2
|
B:GEL935
|
4.3
|
18.3
|
1.0
|
CA
|
B:GLY31
|
4.3
|
18.2
|
1.0
|
CB
|
B:ASP48
|
4.3
|
13.1
|
1.0
|
CA
|
B:TYR27
|
4.4
|
12.9
|
1.0
|
C
|
B:ARG30
|
4.4
|
17.8
|
1.0
|
CA
|
B:GLY29
|
4.4
|
15.5
|
1.0
|
N
|
B:CYS28
|
4.4
|
13.2
|
1.0
|
O5P
|
B:GEL935
|
4.4
|
20.5
|
1.0
|
O3
|
B:GEL935
|
4.4
|
19.6
|
1.0
|
CA
|
B:CYS28
|
4.5
|
13.4
|
1.0
|
N
|
B:ARG30
|
4.6
|
16.6
|
1.0
|
C1
|
B:GEL935
|
4.6
|
19.9
|
1.0
|
C
|
B:CYS28
|
4.6
|
14.0
|
1.0
|
N
|
B:GLY32
|
4.6
|
18.5
|
1.0
|
O
|
B:CYS44
|
4.6
|
12.1
|
1.0
|
CA
|
B:ARG30
|
4.7
|
17.5
|
1.0
|
O
|
B:HOH479
|
4.7
|
34.2
|
1.0
|
CB
|
B:TYR27
|
4.8
|
12.5
|
1.0
|
O
|
B:HOH636
|
4.9
|
50.7
|
1.0
|
O3P
|
B:GEL935
|
4.9
|
20.2
|
1.0
|
CA
|
B:GLY32
|
4.9
|
18.5
|
1.0
|
C31
|
B:GEL935
|
5.0
|
20.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1pob
Go back to
Calcium Binding Sites List in 1pob
Calcium binding site 4 out
of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca804
b:34.1
occ:1.00
|
O
|
B:CYS28
|
2.7
|
13.4
|
1.0
|
O
|
B:GLY25
|
2.9
|
12.7
|
1.0
|
O
|
B:HOH481
|
3.0
|
38.7
|
1.0
|
O
|
B:TYR24
|
3.2
|
12.6
|
1.0
|
C
|
B:CYS28
|
3.4
|
14.0
|
1.0
|
N
|
B:CYS28
|
3.5
|
13.2
|
1.0
|
O
|
B:HOH636
|
3.5
|
50.7
|
1.0
|
C
|
B:GLY25
|
3.7
|
12.8
|
1.0
|
O
|
B:HOH555
|
3.7
|
16.2
|
1.0
|
C
|
B:TYR24
|
3.8
|
12.8
|
1.0
|
C
|
B:CYS26
|
3.8
|
12.7
|
1.0
|
N
|
B:TYR24
|
3.9
|
13.4
|
1.0
|
N
|
B:TYR27
|
3.9
|
12.8
|
1.0
|
CA
|
B:CYS28
|
4.0
|
13.4
|
1.0
|
O
|
B:CYS26
|
4.0
|
13.0
|
1.0
|
C
|
B:TYR27
|
4.0
|
13.0
|
1.0
|
N
|
B:GLY29
|
4.2
|
14.4
|
1.0
|
CA
|
B:CYS26
|
4.2
|
12.8
|
1.0
|
N
|
B:CYS26
|
4.2
|
12.6
|
1.0
|
OD1
|
B:ASP23
|
4.3
|
17.1
|
1.0
|
CD2
|
B:LEU114
|
4.3
|
15.7
|
1.0
|
CA
|
B:TYR27
|
4.4
|
12.9
|
1.0
|
N
|
B:GLY25
|
4.4
|
12.8
|
1.0
|
C
|
B:ASP23
|
4.4
|
13.1
|
1.0
|
CA
|
B:TYR24
|
4.5
|
12.9
|
1.0
|
O
|
B:HOH516
|
4.5
|
41.1
|
1.0
|
CA
|
B:ASP23
|
4.5
|
13.2
|
1.0
|
CA
|
B:GLY29
|
4.6
|
15.5
|
1.0
|
CA
|
B:GLY25
|
4.6
|
12.8
|
1.0
|
CB
|
B:CYS28
|
4.7
|
9.8
|
1.0
|
O
|
B:TYR27
|
4.8
|
13.5
|
1.0
|
O
|
B:HOH480
|
4.9
|
33.0
|
1.0
|
CD1
|
B:LEU114
|
5.0
|
18.4
|
1.0
|
|
Reference:
S.P.White,
D.L.Scott,
Z.Otwinowski,
M.H.Gelb,
P.B.Sigler.
Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue. Science V. 250 1560 1990.
ISSN: ISSN 0036-8075
PubMed: 2274787
Page generated: Thu Jul 11 13:49:58 2024
|