Calcium in PDB 2wfk: Calcium Bound LIPL32
Protein crystallography data
The structure of Calcium Bound LIPL32, PDB code: 2wfk
was solved by
J.-Y.Tung,
C.-W.Yang,
Y.-J.Sun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
27.259 /
2.30
|
|
Space group
|
P 43 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.905,
121.905,
206.784,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
21.89 /
26.18
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Calcium Bound LIPL32
(pdb code 2wfk). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Calcium Bound LIPL32, PDB code: 2wfk:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 2wfk
Go back to
Calcium Binding Sites List in 2wfk
Calcium binding site 1 out
of 5 in the Calcium Bound LIPL32
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Calcium Bound LIPL32 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1250
b:41.8
occ:1.00
|
OD1
|
A:ASP113
|
2.4
|
42.1
|
1.0
|
|
O
|
A:TYR159
|
2.4
|
35.4
|
1.0
|
|
O
|
A:THR114
|
2.5
|
32.0
|
1.0
|
|
OD1
|
A:ASP146
|
2.6
|
43.2
|
1.0
|
|
OD2
|
A:ASP145
|
2.6
|
45.3
|
1.0
|
|
O
|
A:ASP145
|
2.6
|
36.3
|
1.0
|
|
C
|
A:ASP145
|
3.2
|
35.9
|
1.0
|
|
C
|
A:TYR159
|
3.5
|
36.8
|
1.0
|
|
CG
|
A:ASP113
|
3.5
|
38.9
|
1.0
|
|
CG
|
A:ASP145
|
3.5
|
42.7
|
1.0
|
|
C
|
A:THR114
|
3.5
|
33.0
|
1.0
|
|
N
|
A:THR114
|
3.7
|
30.8
|
1.0
|
|
CG
|
A:ASP146
|
3.7
|
43.5
|
1.0
|
|
CA
|
A:ASP145
|
3.8
|
35.1
|
1.0
|
|
CB
|
A:TYR159
|
3.9
|
39.4
|
1.0
|
|
N
|
A:ASP146
|
3.9
|
37.7
|
1.0
|
|
CA
|
A:TYR159
|
4.0
|
37.6
|
1.0
|
|
OG
|
A:SER161
|
4.0
|
35.6
|
1.0
|
|
OG1
|
A:THR114
|
4.0
|
35.8
|
1.0
|
|
C
|
A:ASP113
|
4.1
|
32.2
|
1.0
|
|
CA
|
A:THR114
|
4.1
|
31.6
|
1.0
|
|
OD2
|
A:ASP113
|
4.1
|
39.6
|
1.0
|
|
CA
|
A:ASP146
|
4.2
|
41.4
|
1.0
|
|
CB
|
A:ASP145
|
4.2
|
40.0
|
1.0
|
|
OD1
|
A:ASP145
|
4.4
|
44.3
|
1.0
|
|
CB
|
A:ASP146
|
4.5
|
42.0
|
1.0
|
|
OD2
|
A:ASP146
|
4.5
|
45.0
|
1.0
|
|
CB
|
A:ASP113
|
4.6
|
35.0
|
1.0
|
|
CA
|
A:ASP113
|
4.6
|
32.6
|
1.0
|
|
N
|
A:ASN160
|
4.6
|
36.0
|
1.0
|
|
N
|
A:TRP115
|
4.6
|
36.7
|
1.0
|
|
O
|
A:ASP113
|
4.6
|
33.0
|
1.0
|
|
CB
|
A:TYR198
|
4.7
|
38.1
|
1.0
|
|
CB
|
A:THR114
|
4.7
|
33.1
|
1.0
|
|
CG
|
A:TYR159
|
4.7
|
41.2
|
1.0
|
|
C
|
A:ASN160
|
4.8
|
34.3
|
1.0
|
|
O
|
A:ASN160
|
4.9
|
35.6
|
1.0
|
|
CA
|
A:ASN160
|
4.9
|
34.1
|
1.0
|
|
CA
|
A:TRP115
|
4.9
|
33.3
|
1.0
|
|
O
|
A:HOH2105
|
5.0
|
34.1
|
1.0
|
|
Calcium binding site 2 out
of 5 in 2wfk
Go back to
Calcium Binding Sites List in 2wfk
Calcium binding site 2 out
of 5 in the Calcium Bound LIPL32
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Calcium Bound LIPL32 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1250
b:42.5
occ:1.00
|
O
|
B:TYR159
|
2.4
|
34.7
|
1.0
|
|
O
|
B:THR114
|
2.5
|
37.1
|
1.0
|
|
OD1
|
B:ASP113
|
2.5
|
39.2
|
1.0
|
|
OD1
|
B:ASP146
|
2.6
|
43.8
|
1.0
|
|
O
|
B:ASP145
|
2.6
|
40.1
|
1.0
|
|
OD2
|
B:ASP145
|
2.7
|
40.5
|
1.0
|
|
C
|
B:ASP145
|
3.1
|
39.7
|
1.0
|
|
C
|
B:TYR159
|
3.5
|
36.2
|
1.0
|
|
CG
|
B:ASP145
|
3.5
|
38.9
|
1.0
|
|
C
|
B:THR114
|
3.5
|
36.1
|
1.0
|
|
CG
|
B:ASP113
|
3.6
|
39.1
|
1.0
|
|
N
|
B:THR114
|
3.7
|
32.1
|
1.0
|
|
CA
|
B:ASP145
|
3.7
|
37.1
|
1.0
|
|
CG
|
B:ASP146
|
3.7
|
43.9
|
1.0
|
|
N
|
B:ASP146
|
3.8
|
40.5
|
1.0
|
|
NZ
|
E:LYS131
|
3.9
|
47.5
|
1.0
|
|
CB
|
B:TYR159
|
3.9
|
40.0
|
1.0
|
|
OG
|
B:SER161
|
4.0
|
38.7
|
1.0
|
|
CA
|
B:TYR159
|
4.0
|
37.4
|
1.0
|
|
OG1
|
B:THR114
|
4.0
|
37.6
|
1.0
|
|
CA
|
B:ASP146
|
4.1
|
42.0
|
1.0
|
|
CA
|
B:THR114
|
4.1
|
33.9
|
1.0
|
|
C
|
B:ASP113
|
4.1
|
32.2
|
1.0
|
|
CB
|
B:ASP145
|
4.2
|
38.7
|
1.0
|
|
OD2
|
B:ASP113
|
4.2
|
39.4
|
1.0
|
|
OD1
|
B:ASP145
|
4.3
|
40.3
|
1.0
|
|
CB
|
B:ASP146
|
4.5
|
43.0
|
1.0
|
|
N
|
B:ASN160
|
4.6
|
35.9
|
1.0
|
|
OD2
|
B:ASP146
|
4.6
|
45.6
|
1.0
|
|
N
|
B:TRP115
|
4.6
|
37.0
|
1.0
|
|
CA
|
B:ASP113
|
4.6
|
33.7
|
1.0
|
|
O
|
B:ASP113
|
4.6
|
30.0
|
1.0
|
|
CB
|
B:ASP113
|
4.7
|
35.6
|
1.0
|
|
CB
|
B:THR114
|
4.7
|
35.9
|
1.0
|
|
CB
|
B:TYR198
|
4.7
|
41.2
|
1.0
|
|
C
|
B:ASN160
|
4.8
|
37.5
|
1.0
|
|
CG
|
B:TYR159
|
4.8
|
45.4
|
1.0
|
|
CA
|
B:TRP115
|
4.9
|
33.8
|
1.0
|
|
O
|
B:ASN160
|
4.9
|
38.4
|
1.0
|
|
CA
|
B:ASN160
|
4.9
|
36.5
|
1.0
|
|
O
|
B:HOH2113
|
4.9
|
36.2
|
1.0
|
|
N
|
B:SER161
|
5.0
|
36.7
|
1.0
|
|
Calcium binding site 3 out
of 5 in 2wfk
Go back to
Calcium Binding Sites List in 2wfk
Calcium binding site 3 out
of 5 in the Calcium Bound LIPL32
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Calcium Bound LIPL32 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1250
b:45.2
occ:1.00
|
OD1
|
C:ASP113
|
2.5
|
42.7
|
1.0
|
|
O
|
C:THR114
|
2.5
|
43.0
|
1.0
|
|
O
|
C:TYR159
|
2.5
|
44.4
|
1.0
|
|
OD2
|
C:ASP145
|
2.6
|
44.1
|
1.0
|
|
OD1
|
C:ASP146
|
2.6
|
45.1
|
1.0
|
|
O
|
C:ASP145
|
2.7
|
40.3
|
1.0
|
|
C
|
C:ASP145
|
3.1
|
41.5
|
1.0
|
|
CG
|
C:ASP145
|
3.4
|
45.3
|
1.0
|
|
CG
|
C:ASP113
|
3.5
|
43.5
|
1.0
|
|
C
|
C:TYR159
|
3.5
|
44.2
|
1.0
|
|
C
|
C:THR114
|
3.6
|
42.9
|
1.0
|
|
CG
|
C:ASP146
|
3.6
|
48.7
|
1.0
|
|
CA
|
C:ASP145
|
3.7
|
42.4
|
1.0
|
|
N
|
C:THR114
|
3.8
|
39.2
|
1.0
|
|
N
|
C:ASP146
|
3.8
|
44.4
|
1.0
|
|
CB
|
C:TYR159
|
3.9
|
45.4
|
1.0
|
|
CA
|
C:TYR159
|
4.0
|
43.9
|
1.0
|
|
OG1
|
C:THR114
|
4.1
|
42.6
|
1.0
|
|
OD2
|
C:ASP113
|
4.1
|
45.0
|
1.0
|
|
CA
|
C:ASP146
|
4.1
|
46.7
|
1.0
|
|
OG
|
C:SER161
|
4.1
|
37.7
|
1.0
|
|
CB
|
C:ASP145
|
4.1
|
43.0
|
1.0
|
|
C
|
C:ASP113
|
4.1
|
39.4
|
1.0
|
|
CA
|
C:THR114
|
4.2
|
40.6
|
1.0
|
|
OD1
|
C:ASP145
|
4.2
|
49.9
|
1.0
|
|
NZ
|
B:LYS131
|
4.4
|
51.8
|
1.0
|
|
OD2
|
C:ASP146
|
4.4
|
53.1
|
1.0
|
|
CB
|
C:ASP146
|
4.5
|
46.6
|
1.0
|
|
O
|
C:ASP113
|
4.6
|
40.9
|
1.0
|
|
CB
|
C:ASP113
|
4.6
|
41.4
|
1.0
|
|
N
|
C:ASN160
|
4.7
|
43.2
|
1.0
|
|
CB
|
C:TYR198
|
4.7
|
43.7
|
1.0
|
|
CA
|
C:ASP113
|
4.7
|
39.7
|
1.0
|
|
N
|
C:TRP115
|
4.7
|
43.7
|
1.0
|
|
CG
|
C:TYR159
|
4.7
|
47.6
|
1.0
|
|
CB
|
C:THR114
|
4.8
|
40.2
|
1.0
|
|
C
|
C:ASN160
|
4.8
|
39.8
|
1.0
|
|
O
|
C:ASN160
|
4.9
|
38.2
|
1.0
|
|
Calcium binding site 4 out
of 5 in 2wfk
Go back to
Calcium Binding Sites List in 2wfk
Calcium binding site 4 out
of 5 in the Calcium Bound LIPL32
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Calcium Bound LIPL32 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1250
b:54.3
occ:1.00
|
O
|
D:THR114
|
2.4
|
44.4
|
1.0
|
|
O
|
D:TYR159
|
2.5
|
42.3
|
1.0
|
|
OD1
|
D:ASP113
|
2.5
|
46.1
|
1.0
|
|
OD1
|
D:ASP146
|
2.6
|
51.1
|
1.0
|
|
O
|
D:ASP145
|
2.6
|
48.2
|
1.0
|
|
OD2
|
D:ASP145
|
2.7
|
52.1
|
1.0
|
|
C
|
D:ASP145
|
3.1
|
46.6
|
1.0
|
|
C
|
D:THR114
|
3.5
|
43.3
|
1.0
|
|
CG
|
D:ASP145
|
3.5
|
53.3
|
1.0
|
|
C
|
D:TYR159
|
3.5
|
40.4
|
1.0
|
|
CG
|
D:ASP113
|
3.6
|
46.0
|
1.0
|
|
CA
|
D:ASP145
|
3.7
|
47.9
|
1.0
|
|
N
|
D:THR114
|
3.7
|
42.0
|
1.0
|
|
CG
|
D:ASP146
|
3.8
|
52.1
|
1.0
|
|
N
|
D:ASP146
|
3.8
|
49.4
|
1.0
|
|
OG
|
D:SER161
|
3.9
|
38.4
|
1.0
|
|
OG1
|
D:THR114
|
3.9
|
43.6
|
1.0
|
|
CB
|
D:TYR159
|
4.0
|
42.2
|
1.0
|
|
CA
|
D:THR114
|
4.1
|
42.9
|
1.0
|
|
CA
|
D:TYR159
|
4.1
|
40.2
|
1.0
|
|
CA
|
D:ASP146
|
4.1
|
49.3
|
1.0
|
|
CB
|
D:ASP145
|
4.1
|
51.1
|
1.0
|
|
C
|
D:ASP113
|
4.1
|
43.7
|
1.0
|
|
OD2
|
D:ASP113
|
4.2
|
46.7
|
1.0
|
|
NZ
|
A:LYS131
|
4.2
|
49.7
|
1.0
|
|
OD1
|
D:ASP145
|
4.3
|
55.8
|
1.0
|
|
CB
|
D:ASP146
|
4.5
|
48.8
|
1.0
|
|
N
|
D:TRP115
|
4.5
|
43.0
|
1.0
|
|
O
|
D:ASP113
|
4.6
|
45.5
|
1.0
|
|
CB
|
D:ASP113
|
4.6
|
46.5
|
1.0
|
|
CA
|
D:ASP113
|
4.6
|
44.5
|
1.0
|
|
N
|
D:ASN160
|
4.6
|
40.8
|
1.0
|
|
CB
|
D:THR114
|
4.6
|
40.1
|
1.0
|
|
OD2
|
D:ASP146
|
4.7
|
53.8
|
1.0
|
|
CB
|
D:TYR198
|
4.7
|
50.4
|
1.0
|
|
C
|
D:ASN160
|
4.7
|
40.5
|
1.0
|
|
CA
|
D:TRP115
|
4.8
|
45.0
|
1.0
|
|
CG
|
D:TYR159
|
4.9
|
44.1
|
1.0
|
|
O
|
D:ASN160
|
4.9
|
36.8
|
1.0
|
|
CA
|
D:ASN160
|
4.9
|
40.7
|
1.0
|
|
N
|
D:SER161
|
4.9
|
39.8
|
1.0
|
|
Calcium binding site 5 out
of 5 in 2wfk
Go back to
Calcium Binding Sites List in 2wfk
Calcium binding site 5 out
of 5 in the Calcium Bound LIPL32
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Calcium Bound LIPL32 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1250
b:54.0
occ:1.00
|
OD1
|
E:ASP113
|
2.5
|
49.3
|
1.0
|
|
O
|
E:TYR159
|
2.5
|
49.9
|
1.0
|
|
O
|
E:THR114
|
2.5
|
46.9
|
1.0
|
|
OD1
|
E:ASP146
|
2.6
|
54.5
|
1.0
|
|
OD2
|
E:ASP145
|
2.6
|
53.9
|
1.0
|
|
O
|
E:ASP145
|
2.7
|
46.6
|
1.0
|
|
C
|
E:ASP145
|
3.1
|
48.3
|
1.0
|
|
CG
|
E:ASP145
|
3.5
|
51.5
|
1.0
|
|
C
|
E:TYR159
|
3.5
|
49.9
|
1.0
|
|
CG
|
E:ASP113
|
3.6
|
47.2
|
1.0
|
|
C
|
E:THR114
|
3.6
|
46.5
|
1.0
|
|
CG
|
E:ASP146
|
3.7
|
53.9
|
1.0
|
|
CA
|
E:ASP145
|
3.7
|
49.9
|
1.0
|
|
N
|
E:ASP146
|
3.8
|
50.8
|
1.0
|
|
N
|
E:THR114
|
3.8
|
46.8
|
1.0
|
|
CB
|
E:TYR159
|
3.9
|
51.4
|
1.0
|
|
CA
|
E:TYR159
|
4.0
|
50.2
|
1.0
|
|
OG
|
E:SER161
|
4.0
|
45.0
|
1.0
|
|
CA
|
E:ASP146
|
4.1
|
54.1
|
1.0
|
|
OG1
|
E:THR114
|
4.1
|
40.8
|
1.0
|
|
CB
|
E:ASP145
|
4.1
|
50.5
|
1.0
|
|
OD2
|
E:ASP113
|
4.1
|
46.3
|
1.0
|
|
C
|
E:ASP113
|
4.2
|
46.5
|
1.0
|
|
CA
|
E:THR114
|
4.2
|
44.4
|
1.0
|
|
OD1
|
E:ASP145
|
4.3
|
51.7
|
1.0
|
|
CB
|
E:ASP146
|
4.4
|
54.0
|
1.0
|
|
OD2
|
E:ASP146
|
4.5
|
54.3
|
1.0
|
|
N
|
E:ASN160
|
4.6
|
49.2
|
1.0
|
|
O
|
E:ASP113
|
4.7
|
46.2
|
1.0
|
|
CB
|
E:ASP113
|
4.7
|
46.8
|
1.0
|
|
CB
|
E:TYR198
|
4.7
|
49.3
|
1.0
|
|
CA
|
E:ASP113
|
4.7
|
46.8
|
1.0
|
|
N
|
E:TRP115
|
4.7
|
46.1
|
1.0
|
|
CG
|
E:TYR159
|
4.8
|
50.7
|
1.0
|
|
C
|
E:ASN160
|
4.8
|
45.9
|
1.0
|
|
CB
|
E:THR114
|
4.8
|
40.8
|
1.0
|
|
O
|
E:ASN160
|
4.9
|
44.7
|
1.0
|
|
CA
|
E:ASN160
|
5.0
|
47.1
|
1.0
|
|
Reference:
J.-Y.Tung,
C.-W.Yang,
S.Chou,
C.Lin,
Y.-J.Sun.
Calcium Binds to LIPL32, A Lipoprotein From Pathogenic Leptospira, and Modulates Fibronectin Binding. J.Biol.Chem. V. 285 3245 2010.
ISSN: ISSN 0021-9258
PubMed: 19948735
DOI: 10.1074/JBC.M109.006320
Page generated: Fri Jul 12 18:37:42 2024
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