Calcium in PDB 6py1: Structure of the Crd of CLEC10A
Protein crystallography data
The structure of Structure of the Crd of CLEC10A, PDB code: 6py1
was solved by
G.Birrane,
P.V.Murphy,
A.Gabba,
J.G.Luz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.74 /
1.70
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.825,
51.825,
112.855,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.5 /
18.8
|
Other elements in 6py1:
The structure of Structure of the Crd of CLEC10A also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of the Crd of CLEC10A
(pdb code 6py1). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Structure of the Crd of CLEC10A, PDB code: 6py1:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6py1
Go back to
Calcium Binding Sites List in 6py1
Calcium binding site 1 out
of 4 in the Structure of the Crd of CLEC10A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of the Crd of CLEC10A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:15.1
occ:1.00
|
O
|
A:VAL218
|
2.3
|
13.3
|
1.0
|
ND2
|
A:ASN220
|
2.3
|
15.9
|
1.0
|
O
|
A:HOH569
|
2.3
|
18.0
|
1.0
|
OE1
|
A:GLU224
|
2.4
|
17.2
|
1.0
|
O
|
A:HOH594
|
2.4
|
17.3
|
1.0
|
OE2
|
A:GLU305
|
2.5
|
16.7
|
1.0
|
OE2
|
A:GLU224
|
2.7
|
16.4
|
1.0
|
OE1
|
A:GLU305
|
2.7
|
15.1
|
1.0
|
CD
|
A:GLU224
|
2.9
|
16.7
|
1.0
|
CD
|
A:GLU305
|
2.9
|
15.5
|
1.0
|
C
|
A:VAL218
|
3.5
|
12.6
|
1.0
|
CG
|
A:ASN220
|
3.6
|
20.4
|
1.0
|
CB
|
A:VAL218
|
4.3
|
13.8
|
1.0
|
CA
|
A:VAL218
|
4.3
|
12.4
|
1.0
|
N
|
A:ASN220
|
4.3
|
15.7
|
1.0
|
CB
|
A:ASN220
|
4.3
|
18.3
|
1.0
|
N
|
A:VAL218
|
4.4
|
11.4
|
1.0
|
OH
|
A:TYR193
|
4.4
|
14.4
|
1.0
|
CG
|
A:GLU224
|
4.4
|
15.6
|
1.0
|
CG
|
A:GLU305
|
4.5
|
16.0
|
1.0
|
OD1
|
A:ASN220
|
4.5
|
25.5
|
1.0
|
N
|
A:ILE219
|
4.5
|
12.0
|
1.0
|
CG1
|
A:VAL218
|
4.6
|
13.6
|
1.0
|
O
|
A:HOH513
|
4.6
|
20.7
|
1.0
|
CA
|
A:ILE219
|
4.7
|
13.4
|
1.0
|
O
|
A:HOH562
|
4.7
|
33.1
|
1.0
|
OG
|
A:SER191
|
4.8
|
22.2
|
1.0
|
O
|
A:HOH580
|
4.8
|
27.2
|
1.0
|
C
|
A:ILE219
|
4.9
|
14.3
|
1.0
|
CA
|
A:ASN220
|
5.0
|
16.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6py1
Go back to
Calcium Binding Sites List in 6py1
Calcium binding site 2 out
of 4 in the Structure of the Crd of CLEC10A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of the Crd of CLEC10A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:20.5
occ:1.00
|
O
|
A:HOH555
|
2.4
|
17.4
|
1.0
|
O
|
A:GLU280
|
2.4
|
14.7
|
1.0
|
OD1
|
A:ASP281
|
2.4
|
17.0
|
1.0
|
OD1
|
A:ASP270
|
2.4
|
17.7
|
1.0
|
O
|
A:HOH590
|
2.5
|
24.6
|
1.0
|
OD1
|
A:ASP243
|
2.6
|
18.9
|
1.0
|
O
|
A:HOH577
|
2.6
|
26.0
|
1.0
|
OD2
|
A:ASP243
|
2.6
|
22.0
|
1.0
|
CG
|
A:ASP243
|
3.0
|
20.4
|
1.0
|
CG
|
A:ASP270
|
3.3
|
20.5
|
1.0
|
C
|
A:GLU280
|
3.4
|
14.4
|
1.0
|
CG
|
A:ASP281
|
3.5
|
18.0
|
1.0
|
CA
|
A:ASP281
|
3.7
|
14.4
|
1.0
|
CB
|
A:ASP270
|
3.9
|
18.1
|
1.0
|
N
|
A:ASP281
|
4.0
|
13.6
|
1.0
|
N
|
A:GLU280
|
4.1
|
13.3
|
1.0
|
CB
|
A:ASP281
|
4.1
|
14.7
|
1.0
|
O
|
A:HOH545
|
4.1
|
20.7
|
1.0
|
OD2
|
A:ASP270
|
4.2
|
21.8
|
1.0
|
CA
|
A:ASP270
|
4.4
|
16.9
|
1.0
|
CA
|
A:GLU280
|
4.4
|
14.7
|
1.0
|
O
|
A:ASP243
|
4.4
|
21.7
|
1.0
|
CB
|
A:ASP243
|
4.5
|
17.4
|
1.0
|
OD2
|
A:ASP281
|
4.6
|
19.4
|
1.0
|
CZ2
|
A:TRP248
|
4.6
|
18.3
|
1.0
|
OD2
|
A:ASP293
|
4.6
|
15.7
|
1.0
|
O
|
A:HOH621
|
4.7
|
14.1
|
1.0
|
O
|
A:HOH570
|
4.9
|
27.2
|
1.0
|
C
|
A:ASP243
|
4.9
|
20.7
|
1.0
|
C
|
A:ASP281
|
5.0
|
13.8
|
1.0
|
O
|
A:HOH535
|
5.0
|
32.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6py1
Go back to
Calcium Binding Sites List in 6py1
Calcium binding site 3 out
of 4 in the Structure of the Crd of CLEC10A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of the Crd of CLEC10A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca405
b:14.2
occ:1.00
|
OD1
|
A:ASP293
|
2.4
|
12.7
|
1.0
|
O4
|
A:A2G401
|
2.4
|
18.1
|
1.0
|
O3
|
A:A2G401
|
2.4
|
16.2
|
1.0
|
OE2
|
A:GLU280
|
2.4
|
15.8
|
1.0
|
OE1
|
A:GLN267
|
2.4
|
13.3
|
1.0
|
OD1
|
A:ASN292
|
2.5
|
12.4
|
1.0
|
O
|
A:ASP293
|
2.5
|
11.7
|
1.0
|
OD1
|
A:ASP269
|
2.5
|
16.0
|
1.0
|
CD
|
A:GLN267
|
3.3
|
16.2
|
1.0
|
C4
|
A:A2G401
|
3.4
|
18.2
|
1.0
|
CG
|
A:ASP293
|
3.4
|
12.4
|
1.0
|
CD
|
A:GLU280
|
3.4
|
15.8
|
1.0
|
CG
|
A:ASN292
|
3.4
|
12.9
|
1.0
|
C3
|
A:A2G401
|
3.4
|
17.9
|
1.0
|
CG
|
A:ASP269
|
3.4
|
18.3
|
1.0
|
C
|
A:ASP293
|
3.5
|
12.4
|
1.0
|
NE2
|
A:GLN267
|
3.7
|
19.6
|
1.0
|
ND2
|
A:ASN292
|
3.7
|
13.1
|
1.0
|
OE1
|
A:GLU280
|
3.8
|
15.9
|
1.0
|
N
|
A:ASP293
|
3.8
|
11.8
|
1.0
|
OD2
|
A:ASP269
|
3.8
|
18.9
|
1.0
|
CA
|
A:ASP293
|
4.0
|
12.1
|
1.0
|
OD2
|
A:ASP293
|
4.1
|
15.7
|
1.0
|
C2
|
A:A2G401
|
4.1
|
20.6
|
1.0
|
CB
|
A:ASP293
|
4.3
|
13.3
|
1.0
|
N
|
A:ASP269
|
4.3
|
18.7
|
1.0
|
CG
|
A:GLN267
|
4.5
|
16.2
|
1.0
|
CG
|
A:GLU280
|
4.6
|
15.2
|
1.0
|
CB
|
A:ASP269
|
4.6
|
16.6
|
1.0
|
N
|
A:ASP294
|
4.7
|
11.6
|
1.0
|
CB
|
A:ASN292
|
4.7
|
11.4
|
1.0
|
CB
|
A:GLU280
|
4.7
|
14.0
|
1.0
|
CB
|
A:TRP271
|
4.7
|
17.3
|
1.0
|
C
|
A:ASN292
|
4.8
|
12.8
|
1.0
|
C5
|
A:A2G401
|
4.8
|
19.4
|
1.0
|
N
|
A:TRP271
|
4.9
|
15.9
|
1.0
|
N
|
A:ASP270
|
4.9
|
16.2
|
1.0
|
CA
|
A:ASP269
|
4.9
|
18.3
|
1.0
|
CA
|
A:ASN292
|
5.0
|
12.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6py1
Go back to
Calcium Binding Sites List in 6py1
Calcium binding site 4 out
of 4 in the Structure of the Crd of CLEC10A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of the Crd of CLEC10A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca406
b:39.5
occ:1.00
|
O
|
A:HOH501
|
2.8
|
17.4
|
0.5
|
N
|
A:LEU216
|
3.1
|
12.5
|
1.0
|
CG
|
A:GLU206
|
3.3
|
26.1
|
1.0
|
NE2
|
A:GLN210
|
3.3
|
18.2
|
0.5
|
O
|
A:HOH511
|
3.4
|
38.3
|
1.0
|
CA
|
A:HIS215
|
3.5
|
14.9
|
1.0
|
O
|
A:GLU206
|
3.6
|
17.4
|
1.0
|
CA
|
A:GLU206
|
3.7
|
16.7
|
1.0
|
C
|
A:HIS215
|
3.8
|
13.2
|
1.0
|
CB
|
A:HIS215
|
3.8
|
15.7
|
1.0
|
CG
|
A:GLN210
|
3.8
|
18.0
|
0.5
|
CB
|
A:GLU206
|
3.9
|
20.8
|
1.0
|
CB
|
A:LEU216
|
4.0
|
14.7
|
1.0
|
CD
|
A:GLN210
|
4.1
|
19.3
|
0.5
|
CG
|
A:LEU216
|
4.1
|
15.9
|
1.0
|
C
|
A:GLU206
|
4.1
|
17.6
|
1.0
|
CG1
|
A:VAL251
|
4.2
|
17.2
|
1.0
|
CA
|
A:LEU216
|
4.2
|
13.7
|
1.0
|
CG2
|
A:VAL251
|
4.2
|
15.2
|
1.0
|
CB
|
A:VAL251
|
4.3
|
15.5
|
1.0
|
CG
|
A:GLN210
|
4.3
|
22.4
|
0.5
|
NE2
|
A:GLN210
|
4.3
|
24.7
|
0.5
|
CB
|
A:CYS209
|
4.4
|
15.3
|
1.0
|
CD
|
A:GLU206
|
4.5
|
34.1
|
1.0
|
CD1
|
A:LEU216
|
4.5
|
17.2
|
1.0
|
OE1
|
A:GLU206
|
4.6
|
35.4
|
1.0
|
CD
|
A:GLN210
|
4.7
|
24.7
|
0.5
|
O
|
A:ALA214
|
4.8
|
14.9
|
1.0
|
N
|
A:HIS215
|
4.8
|
15.2
|
1.0
|
|
Reference:
G.Birrane,
P.V.Murphy.
Structure of the Carbohydrate Recognition Domain of CLEC10A To Be Published.
Page generated: Tue Jul 16 13:07:51 2024
|