Calcium in PDB 9ks7: Crystal Structure of T. Rubripes Mincle with Glycerol
Protein crystallography data
The structure of Crystal Structure of T. Rubripes Mincle with Glycerol, PDB code: 9ks7
was solved by
T.Ito,
M.Nagae,
S.Yamasaki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.19 /
1.70
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.531,
72.371,
88.646,
90,
94.43,
90
|
|
R / Rfree (%)
|
17.3 /
19.7
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of T. Rubripes Mincle with Glycerol
(pdb code 9ks7). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of T. Rubripes Mincle with Glycerol, PDB code: 9ks7:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 1 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 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 T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:17.3
occ:1.00
|
O
|
A:ILE91
|
2.2
|
15.0
|
1.0
|
|
OD1
|
A:ASN93
|
2.3
|
19.7
|
1.0
|
|
O
|
A:HOH350
|
2.4
|
18.4
|
1.0
|
|
O
|
A:HOH377
|
2.4
|
18.8
|
1.0
|
|
OE2
|
A:GLU175
|
2.5
|
16.6
|
1.0
|
|
OE2
|
A:GLU97
|
2.5
|
16.0
|
1.0
|
|
OE1
|
A:GLU175
|
2.5
|
15.7
|
1.0
|
|
OE1
|
A:GLU97
|
2.8
|
17.8
|
1.0
|
|
CD
|
A:GLU175
|
2.9
|
17.7
|
1.0
|
|
CD
|
A:GLU97
|
3.0
|
14.3
|
1.0
|
|
C
|
A:ILE91
|
3.4
|
13.8
|
1.0
|
|
CG
|
A:ASN93
|
3.5
|
24.7
|
1.0
|
|
CA
|
A:ILE91
|
4.2
|
14.2
|
1.0
|
|
CB
|
A:ILE91
|
4.2
|
14.6
|
1.0
|
|
OH
|
A:TYR66
|
4.2
|
16.4
|
1.0
|
|
CB
|
A:ASN93
|
4.2
|
22.7
|
1.0
|
|
N
|
A:ILE91
|
4.3
|
14.2
|
1.0
|
|
O
|
A:HOH324
|
4.3
|
32.5
|
1.0
|
|
N
|
A:ASN93
|
4.3
|
16.9
|
1.0
|
|
CG
|
A:GLU175
|
4.4
|
15.8
|
1.0
|
|
N
|
A:ILE92
|
4.4
|
15.1
|
1.0
|
|
CG
|
A:GLU97
|
4.5
|
16.9
|
1.0
|
|
O
|
A:HOH387
|
4.5
|
21.3
|
1.0
|
|
ND2
|
A:ASN93
|
4.6
|
21.1
|
1.0
|
|
CG2
|
A:ILE91
|
4.6
|
14.8
|
1.0
|
|
CA
|
A:ILE92
|
4.6
|
15.6
|
1.0
|
|
O
|
A:HOH388
|
4.7
|
32.3
|
1.0
|
|
OG
|
A:SER64
|
4.7
|
19.0
|
1.0
|
|
O
|
A:HOH323
|
4.8
|
24.3
|
1.0
|
|
C
|
A:ILE92
|
4.8
|
17.1
|
1.0
|
|
CA
|
A:ASN93
|
4.9
|
19.4
|
1.0
|
|
Calcium binding site 2 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 2 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 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 T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:16.4
occ:1.00
|
OD1
|
A:ASN162
|
2.4
|
15.3
|
1.0
|
|
OD1
|
A:ASP163
|
2.4
|
17.4
|
1.0
|
|
OD1
|
A:ASN140
|
2.4
|
15.7
|
1.0
|
|
O
|
A:ASP163
|
2.4
|
14.1
|
1.0
|
|
O2
|
A:GOL201
|
2.5
|
19.0
|
1.0
|
|
O1
|
A:GOL201
|
2.5
|
15.8
|
1.0
|
|
OE1
|
A:GLU138
|
2.5
|
17.2
|
1.0
|
|
OE1
|
A:GLU147
|
2.5
|
19.2
|
1.0
|
|
CG
|
A:ASP163
|
3.3
|
15.1
|
1.0
|
|
CG
|
A:ASN162
|
3.4
|
14.8
|
1.0
|
|
CD
|
A:GLU138
|
3.4
|
18.9
|
1.0
|
|
C2
|
A:GOL201
|
3.4
|
22.3
|
1.0
|
|
CG
|
A:ASN140
|
3.4
|
18.1
|
1.0
|
|
C1
|
A:GOL201
|
3.4
|
16.7
|
1.0
|
|
CD
|
A:GLU147
|
3.5
|
21.4
|
1.0
|
|
C
|
A:ASP163
|
3.5
|
15.5
|
1.0
|
|
OE2
|
A:GLU138
|
3.7
|
20.5
|
1.0
|
|
ND2
|
A:ASN162
|
3.8
|
15.2
|
1.0
|
|
OE2
|
A:GLU147
|
3.8
|
17.2
|
1.0
|
|
N
|
A:ASP163
|
3.8
|
13.1
|
1.0
|
|
ND2
|
A:ASN140
|
3.9
|
17.7
|
1.0
|
|
CA
|
A:ASP163
|
4.1
|
11.4
|
1.0
|
|
OD2
|
A:ASP163
|
4.1
|
15.7
|
1.0
|
|
N
|
A:ASN140
|
4.2
|
15.9
|
1.0
|
|
CB
|
A:ASP163
|
4.3
|
12.6
|
1.0
|
|
CB
|
A:TYR142
|
4.3
|
19.5
|
1.0
|
|
N
|
A:TYR142
|
4.5
|
18.9
|
1.0
|
|
CB
|
A:ASN140
|
4.6
|
17.4
|
1.0
|
|
C
|
A:ASN162
|
4.6
|
16.3
|
1.0
|
|
N
|
A:ASN141
|
4.6
|
16.6
|
1.0
|
|
C3
|
A:GOL201
|
4.6
|
41.3
|
1.0
|
|
CG
|
A:GLU138
|
4.6
|
16.6
|
1.0
|
|
CB
|
A:ASN162
|
4.6
|
16.3
|
1.0
|
|
N
|
A:LEU164
|
4.7
|
15.2
|
1.0
|
|
CG
|
A:GLU147
|
4.7
|
16.6
|
1.0
|
|
CA
|
A:ASN140
|
4.7
|
17.2
|
1.0
|
|
CB
|
A:GLU147
|
4.8
|
16.8
|
1.0
|
|
CA
|
A:ASN162
|
4.8
|
16.7
|
1.0
|
|
C
|
A:ASN140
|
4.9
|
16.4
|
1.0
|
|
Calcium binding site 3 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 3 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 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 T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:17.8
occ:1.00
|
O
|
B:ILE91
|
2.2
|
13.8
|
1.0
|
|
OD1
|
B:ASN93
|
2.3
|
19.3
|
1.0
|
|
OE2
|
B:GLU97
|
2.4
|
18.2
|
1.0
|
|
O
|
B:HOH383
|
2.4
|
20.6
|
1.0
|
|
OE2
|
B:GLU175
|
2.5
|
18.5
|
1.0
|
|
O
|
B:HOH359
|
2.5
|
19.1
|
1.0
|
|
OE1
|
B:GLU175
|
2.6
|
18.8
|
1.0
|
|
OE1
|
B:GLU97
|
2.7
|
19.1
|
1.0
|
|
CD
|
B:GLU97
|
2.9
|
16.9
|
1.0
|
|
CD
|
B:GLU175
|
2.9
|
18.8
|
1.0
|
|
C
|
B:ILE91
|
3.4
|
15.3
|
1.0
|
|
CG
|
B:ASN93
|
3.5
|
22.8
|
1.0
|
|
CA
|
B:ILE91
|
4.2
|
15.5
|
1.0
|
|
OH
|
B:TYR66
|
4.2
|
19.2
|
1.0
|
|
N
|
B:ASN93
|
4.2
|
18.1
|
1.0
|
|
CB
|
B:ILE91
|
4.3
|
15.1
|
1.0
|
|
CB
|
B:ASN93
|
4.3
|
23.8
|
1.0
|
|
N
|
B:ILE91
|
4.3
|
15.5
|
1.0
|
|
CG
|
B:GLU97
|
4.4
|
16.9
|
1.0
|
|
N
|
B:ILE92
|
4.4
|
15.3
|
1.0
|
|
CG
|
B:GLU175
|
4.4
|
17.8
|
1.0
|
|
O
|
B:HOH326
|
4.5
|
24.1
|
1.0
|
|
ND2
|
B:ASN93
|
4.5
|
25.5
|
1.0
|
|
CA
|
B:ILE92
|
4.6
|
16.4
|
1.0
|
|
O
|
B:HOH390
|
4.6
|
20.2
|
1.0
|
|
O
|
B:HOH313
|
4.6
|
28.3
|
1.0
|
|
CG2
|
B:ILE91
|
4.7
|
16.4
|
1.0
|
|
OG
|
B:SER64
|
4.7
|
21.1
|
1.0
|
|
O
|
B:HOH392
|
4.7
|
35.1
|
1.0
|
|
C
|
B:ILE92
|
4.8
|
20.1
|
1.0
|
|
CA
|
B:ASN93
|
4.9
|
21.7
|
1.0
|
|
Calcium binding site 4 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 4 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 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 T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:16.1
occ:1.00
|
OD1
|
B:ASP163
|
2.4
|
15.0
|
1.0
|
|
OD1
|
B:ASN140
|
2.4
|
16.3
|
1.0
|
|
O1
|
B:GOL201
|
2.4
|
15.4
|
1.0
|
|
OD1
|
B:ASN162
|
2.4
|
16.3
|
1.0
|
|
OE1
|
B:GLU147
|
2.5
|
17.6
|
1.0
|
|
O
|
B:ASP163
|
2.5
|
13.8
|
1.0
|
|
O2
|
B:GOL201
|
2.5
|
16.9
|
1.0
|
|
OE1
|
B:GLU138
|
2.5
|
16.6
|
1.0
|
|
CG
|
B:ASP163
|
3.3
|
17.6
|
1.0
|
|
C2
|
B:GOL201
|
3.3
|
19.6
|
1.0
|
|
C1
|
B:GOL201
|
3.3
|
14.6
|
1.0
|
|
CD
|
B:GLU138
|
3.4
|
18.4
|
1.0
|
|
CG
|
B:ASN140
|
3.4
|
21.9
|
1.0
|
|
CD
|
B:GLU147
|
3.4
|
19.8
|
1.0
|
|
CG
|
B:ASN162
|
3.4
|
15.3
|
1.0
|
|
C
|
B:ASP163
|
3.6
|
12.4
|
1.0
|
|
OE2
|
B:GLU138
|
3.7
|
19.5
|
1.0
|
|
N
|
B:ASP163
|
3.8
|
13.0
|
1.0
|
|
OE2
|
B:GLU147
|
3.8
|
15.2
|
1.0
|
|
ND2
|
B:ASN162
|
3.8
|
13.6
|
1.0
|
|
ND2
|
B:ASN140
|
3.9
|
18.1
|
1.0
|
|
OD2
|
B:ASP163
|
4.0
|
15.1
|
1.0
|
|
CA
|
B:ASP163
|
4.1
|
11.9
|
1.0
|
|
N
|
B:ASN140
|
4.2
|
15.7
|
1.0
|
|
CB
|
B:ASP163
|
4.3
|
15.2
|
1.0
|
|
CB
|
B:TYR142
|
4.3
|
18.9
|
1.0
|
|
N
|
B:TYR142
|
4.5
|
20.1
|
1.0
|
|
N
|
B:ASN141
|
4.6
|
15.5
|
1.0
|
|
C
|
B:ASN162
|
4.6
|
15.2
|
1.0
|
|
CB
|
B:ASN140
|
4.6
|
18.4
|
1.0
|
|
CG
|
B:GLU138
|
4.6
|
16.0
|
1.0
|
|
N
|
B:LEU164
|
4.7
|
14.7
|
1.0
|
|
CG
|
B:GLU147
|
4.7
|
16.5
|
1.0
|
|
CB
|
B:ASN162
|
4.7
|
14.7
|
1.0
|
|
CA
|
B:ASN140
|
4.8
|
16.8
|
1.0
|
|
C3
|
B:GOL201
|
4.8
|
33.0
|
1.0
|
|
CB
|
B:GLU147
|
4.9
|
13.9
|
1.0
|
|
CA
|
B:ASN162
|
4.9
|
14.1
|
1.0
|
|
C
|
B:ASN140
|
4.9
|
17.3
|
1.0
|
|
CA
|
B:TYR142
|
5.0
|
19.2
|
1.0
|
|
Calcium binding site 5 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 5 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca202
b:16.7
occ:1.00
|
O
|
E:ILE91
|
2.3
|
14.9
|
1.0
|
|
O
|
E:HOH379
|
2.4
|
20.8
|
1.0
|
|
OD1
|
E:ASN93
|
2.4
|
20.6
|
1.0
|
|
OE2
|
E:GLU175
|
2.4
|
16.8
|
1.0
|
|
O
|
E:HOH361
|
2.4
|
17.1
|
1.0
|
|
OE2
|
E:GLU97
|
2.5
|
14.6
|
1.0
|
|
OE1
|
E:GLU175
|
2.6
|
16.1
|
1.0
|
|
OE1
|
E:GLU97
|
2.8
|
18.6
|
1.0
|
|
CD
|
E:GLU175
|
2.9
|
19.9
|
1.0
|
|
CD
|
E:GLU97
|
3.0
|
15.3
|
1.0
|
|
C
|
E:ILE91
|
3.5
|
14.8
|
1.0
|
|
CG
|
E:ASN93
|
3.6
|
23.1
|
1.0
|
|
OH
|
E:TYR66
|
4.2
|
16.8
|
1.0
|
|
CB
|
E:ILE91
|
4.2
|
16.7
|
1.0
|
|
CA
|
E:ILE91
|
4.2
|
14.8
|
1.0
|
|
N
|
E:ILE91
|
4.3
|
13.3
|
1.0
|
|
CB
|
E:ASN93
|
4.3
|
22.4
|
1.0
|
|
N
|
E:ASN93
|
4.3
|
18.4
|
1.0
|
|
CG
|
E:GLU175
|
4.4
|
18.3
|
1.0
|
|
O
|
E:HOH391
|
4.5
|
45.9
|
1.0
|
|
CG
|
E:GLU97
|
4.5
|
14.6
|
1.0
|
|
O
|
E:HOH330
|
4.5
|
20.9
|
1.0
|
|
N
|
E:ILE92
|
4.5
|
15.6
|
1.0
|
|
O
|
E:HOH392
|
4.6
|
23.0
|
1.0
|
|
ND2
|
E:ASN93
|
4.6
|
25.9
|
1.0
|
|
O
|
E:HOH335
|
4.6
|
29.7
|
1.0
|
|
CG2
|
E:ILE91
|
4.6
|
16.5
|
1.0
|
|
CA
|
E:ILE92
|
4.7
|
17.3
|
1.0
|
|
OG
|
E:SER64
|
4.7
|
18.4
|
1.0
|
|
C
|
E:ILE92
|
4.9
|
18.4
|
1.0
|
|
CA
|
E:ASN93
|
5.0
|
22.7
|
1.0
|
|
Calcium binding site 6 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 6 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca203
b:15.9
occ:1.00
|
OD1
|
E:ASP163
|
2.3
|
14.6
|
1.0
|
|
OD1
|
E:ASN140
|
2.4
|
15.8
|
1.0
|
|
OD1
|
E:ASN162
|
2.4
|
16.8
|
1.0
|
|
O
|
E:ASP163
|
2.5
|
13.8
|
1.0
|
|
OE1
|
E:GLU147
|
2.5
|
17.5
|
1.0
|
|
O1
|
E:GOL201
|
2.5
|
15.5
|
1.0
|
|
OE1
|
E:GLU138
|
2.5
|
17.4
|
1.0
|
|
O2
|
E:GOL201
|
2.6
|
16.6
|
1.0
|
|
CG
|
E:ASP163
|
3.3
|
16.0
|
1.0
|
|
CG
|
E:ASN140
|
3.4
|
19.8
|
1.0
|
|
C1
|
E:GOL201
|
3.4
|
17.6
|
1.0
|
|
CG
|
E:ASN162
|
3.4
|
17.0
|
1.0
|
|
C2
|
E:GOL201
|
3.4
|
25.2
|
1.0
|
|
CD
|
E:GLU138
|
3.4
|
18.9
|
1.0
|
|
CD
|
E:GLU147
|
3.5
|
17.4
|
1.0
|
|
C
|
E:ASP163
|
3.5
|
14.1
|
1.0
|
|
OE2
|
E:GLU138
|
3.7
|
18.8
|
1.0
|
|
N
|
E:ASP163
|
3.8
|
15.2
|
1.0
|
|
ND2
|
E:ASN162
|
3.8
|
15.5
|
1.0
|
|
OE2
|
E:GLU147
|
3.8
|
17.8
|
1.0
|
|
ND2
|
E:ASN140
|
4.0
|
18.8
|
1.0
|
|
OD2
|
E:ASP163
|
4.0
|
14.9
|
1.0
|
|
CA
|
E:ASP163
|
4.0
|
13.4
|
1.0
|
|
N
|
E:ASN140
|
4.2
|
16.2
|
1.0
|
|
CB
|
E:ASP163
|
4.3
|
12.9
|
1.0
|
|
CB
|
E:TYR142
|
4.4
|
18.2
|
1.0
|
|
N
|
E:TYR142
|
4.5
|
20.2
|
1.0
|
|
CB
|
E:ASN140
|
4.6
|
18.9
|
1.0
|
|
N
|
E:ASN141
|
4.6
|
15.0
|
1.0
|
|
C
|
E:ASN162
|
4.6
|
14.0
|
1.0
|
|
CG
|
E:GLU138
|
4.6
|
17.2
|
1.0
|
|
CB
|
E:ASN162
|
4.7
|
14.5
|
1.0
|
|
N
|
E:LEU164
|
4.7
|
14.3
|
1.0
|
|
CG
|
E:GLU147
|
4.7
|
16.3
|
1.0
|
|
CA
|
E:ASN140
|
4.8
|
17.0
|
1.0
|
|
C3
|
E:GOL201
|
4.8
|
30.9
|
1.0
|
|
CB
|
E:GLU147
|
4.8
|
15.5
|
1.0
|
|
CA
|
E:ASN162
|
4.9
|
13.0
|
1.0
|
|
C
|
E:ASN140
|
5.0
|
16.3
|
1.0
|
|
Calcium binding site 7 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 7 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca202
b:17.0
occ:1.00
|
O
|
G:ILE91
|
2.3
|
15.4
|
1.0
|
|
OD1
|
G:ASN93
|
2.4
|
19.8
|
1.0
|
|
O
|
G:HOH349
|
2.4
|
18.0
|
1.0
|
|
OE2
|
G:GLU175
|
2.5
|
16.6
|
1.0
|
|
OE2
|
G:GLU97
|
2.5
|
17.6
|
1.0
|
|
O
|
G:HOH375
|
2.5
|
21.3
|
1.0
|
|
OE1
|
G:GLU175
|
2.5
|
17.0
|
1.0
|
|
OE1
|
G:GLU97
|
2.8
|
19.0
|
1.0
|
|
CD
|
G:GLU175
|
2.8
|
18.5
|
1.0
|
|
CD
|
G:GLU97
|
2.9
|
22.0
|
1.0
|
|
C
|
G:ILE91
|
3.5
|
13.0
|
1.0
|
|
CG
|
G:ASN93
|
3.6
|
26.5
|
1.0
|
|
CB
|
G:ILE91
|
4.2
|
14.7
|
1.0
|
|
CA
|
G:ILE91
|
4.2
|
15.3
|
1.0
|
|
OH
|
G:TYR66
|
4.3
|
17.6
|
1.0
|
|
N
|
G:ILE91
|
4.3
|
15.2
|
1.0
|
|
N
|
G:ASN93
|
4.3
|
17.3
|
1.0
|
|
CG
|
G:GLU175
|
4.4
|
17.0
|
1.0
|
|
CB
|
G:ASN93
|
4.4
|
21.7
|
1.0
|
|
CG
|
G:GLU97
|
4.4
|
17.7
|
1.0
|
|
N
|
G:ILE92
|
4.5
|
15.0
|
1.0
|
|
O
|
G:HOH311
|
4.5
|
29.5
|
1.0
|
|
O
|
G:HOH379
|
4.6
|
29.6
|
1.0
|
|
O
|
G:HOH386
|
4.6
|
22.2
|
1.0
|
|
ND2
|
G:ASN93
|
4.6
|
23.2
|
1.0
|
|
CG2
|
G:ILE91
|
4.6
|
18.4
|
1.0
|
|
O
|
G:HOH341
|
4.7
|
28.7
|
1.0
|
|
CA
|
G:ILE92
|
4.7
|
15.7
|
1.0
|
|
OG
|
G:SER64
|
4.8
|
21.8
|
1.0
|
|
C
|
G:ILE92
|
4.9
|
17.4
|
1.0
|
|
Calcium binding site 8 out
of 8 in 9ks7
Go back to
Calcium Binding Sites List in 9ks7
Calcium binding site 8 out
of 8 in the Crystal Structure of T. Rubripes Mincle with Glycerol
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of T. Rubripes Mincle with Glycerol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca203
b:16.2
occ:1.00
|
OD1
|
G:ASP163
|
2.3
|
14.3
|
1.0
|
|
OD1
|
G:ASN140
|
2.4
|
16.1
|
1.0
|
|
OD1
|
G:ASN162
|
2.4
|
15.8
|
1.0
|
|
O
|
G:ASP163
|
2.5
|
14.1
|
1.0
|
|
OE1
|
G:GLU147
|
2.5
|
17.1
|
1.0
|
|
O1
|
G:GOL201
|
2.5
|
15.4
|
1.0
|
|
OE1
|
G:GLU138
|
2.5
|
15.7
|
1.0
|
|
O2
|
G:GOL201
|
2.6
|
20.0
|
1.0
|
|
CG
|
G:ASP163
|
3.3
|
16.5
|
1.0
|
|
CD
|
G:GLU138
|
3.4
|
19.6
|
1.0
|
|
CG
|
G:ASN140
|
3.4
|
22.9
|
1.0
|
|
CG
|
G:ASN162
|
3.4
|
14.8
|
1.0
|
|
C2
|
G:GOL201
|
3.4
|
21.2
|
1.0
|
|
C1
|
G:GOL201
|
3.4
|
17.0
|
1.0
|
|
CD
|
G:GLU147
|
3.5
|
18.1
|
1.0
|
|
C
|
G:ASP163
|
3.5
|
13.2
|
1.0
|
|
OE2
|
G:GLU138
|
3.7
|
18.7
|
1.0
|
|
N
|
G:ASP163
|
3.8
|
12.9
|
1.0
|
|
ND2
|
G:ASN162
|
3.8
|
15.0
|
1.0
|
|
OE2
|
G:GLU147
|
3.9
|
18.6
|
1.0
|
|
ND2
|
G:ASN140
|
4.0
|
19.5
|
1.0
|
|
OD2
|
G:ASP163
|
4.0
|
19.1
|
1.0
|
|
CA
|
G:ASP163
|
4.0
|
12.9
|
1.0
|
|
N
|
G:ASN140
|
4.1
|
16.1
|
1.0
|
|
CB
|
G:ASP163
|
4.2
|
12.7
|
1.0
|
|
CB
|
G:TYR142
|
4.4
|
17.4
|
1.0
|
|
N
|
G:TYR142
|
4.5
|
21.4
|
1.0
|
|
N
|
G:ASN141
|
4.6
|
16.5
|
1.0
|
|
CB
|
G:ASN140
|
4.6
|
17.5
|
1.0
|
|
C
|
G:ASN162
|
4.6
|
13.1
|
1.0
|
|
CG
|
G:GLU138
|
4.6
|
16.1
|
1.0
|
|
CB
|
G:ASN162
|
4.7
|
13.7
|
1.0
|
|
N
|
G:LEU164
|
4.7
|
13.9
|
1.0
|
|
CG
|
G:GLU147
|
4.7
|
16.6
|
1.0
|
|
CA
|
G:ASN140
|
4.7
|
18.5
|
1.0
|
|
CB
|
G:GLU147
|
4.8
|
15.1
|
1.0
|
|
C3
|
G:GOL201
|
4.8
|
27.6
|
1.0
|
|
CA
|
G:ASN162
|
4.9
|
13.7
|
1.0
|
|
C
|
G:ASN140
|
4.9
|
17.8
|
1.0
|
|
Reference:
T.Ito,
C.Guenther,
E.Ishikawa,
T.Yabuki,
M.Nagae,
Y.Nakatani,
S.Yamasaki.
Phylogenetic and Structural Insights Into the Origin of C-Type Lectin Mincle in Vertebrates. Immunogenetics V. 77 18 2025.
ISSN: ISSN 0093-7711
PubMed: 40119899
DOI: 10.1007/S00251-025-01375-X
Page generated: Thu Jul 10 10:12:53 2025
|
