Calcium in PDB 5vh2: Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
Protein crystallography data
The structure of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D, PDB code: 5vh2
was solved by
D.J.Termine,
A.Jaiganesh,
M.Sotomayor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
33.99 /
2.84
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.738,
47.210,
113.044,
89.95,
90.02,
115.76
|
|
R / Rfree (%)
|
23.8 /
27.2
|
Other elements in 5vh2:
The structure of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
(pdb code 5vh2). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D, PDB code: 5vh2:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 1 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1401
b:26.8
occ:1.00
|
OD2
|
A:ASP1214
|
2.1
|
28.4
|
1.0
|
|
OD2
|
A:ASP1264
|
2.1
|
25.7
|
1.0
|
|
O
|
A:GLU1181
|
2.2
|
26.4
|
1.0
|
|
O
|
A:GLY1218
|
2.6
|
27.2
|
1.0
|
|
OD2
|
A:ASP1212
|
2.9
|
25.6
|
1.0
|
|
OD1
|
A:ASP1212
|
3.2
|
27.0
|
1.0
|
|
CG
|
A:ASP1214
|
3.2
|
29.2
|
1.0
|
|
CG
|
A:ASP1264
|
3.3
|
25.2
|
1.0
|
|
CG
|
A:ASP1212
|
3.4
|
26.1
|
1.0
|
|
C
|
A:GLU1181
|
3.4
|
26.3
|
1.0
|
|
C
|
A:GLY1218
|
3.6
|
27.9
|
1.0
|
|
ND2
|
A:ASN1270
|
3.8
|
25.7
|
1.0
|
|
CB
|
A:ASP1264
|
3.8
|
25.0
|
1.0
|
|
CB
|
A:ASP1214
|
3.9
|
29.6
|
1.0
|
|
N
|
A:GLU1181
|
4.0
|
28.3
|
1.0
|
|
OD1
|
A:ASP1214
|
4.1
|
29.8
|
1.0
|
|
CA
|
A:GLY1218
|
4.2
|
28.5
|
1.0
|
|
OD1
|
A:ASP1264
|
4.3
|
24.9
|
1.0
|
|
CA
|
A:GLU1181
|
4.3
|
27.3
|
1.0
|
|
N
|
A:ALA1182
|
4.4
|
25.4
|
1.0
|
|
CA
|
A:ALA1182
|
4.5
|
24.5
|
1.0
|
|
N
|
A:ASP1180
|
4.7
|
29.5
|
1.0
|
|
N
|
A:GLY1219
|
4.7
|
28.1
|
1.0
|
|
C
|
A:ASN1179
|
4.9
|
28.7
|
1.0
|
|
CG
|
A:ASN1270
|
4.9
|
24.9
|
1.0
|
|
CG
|
A:GLU1181
|
4.9
|
27.7
|
1.0
|
|
CB
|
A:ASP1212
|
4.9
|
25.8
|
1.0
|
|
Calcium binding site 2 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 2 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1402
b:27.4
occ:1.00
|
OD1
|
A:ASN1282
|
2.2
|
27.0
|
1.0
|
|
OE2
|
A:GLU1197
|
2.2
|
26.0
|
1.0
|
|
O
|
A:GLU1283
|
2.3
|
27.8
|
1.0
|
|
OD1
|
A:ASP1318
|
2.4
|
32.4
|
1.0
|
|
OD1
|
A:ASP1285
|
2.5
|
35.6
|
1.0
|
|
OE1
|
A:GLU1251
|
2.7
|
27.6
|
1.0
|
|
OE2
|
A:GLU1251
|
2.8
|
27.0
|
1.0
|
|
CD
|
A:GLU1251
|
3.1
|
27.4
|
1.0
|
|
CD
|
A:GLU1197
|
3.3
|
25.4
|
1.0
|
|
CG
|
A:ASN1282
|
3.4
|
26.9
|
1.0
|
|
CA
|
A:CA1403
|
3.5
|
27.0
|
1.0
|
|
C
|
A:GLU1283
|
3.5
|
27.8
|
1.0
|
|
CG
|
A:ASP1285
|
3.6
|
37.1
|
1.0
|
|
CG
|
A:ASP1318
|
3.6
|
31.3
|
1.0
|
|
N
|
A:GLU1283
|
3.6
|
26.4
|
1.0
|
|
OE1
|
A:GLU1197
|
3.8
|
25.3
|
1.0
|
|
OD2
|
A:ASP1285
|
4.1
|
38.3
|
1.0
|
|
N
|
A:ASP1285
|
4.2
|
35.3
|
1.0
|
|
ND2
|
A:ASN1282
|
4.2
|
27.7
|
1.0
|
|
CB
|
A:ASP1318
|
4.2
|
30.5
|
1.0
|
|
CA
|
A:GLU1283
|
4.2
|
27.0
|
1.0
|
|
CG
|
A:GLU1286
|
4.2
|
32.2
|
1.0
|
|
C
|
A:ASN1282
|
4.4
|
26.1
|
1.0
|
|
CA
|
A:ASN1282
|
4.4
|
25.6
|
1.0
|
|
CB
|
A:TYR1250
|
4.4
|
24.6
|
1.0
|
|
CB
|
A:ASN1282
|
4.5
|
26.1
|
1.0
|
|
N
|
A:LEU1284
|
4.5
|
28.6
|
1.0
|
|
CG
|
A:GLU1251
|
4.6
|
27.6
|
1.0
|
|
CA
|
A:ASP1318
|
4.6
|
29.4
|
1.0
|
|
CG
|
A:GLU1197
|
4.6
|
24.8
|
1.0
|
|
OD2
|
A:ASP1318
|
4.7
|
30.9
|
1.0
|
|
CB
|
A:ASP1285
|
4.7
|
37.7
|
1.0
|
|
CA
|
A:LEU1284
|
4.7
|
29.6
|
1.0
|
|
CA
|
A:ASP1285
|
4.9
|
36.0
|
1.0
|
|
CD2
|
A:TYR1250
|
4.9
|
25.4
|
1.0
|
|
C
|
A:LEU1284
|
5.0
|
29.7
|
1.0
|
|
Calcium binding site 3 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 3 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1403
b:27.0
occ:1.00
|
OE2
|
A:GLU1251
|
2.0
|
27.0
|
1.0
|
|
OE1
|
A:GLU1286
|
2.3
|
34.3
|
1.0
|
|
OD1
|
A:ASP1249
|
2.5
|
25.9
|
1.0
|
|
OD2
|
A:ASP1285
|
2.6
|
38.3
|
1.0
|
|
OD1
|
A:ASP1285
|
2.6
|
35.6
|
1.0
|
|
OE1
|
A:GLU1197
|
2.7
|
25.3
|
1.0
|
|
CG
|
A:ASP1285
|
2.9
|
37.1
|
1.0
|
|
CD
|
A:GLU1251
|
3.2
|
27.4
|
1.0
|
|
CD
|
A:GLU1286
|
3.2
|
33.1
|
1.0
|
|
CG
|
A:GLU1286
|
3.3
|
32.2
|
1.0
|
|
CD
|
A:GLU1197
|
3.4
|
25.4
|
1.0
|
|
CA
|
A:CA1402
|
3.5
|
27.4
|
1.0
|
|
OE2
|
A:GLU1197
|
3.5
|
26.0
|
1.0
|
|
CG
|
A:ASP1249
|
3.7
|
25.6
|
1.0
|
|
CG
|
A:GLU1251
|
4.0
|
27.6
|
1.0
|
|
OE1
|
A:GLU1251
|
4.0
|
27.6
|
1.0
|
|
CB
|
A:GLU1251
|
4.1
|
26.9
|
1.0
|
|
N
|
A:GLU1251
|
4.2
|
25.3
|
1.0
|
|
OE2
|
A:GLU1286
|
4.3
|
32.7
|
1.0
|
|
N
|
A:TYR1250
|
4.4
|
24.2
|
1.0
|
|
OD2
|
A:ASP1249
|
4.4
|
26.1
|
1.0
|
|
CB
|
A:ASP1285
|
4.4
|
37.7
|
1.0
|
|
OD1
|
A:ASP1318
|
4.6
|
32.4
|
1.0
|
|
CA
|
A:ASP1249
|
4.6
|
24.2
|
1.0
|
|
O
|
A:ASP1285
|
4.7
|
35.2
|
1.0
|
|
CB
|
A:ASP1249
|
4.7
|
24.7
|
1.0
|
|
CB
|
A:GLU1286
|
4.7
|
31.0
|
1.0
|
|
CG
|
A:GLU1197
|
4.8
|
24.8
|
1.0
|
|
C
|
A:ASP1285
|
4.8
|
34.6
|
1.0
|
|
CA
|
A:GLU1251
|
4.8
|
25.9
|
1.0
|
|
C
|
A:ASP1249
|
4.9
|
23.9
|
1.0
|
|
CB
|
A:TYR1250
|
4.9
|
24.6
|
1.0
|
|
Calcium binding site 4 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 4 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1401
b:21.6
occ:1.00
|
O
|
B:GLY1218
|
2.0
|
21.1
|
1.0
|
|
OD2
|
B:ASP1212
|
2.3
|
21.1
|
1.0
|
|
OD2
|
B:ASP1264
|
2.4
|
21.0
|
1.0
|
|
O
|
B:GLU1181
|
2.4
|
22.3
|
1.0
|
|
OD2
|
B:ASP1214
|
2.5
|
22.6
|
1.0
|
|
OD1
|
B:ASP1212
|
2.5
|
22.0
|
1.0
|
|
CG
|
B:ASP1212
|
2.8
|
21.5
|
1.0
|
|
CG
|
B:ASP1214
|
3.1
|
22.9
|
1.0
|
|
C
|
B:GLY1218
|
3.2
|
21.1
|
1.0
|
|
CG
|
B:ASP1264
|
3.4
|
20.5
|
1.0
|
|
CB
|
B:ASP1264
|
3.6
|
20.2
|
1.0
|
|
C
|
B:GLU1181
|
3.6
|
22.7
|
1.0
|
|
CB
|
B:ASP1214
|
3.6
|
22.6
|
1.0
|
|
OD1
|
B:ASP1214
|
3.9
|
23.4
|
1.0
|
|
CA
|
B:GLY1218
|
3.9
|
21.1
|
1.0
|
|
CB
|
B:ASN1179
|
4.2
|
22.4
|
1.0
|
|
N
|
B:GLY1219
|
4.2
|
21.1
|
1.0
|
|
CB
|
B:ASP1212
|
4.2
|
21.2
|
1.0
|
|
ND2
|
B:ASN1179
|
4.3
|
22.4
|
1.0
|
|
N
|
B:GLU1181
|
4.3
|
23.7
|
1.0
|
|
CA
|
B:GLY1219
|
4.4
|
21.1
|
1.0
|
|
CA
|
B:GLU1181
|
4.5
|
23.5
|
1.0
|
|
OD1
|
B:ASP1264
|
4.5
|
20.3
|
1.0
|
|
N
|
B:ALA1182
|
4.5
|
22.6
|
1.0
|
|
ND2
|
B:ASN1270
|
4.5
|
21.8
|
1.0
|
|
CA
|
B:ALA1182
|
4.6
|
22.0
|
1.0
|
|
CG
|
B:GLU1181
|
4.7
|
23.5
|
1.0
|
|
CG
|
B:ASN1179
|
4.7
|
22.4
|
1.0
|
|
N
|
B:ASP1214
|
4.9
|
23.0
|
1.0
|
|
CA
|
B:ASP1214
|
4.9
|
23.1
|
1.0
|
|
Calcium binding site 5 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 5 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1402
b:19.6
occ:1.00
|
OD1
|
B:ASP1249
|
2.2
|
19.5
|
1.0
|
|
OD2
|
B:ASP1285
|
2.2
|
38.2
|
1.0
|
|
OE1
|
B:GLU1197
|
2.4
|
19.0
|
1.0
|
|
OE2
|
B:GLU1251
|
2.7
|
19.6
|
1.0
|
|
OE1
|
B:GLU1286
|
2.7
|
36.8
|
1.0
|
|
CG
|
B:ASP1285
|
3.0
|
36.3
|
1.0
|
|
OD1
|
B:ASP1285
|
3.0
|
35.2
|
1.0
|
|
CD
|
B:GLU1197
|
3.3
|
19.0
|
1.0
|
|
CG
|
B:ASP1249
|
3.3
|
19.5
|
1.0
|
|
OE2
|
B:GLU1197
|
3.6
|
19.1
|
1.0
|
|
CD
|
B:GLU1286
|
3.7
|
34.9
|
1.0
|
|
CD
|
B:GLU1251
|
3.9
|
19.6
|
1.0
|
|
CA
|
B:ASP1249
|
4.0
|
18.9
|
1.0
|
|
CA
|
B:CA1403
|
4.0
|
19.5
|
1.0
|
|
N
|
B:TYR1250
|
4.0
|
18.8
|
1.0
|
|
CG
|
B:GLU1286
|
4.1
|
33.4
|
1.0
|
|
OD2
|
B:ASP1249
|
4.1
|
19.8
|
1.0
|
|
CB
|
B:ASP1249
|
4.1
|
19.2
|
1.0
|
|
N
|
B:GLU1251
|
4.4
|
19.2
|
1.0
|
|
CB
|
B:ASP1285
|
4.4
|
35.4
|
1.0
|
|
C
|
B:ASP1249
|
4.4
|
18.8
|
1.0
|
|
CG
|
B:GLU1197
|
4.5
|
18.8
|
1.0
|
|
CB
|
B:GLU1251
|
4.6
|
19.9
|
1.0
|
|
CG
|
B:GLU1251
|
4.7
|
19.9
|
1.0
|
|
OE2
|
B:GLU1286
|
4.8
|
34.3
|
1.0
|
|
OE1
|
B:GLU1251
|
4.8
|
19.6
|
1.0
|
|
O
|
B:LEU1248
|
4.9
|
18.9
|
1.0
|
|
O
|
B:ASP1285
|
4.9
|
33.8
|
1.0
|
|
CB
|
B:TYR1250
|
5.0
|
18.8
|
1.0
|
|
CA
|
B:TYR1250
|
5.0
|
18.8
|
1.0
|
|
Calcium binding site 6 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 6 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1403
b:19.5
occ:1.00
|
OD1
|
B:ASN1282
|
2.2
|
19.2
|
1.0
|
|
OD1
|
B:ASP1318
|
2.3
|
31.8
|
1.0
|
|
OE2
|
B:GLU1197
|
2.4
|
19.1
|
1.0
|
|
OD1
|
B:ASP1285
|
2.5
|
35.2
|
1.0
|
|
O
|
B:GLU1283
|
2.5
|
19.6
|
1.0
|
|
OE1
|
B:GLU1251
|
2.5
|
19.6
|
1.0
|
|
OE2
|
B:GLU1251
|
2.6
|
19.6
|
1.0
|
|
CD
|
B:GLU1251
|
2.9
|
19.6
|
1.0
|
|
CG
|
B:ASN1282
|
3.4
|
19.1
|
1.0
|
|
CD
|
B:GLU1197
|
3.5
|
19.0
|
1.0
|
|
CG
|
B:ASP1318
|
3.5
|
30.3
|
1.0
|
|
CG
|
B:ASP1285
|
3.6
|
36.3
|
1.0
|
|
C
|
B:GLU1283
|
3.7
|
19.6
|
1.0
|
|
N
|
B:GLU1283
|
3.9
|
19.1
|
1.0
|
|
OE1
|
B:GLU1197
|
3.9
|
19.0
|
1.0
|
|
CA
|
B:CA1402
|
4.0
|
19.6
|
1.0
|
|
CG
|
B:GLU1286
|
4.0
|
33.4
|
1.0
|
|
CB
|
B:ASP1318
|
4.1
|
29.7
|
1.0
|
|
OD2
|
B:ASP1285
|
4.2
|
38.2
|
1.0
|
|
ND2
|
B:ASN1282
|
4.2
|
19.2
|
1.0
|
|
N
|
B:ASP1285
|
4.2
|
32.2
|
1.0
|
|
CG
|
B:GLU1251
|
4.4
|
19.9
|
1.0
|
|
CA
|
B:GLU1283
|
4.4
|
19.3
|
1.0
|
|
CA
|
B:ASP1318
|
4.4
|
30.1
|
1.0
|
|
CB
|
B:TYR1250
|
4.5
|
18.8
|
1.0
|
|
OD2
|
B:ASP1318
|
4.5
|
29.3
|
1.0
|
|
CA
|
B:ASN1282
|
4.6
|
18.8
|
1.0
|
|
CB
|
B:ASN1282
|
4.6
|
18.9
|
1.0
|
|
C
|
B:ASN1282
|
4.6
|
18.9
|
1.0
|
|
N
|
B:LEU1284
|
4.7
|
19.8
|
1.0
|
|
CB
|
B:ASP1285
|
4.7
|
35.4
|
1.0
|
|
CG
|
B:GLU1197
|
4.8
|
18.8
|
1.0
|
|
CA
|
B:LEU1284
|
4.8
|
20.2
|
1.0
|
|
CD2
|
B:TYR1250
|
4.9
|
18.9
|
1.0
|
|
CB
|
B:GLU1286
|
4.9
|
31.5
|
1.0
|
|
CA
|
B:ASP1285
|
4.9
|
33.1
|
1.0
|
|
N
|
B:GLU1286
|
5.0
|
31.3
|
1.0
|
|
OE1
|
B:GLU1286
|
5.0
|
36.8
|
1.0
|
|
Calcium binding site 7 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 7 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1401
b:16.9
occ:1.00
|
OE1
|
C:GLU1286
|
2.2
|
16.5
|
1.0
|
|
OD1
|
C:ASP1249
|
2.3
|
17.0
|
1.0
|
|
OE2
|
C:GLU1251
|
2.4
|
17.2
|
1.0
|
|
OD2
|
C:ASP1285
|
2.4
|
19.2
|
1.0
|
|
OE1
|
C:GLU1197
|
2.8
|
15.9
|
1.0
|
|
OD1
|
C:ASP1285
|
2.9
|
18.2
|
1.0
|
|
CG
|
C:ASP1285
|
3.0
|
19.1
|
1.0
|
|
CD
|
C:GLU1286
|
3.2
|
16.3
|
1.0
|
|
CG
|
C:ASP1249
|
3.4
|
17.1
|
1.0
|
|
CG
|
C:GLU1286
|
3.6
|
16.1
|
1.0
|
|
CD
|
C:GLU1251
|
3.6
|
17.7
|
1.0
|
|
CD
|
C:GLU1197
|
3.6
|
15.7
|
1.0
|
|
OE2
|
C:GLU1197
|
3.8
|
15.9
|
1.0
|
|
CA
|
C:CA1402
|
3.9
|
16.9
|
1.0
|
|
OD2
|
C:ASP1249
|
4.1
|
17.7
|
1.0
|
|
CB
|
C:GLU1251
|
4.2
|
18.2
|
1.0
|
|
CG
|
C:GLU1251
|
4.3
|
18.4
|
1.0
|
|
OE2
|
C:GLU1286
|
4.3
|
16.3
|
1.0
|
|
N
|
C:GLU1251
|
4.3
|
17.2
|
1.0
|
|
N
|
C:TYR1250
|
4.4
|
16.1
|
1.0
|
|
CB
|
C:ASP1249
|
4.4
|
16.7
|
1.0
|
|
CB
|
C:ASP1285
|
4.4
|
20.1
|
1.0
|
|
CA
|
C:ASP1249
|
4.4
|
16.1
|
1.0
|
|
OE1
|
C:GLU1251
|
4.5
|
17.7
|
1.0
|
|
O
|
C:ASP1285
|
4.7
|
18.8
|
1.0
|
|
C
|
C:ASP1249
|
4.8
|
16.2
|
1.0
|
|
CG
|
C:GLU1197
|
4.9
|
15.2
|
1.0
|
|
C
|
C:ASP1285
|
4.9
|
18.6
|
1.0
|
|
CA
|
C:GLU1251
|
4.9
|
17.9
|
1.0
|
|
Calcium binding site 8 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 8 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 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 Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1402
b:16.9
occ:1.00
|
OD1
|
C:ASP1318
|
2.1
|
16.9
|
1.0
|
|
OD1
|
C:ASN1282
|
2.3
|
16.8
|
1.0
|
|
O
|
C:GLU1283
|
2.4
|
16.3
|
1.0
|
|
OD1
|
C:ASP1285
|
2.4
|
18.2
|
1.0
|
|
OE1
|
C:GLU1251
|
2.5
|
17.7
|
1.0
|
|
OE2
|
C:GLU1197
|
2.7
|
15.9
|
1.0
|
|
OE2
|
C:GLU1251
|
2.7
|
17.2
|
1.0
|
|
CD
|
C:GLU1251
|
2.9
|
17.7
|
1.0
|
|
CG
|
C:ASP1318
|
3.3
|
16.7
|
1.0
|
|
CG
|
C:ASN1282
|
3.5
|
16.9
|
1.0
|
|
CG
|
C:ASP1285
|
3.6
|
19.1
|
1.0
|
|
C
|
C:GLU1283
|
3.6
|
16.0
|
1.0
|
|
CD
|
C:GLU1197
|
3.7
|
15.7
|
1.0
|
|
CG
|
C:GLU1286
|
3.9
|
16.1
|
1.0
|
|
CA
|
C:CA1401
|
3.9
|
16.9
|
1.0
|
|
N
|
C:GLU1283
|
3.9
|
15.7
|
1.0
|
|
CB
|
C:ASP1318
|
4.0
|
16.4
|
1.0
|
|
N
|
C:ASP1285
|
4.0
|
19.4
|
1.0
|
|
OE1
|
C:GLU1197
|
4.1
|
15.9
|
1.0
|
|
ND2
|
C:ASN1282
|
4.2
|
17.5
|
1.0
|
|
OD2
|
C:ASP1285
|
4.2
|
19.2
|
1.0
|
|
CA
|
C:ASP1318
|
4.3
|
15.5
|
1.0
|
|
OD2
|
C:ASP1318
|
4.4
|
16.9
|
1.0
|
|
CG
|
C:GLU1251
|
4.4
|
18.4
|
1.0
|
|
CA
|
C:GLU1283
|
4.4
|
15.6
|
1.0
|
|
N
|
C:LEU1284
|
4.6
|
16.1
|
1.0
|
|
C
|
C:ASN1282
|
4.7
|
15.8
|
1.0
|
|
CA
|
C:ASN1282
|
4.7
|
15.9
|
1.0
|
|
CB
|
C:ASP1285
|
4.7
|
20.1
|
1.0
|
|
CB
|
C:ASN1282
|
4.7
|
16.5
|
1.0
|
|
CA
|
C:LEU1284
|
4.7
|
16.5
|
1.0
|
|
CB
|
C:TYR1250
|
4.7
|
16.2
|
1.0
|
|
CA
|
C:ASP1285
|
4.8
|
19.7
|
1.0
|
|
CB
|
C:GLU1286
|
4.8
|
16.0
|
1.0
|
|
N
|
C:GLU1286
|
4.8
|
17.8
|
1.0
|
|
C
|
C:LEU1284
|
4.9
|
16.4
|
1.0
|
|
O
|
C:ASP1318
|
4.9
|
15.9
|
1.0
|
|
OE1
|
C:GLU1286
|
4.9
|
16.5
|
1.0
|
|
C
|
C:ASP1285
|
5.0
|
18.6
|
1.0
|
|
CD
|
C:GLU1286
|
5.0
|
16.3
|
1.0
|
|
Calcium binding site 9 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 9 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1401
b:22.8
occ:1.00
|
O
|
D:GLU1283
|
2.2
|
22.6
|
1.0
|
|
OD1
|
D:ASP1318
|
2.3
|
30.5
|
1.0
|
|
OD1
|
D:ASN1282
|
2.3
|
21.9
|
1.0
|
|
OD1
|
D:ASP1285
|
2.3
|
31.9
|
1.0
|
|
OE2
|
D:GLU1197
|
2.4
|
22.2
|
1.0
|
|
OE1
|
D:GLU1251
|
2.7
|
23.1
|
1.0
|
|
OE2
|
D:GLU1251
|
2.8
|
23.4
|
1.0
|
|
CD
|
D:GLU1251
|
3.1
|
23.4
|
1.0
|
|
C
|
D:GLU1283
|
3.4
|
22.5
|
1.0
|
|
CG
|
D:ASP1285
|
3.4
|
32.5
|
1.0
|
|
CD
|
D:GLU1197
|
3.5
|
22.2
|
1.0
|
|
CG
|
D:ASP1318
|
3.5
|
29.9
|
1.0
|
|
CG
|
D:ASN1282
|
3.5
|
21.6
|
1.0
|
|
N
|
D:GLU1283
|
3.7
|
21.6
|
1.0
|
|
OE1
|
D:GLU1197
|
3.9
|
22.5
|
1.0
|
|
N
|
D:ASP1285
|
4.0
|
31.4
|
1.0
|
|
CA
|
D:CA1402
|
4.0
|
23.9
|
1.0
|
|
CG
|
D:GLU1286
|
4.1
|
30.5
|
1.0
|
|
OD2
|
D:ASP1285
|
4.1
|
33.1
|
1.0
|
|
CB
|
D:ASP1318
|
4.1
|
29.6
|
1.0
|
|
CA
|
D:GLU1283
|
4.2
|
22.0
|
1.0
|
|
ND2
|
D:ASN1282
|
4.3
|
21.9
|
1.0
|
|
N
|
D:LEU1284
|
4.5
|
22.9
|
1.0
|
|
C
|
D:ASN1282
|
4.5
|
21.3
|
1.0
|
|
CA
|
D:ASP1318
|
4.5
|
29.3
|
1.0
|
|
OD2
|
D:ASP1318
|
4.5
|
29.6
|
1.0
|
|
CA
|
D:ASN1282
|
4.5
|
21.1
|
1.0
|
|
CB
|
D:ASP1285
|
4.5
|
32.5
|
1.0
|
|
CG
|
D:GLU1251
|
4.6
|
24.2
|
1.0
|
|
CB
|
D:ASN1282
|
4.6
|
21.2
|
1.0
|
|
CA
|
D:LEU1284
|
4.6
|
23.4
|
1.0
|
|
CB
|
D:TYR1250
|
4.6
|
21.5
|
1.0
|
|
CA
|
D:ASP1285
|
4.7
|
31.6
|
1.0
|
|
CG
|
D:GLU1197
|
4.7
|
22.0
|
1.0
|
|
C
|
D:LEU1284
|
4.8
|
24.1
|
1.0
|
|
N
|
D:GLU1286
|
4.9
|
30.4
|
1.0
|
|
CB
|
D:GLU1286
|
4.9
|
29.8
|
1.0
|
|
C
|
D:ASP1285
|
4.9
|
31.1
|
1.0
|
|
Calcium binding site 10 out
of 10 in 5vh2
Go back to
Calcium Binding Sites List in 5vh2
Calcium binding site 10 out
of 10 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1402
b:23.9
occ:1.00
|
OD2
|
D:ASP1285
|
2.2
|
33.1
|
1.0
|
|
OD1
|
D:ASP1249
|
2.3
|
23.9
|
1.0
|
|
OE1
|
D:GLU1197
|
2.4
|
22.5
|
1.0
|
|
OE1
|
D:GLU1286
|
2.7
|
31.5
|
1.0
|
|
OE2
|
D:GLU1251
|
2.7
|
23.4
|
1.0
|
|
CG
|
D:ASP1285
|
2.9
|
32.5
|
1.0
|
|
OD1
|
D:ASP1285
|
3.0
|
31.9
|
1.0
|
|
CD
|
D:GLU1197
|
3.2
|
22.2
|
1.0
|
|
CG
|
D:ASP1249
|
3.4
|
24.3
|
1.0
|
|
OE2
|
D:GLU1197
|
3.6
|
22.2
|
1.0
|
|
CD
|
D:GLU1286
|
3.7
|
30.9
|
1.0
|
|
CD
|
D:GLU1251
|
4.0
|
23.4
|
1.0
|
|
CA
|
D:CA1401
|
4.0
|
22.8
|
1.0
|
|
CG
|
D:GLU1286
|
4.1
|
30.5
|
1.0
|
|
CA
|
D:ASP1249
|
4.1
|
22.9
|
1.0
|
|
N
|
D:TYR1250
|
4.2
|
22.0
|
1.0
|
|
OD2
|
D:ASP1249
|
4.2
|
25.2
|
1.0
|
|
CB
|
D:ASP1249
|
4.2
|
23.8
|
1.0
|
|
CB
|
D:ASP1285
|
4.3
|
32.5
|
1.0
|
|
CG
|
D:GLU1197
|
4.4
|
22.0
|
1.0
|
|
N
|
D:GLU1251
|
4.5
|
22.8
|
1.0
|
|
C
|
D:ASP1249
|
4.5
|
22.3
|
1.0
|
|
CB
|
D:GLU1251
|
4.7
|
24.3
|
1.0
|
|
CG
|
D:GLU1251
|
4.8
|
24.2
|
1.0
|
|
OE2
|
D:GLU1286
|
4.8
|
30.6
|
1.0
|
|
OE1
|
D:GLU1251
|
4.8
|
23.1
|
1.0
|
|
O
|
D:ASP1285
|
4.9
|
31.4
|
1.0
|
|
Reference:
A.Jaiganesh,
P.De-La-Torre,
A.A.Patel,
D.J.Termine,
F.Velez-Cortes,
C.Chen,
M.Sotomayor.
Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness. Structure V. 26 1210 2018.
ISSN: ISSN 1878-4186
PubMed: 30033219
DOI: 10.1016/J.STR.2018.06.003
Page generated: Wed Jul 9 10:47:47 2025
|
