Calcium in PDB 3kq4: Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
Protein crystallography data
The structure of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin, PDB code: 3kq4
was solved by
C.B.F.Andersen,
M.Madsen,
S.K.Moestrup,
G.R.Andersen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.85 /
3.30
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.684,
204.179,
410.023,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
21.1 /
24.3
|
Other elements in 3kq4:
The structure of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
(pdb code 3kq4). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin, PDB code: 3kq4:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 1 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2014
b:0.7
occ:1.00
|
OE1
|
B:GLU980
|
2.3
|
0.9
|
1.0
|
|
O
|
B:ASP1029
|
2.3
|
0.9
|
1.0
|
|
OD1
|
B:ASP988
|
2.3
|
0.6
|
1.0
|
|
OD1
|
B:ASP1027
|
2.3
|
0.9
|
1.0
|
|
O
|
B:LEU1030
|
2.3
|
0.7
|
1.0
|
|
O
|
B:ASP1027
|
3.1
|
0.8
|
1.0
|
|
C
|
B:ASP1029
|
3.2
|
0.4
|
1.0
|
|
C
|
B:LEU1030
|
3.3
|
0.8
|
1.0
|
|
CD
|
B:GLU980
|
3.4
|
0.5
|
1.0
|
|
CG
|
B:ASP988
|
3.5
|
0.9
|
1.0
|
|
CG
|
B:ASP1027
|
3.5
|
0.5
|
1.0
|
|
N
|
B:LEU1030
|
3.7
|
0.1
|
1.0
|
|
CA
|
B:LEU1030
|
3.7
|
0.8
|
1.0
|
|
C
|
B:ASP1027
|
3.8
|
0.8
|
1.0
|
|
CB
|
B:LEU1030
|
3.8
|
0.4
|
1.0
|
|
OE2
|
B:GLU980
|
4.1
|
0.1
|
1.0
|
|
N
|
B:ASP1027
|
4.1
|
0.9
|
1.0
|
|
N
|
B:ASP1029
|
4.2
|
0.2
|
1.0
|
|
OD2
|
B:ASP988
|
4.2
|
0.7
|
1.0
|
|
OD2
|
B:ASP1027
|
4.3
|
0.6
|
1.0
|
|
CA
|
B:ASP1029
|
4.3
|
0.6
|
1.0
|
|
CA
|
B:ASP1027
|
4.3
|
0.7
|
1.0
|
|
CB
|
B:ASP988
|
4.4
|
0.4
|
1.0
|
|
C
|
B:SER1028
|
4.4
|
0.6
|
1.0
|
|
CG
|
B:GLU980
|
4.5
|
0.8
|
1.0
|
|
CB
|
B:ASP1027
|
4.5
|
0.7
|
1.0
|
|
N
|
B:SER1028
|
4.5
|
0.6
|
1.0
|
|
N
|
B:ALA1031
|
4.5
|
0.7
|
1.0
|
|
O
|
B:SER1028
|
4.7
|
0.6
|
1.0
|
|
CB
|
B:GLU980
|
4.7
|
0.4
|
1.0
|
|
CG
|
B:LEU1030
|
4.7
|
0.2
|
1.0
|
|
OH
|
B:TYR952
|
4.8
|
0.2
|
1.0
|
|
Calcium binding site 2 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 2 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2015
b:54.5
occ:1.00
|
O
|
B:ASP1149
|
2.3
|
0.3
|
1.0
|
|
OE1
|
B:GLU1096
|
2.3
|
78.8
|
1.0
|
|
OD2
|
B:ASP1146
|
2.3
|
66.4
|
1.0
|
|
O
|
B:ILE1148
|
2.3
|
69.2
|
1.0
|
|
OD2
|
B:ASP1105
|
2.3
|
77.9
|
1.0
|
|
OD1
|
B:ASP1105
|
2.7
|
82.3
|
1.0
|
|
CG
|
B:ASP1105
|
2.9
|
78.2
|
1.0
|
|
C
|
B:ASP1149
|
3.3
|
0.7
|
1.0
|
|
C
|
B:ILE1148
|
3.4
|
72.1
|
1.0
|
|
CG
|
B:ASP1146
|
3.5
|
68.5
|
1.0
|
|
CD
|
B:GLU1096
|
3.5
|
77.1
|
1.0
|
|
CB
|
B:ASP1149
|
3.7
|
0.1
|
1.0
|
|
CA
|
B:ASP1149
|
3.8
|
0.9
|
1.0
|
|
N
|
B:ASP1149
|
3.9
|
0.4
|
1.0
|
|
O
|
B:ASP1146
|
3.9
|
90.0
|
1.0
|
|
NZ
|
A:LYS159
|
4.0
|
64.4
|
1.0
|
|
N
|
B:ASP1146
|
4.0
|
80.0
|
1.0
|
|
OD1
|
B:ASN1070
|
4.1
|
74.1
|
1.0
|
|
OD1
|
B:ASP1146
|
4.2
|
64.6
|
1.0
|
|
CB
|
B:GLU1096
|
4.3
|
73.2
|
1.0
|
|
CB
|
B:ASP1105
|
4.3
|
66.9
|
1.0
|
|
OE2
|
B:GLU1096
|
4.3
|
78.3
|
1.0
|
|
C
|
B:ASP1146
|
4.4
|
90.6
|
1.0
|
|
N
|
B:THR1150
|
4.5
|
67.8
|
1.0
|
|
N
|
B:ILE1148
|
4.5
|
81.5
|
1.0
|
|
CG
|
B:GLU1096
|
4.5
|
74.4
|
1.0
|
|
CA
|
B:ASP1146
|
4.5
|
84.7
|
1.0
|
|
CA
|
B:ILE1148
|
4.5
|
80.8
|
1.0
|
|
OH
|
B:TYR1068
|
4.6
|
57.1
|
1.0
|
|
CB
|
B:ASP1146
|
4.6
|
76.9
|
1.0
|
|
CB
|
B:SER1145
|
4.9
|
70.3
|
1.0
|
|
C
|
B:SER1145
|
5.0
|
72.4
|
1.0
|
|
CA
|
B:THR1150
|
5.0
|
70.2
|
1.0
|
|
Calcium binding site 3 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 3 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2016
b:0.7
occ:1.00
|
OE2
|
B:GLU1213
|
2.3
|
0.5
|
1.0
|
|
OD1
|
B:ASP1262
|
2.3
|
0.0
|
1.0
|
|
O
|
B:GLY1264
|
2.3
|
0.5
|
1.0
|
|
OD1
|
B:ASP1221
|
2.3
|
0.7
|
1.0
|
|
O
|
B:GLN1265
|
2.3
|
0.2
|
1.0
|
|
O
|
B:ASP1262
|
2.3
|
0.9
|
1.0
|
|
OD2
|
B:ASP1221
|
2.7
|
0.0
|
1.0
|
|
CG
|
B:ASP1221
|
2.8
|
0.3
|
1.0
|
|
C
|
B:GLY1264
|
3.3
|
0.9
|
1.0
|
|
C
|
B:ASP1262
|
3.3
|
0.5
|
1.0
|
|
C
|
B:GLN1265
|
3.4
|
0.8
|
1.0
|
|
CG
|
B:ASP1262
|
3.4
|
0.7
|
1.0
|
|
CD
|
B:GLU1213
|
3.4
|
0.3
|
1.0
|
|
NE2
|
B:GLN1266
|
3.6
|
0.7
|
1.0
|
|
N
|
B:ASP1262
|
3.7
|
0.8
|
1.0
|
|
O
|
B:GLU1263
|
3.9
|
0.6
|
1.0
|
|
CA
|
B:GLN1265
|
3.9
|
0.6
|
1.0
|
|
CA
|
B:ASP1262
|
3.9
|
0.5
|
1.0
|
|
N
|
B:GLN1265
|
4.0
|
0.1
|
1.0
|
|
CB
|
B:GLN1265
|
4.0
|
0.1
|
1.0
|
|
C
|
B:GLU1263
|
4.1
|
0.3
|
1.0
|
|
OE1
|
B:GLU1213
|
4.1
|
0.1
|
1.0
|
|
OD2
|
B:ASP1262
|
4.2
|
0.1
|
1.0
|
|
CB
|
B:ASP1262
|
4.2
|
0.1
|
1.0
|
|
N
|
B:GLY1264
|
4.3
|
0.3
|
1.0
|
|
CA
|
B:GLY1264
|
4.3
|
0.2
|
1.0
|
|
CB
|
B:ASP1221
|
4.3
|
0.9
|
1.0
|
|
CG
|
B:GLU1213
|
4.4
|
0.5
|
1.0
|
|
CD
|
B:GLN1266
|
4.4
|
0.6
|
1.0
|
|
N
|
B:GLU1263
|
4.4
|
0.8
|
1.0
|
|
C
|
B:THR1261
|
4.5
|
0.1
|
1.0
|
|
N
|
B:GLN1266
|
4.5
|
0.8
|
1.0
|
|
CB
|
B:THR1261
|
4.7
|
0.6
|
1.0
|
|
CA
|
B:THR1261
|
4.8
|
0.6
|
1.0
|
|
CG
|
B:GLN1265
|
4.8
|
0.1
|
1.0
|
|
CA
|
B:GLU1263
|
4.8
|
0.2
|
1.0
|
|
OH
|
B:TYR1185
|
5.0
|
0.8
|
1.0
|
|
Calcium binding site 4 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 4 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2017
b:82.6
occ:1.00
|
OE2
|
B:GLU1328
|
2.3
|
84.0
|
1.0
|
|
O
|
B:VAL1375
|
2.3
|
91.4
|
1.0
|
|
OD2
|
B:ASP1336
|
2.3
|
87.7
|
1.0
|
|
OD1
|
B:ASP1373
|
2.3
|
95.2
|
1.0
|
|
CG
|
B:ASP1336
|
3.2
|
87.4
|
1.0
|
|
CD
|
B:GLU1328
|
3.3
|
84.8
|
1.0
|
|
OD1
|
B:ASP1336
|
3.5
|
82.3
|
1.0
|
|
C
|
B:VAL1375
|
3.5
|
91.9
|
1.0
|
|
CG
|
B:ASP1373
|
3.6
|
90.2
|
1.0
|
|
CG
|
B:GLU1328
|
3.7
|
93.4
|
1.0
|
|
O
|
B:ASP1373
|
3.8
|
94.6
|
1.0
|
|
OG1
|
B:THR1372
|
3.9
|
0.5
|
1.0
|
|
N
|
B:VAL1375
|
4.0
|
91.9
|
1.0
|
|
CE1
|
B:TYR1300
|
4.1
|
65.1
|
1.0
|
|
N
|
B:ASP1373
|
4.2
|
98.2
|
1.0
|
|
OH
|
B:TYR1300
|
4.2
|
67.8
|
1.0
|
|
C
|
B:ASP1373
|
4.2
|
92.5
|
1.0
|
|
OD2
|
B:ASP1373
|
4.3
|
85.0
|
1.0
|
|
OE2
|
B:GLU1379
|
4.4
|
70.2
|
1.0
|
|
CA
|
B:VAL1375
|
4.4
|
91.1
|
1.0
|
|
N
|
B:GLY1376
|
4.4
|
85.8
|
1.0
|
|
CA
|
B:GLY1376
|
4.4
|
87.6
|
1.0
|
|
OE1
|
B:GLU1328
|
4.4
|
79.2
|
1.0
|
|
CB
|
B:ASP1336
|
4.6
|
93.9
|
1.0
|
|
CB
|
B:ASP1373
|
4.6
|
89.2
|
1.0
|
|
CA
|
B:ASP1373
|
4.6
|
92.6
|
1.0
|
|
CZ
|
B:TYR1300
|
4.6
|
70.2
|
1.0
|
|
CG2
|
B:VAL1375
|
4.8
|
90.1
|
1.0
|
|
NH1
|
A:ARG323
|
4.9
|
73.6
|
1.0
|
|
N
|
B:GLY1374
|
4.9
|
69.6
|
1.0
|
|
CB
|
B:GLU1328
|
5.0
|
93.5
|
1.0
|
|
Calcium binding site 5 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 5 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca2014
b:0.1
occ:1.00
|
O
|
D:ASP1029
|
2.3
|
0.0
|
1.0
|
|
OE1
|
D:GLU980
|
2.3
|
0.3
|
1.0
|
|
OD1
|
D:ASP988
|
2.3
|
0.8
|
1.0
|
|
OD1
|
D:ASP1027
|
2.3
|
0.2
|
1.0
|
|
O
|
D:LEU1030
|
2.3
|
0.5
|
1.0
|
|
O
|
D:ASP1027
|
3.1
|
0.9
|
1.0
|
|
C
|
D:ASP1029
|
3.2
|
0.5
|
1.0
|
|
C
|
D:LEU1030
|
3.3
|
0.1
|
1.0
|
|
CD
|
D:GLU980
|
3.4
|
0.9
|
1.0
|
|
CG
|
D:ASP988
|
3.5
|
1.0
|
1.0
|
|
CG
|
D:ASP1027
|
3.5
|
0.2
|
1.0
|
|
N
|
D:LEU1030
|
3.7
|
0.6
|
1.0
|
|
CA
|
D:LEU1030
|
3.7
|
0.3
|
1.0
|
|
C
|
D:ASP1027
|
3.8
|
0.5
|
1.0
|
|
CB
|
D:LEU1030
|
3.8
|
0.8
|
1.0
|
|
OE2
|
D:GLU980
|
4.1
|
0.6
|
1.0
|
|
N
|
D:ASP1027
|
4.1
|
0.3
|
1.0
|
|
N
|
D:ASP1029
|
4.2
|
0.0
|
1.0
|
|
OD2
|
D:ASP988
|
4.2
|
0.1
|
1.0
|
|
OD2
|
D:ASP1027
|
4.3
|
0.1
|
1.0
|
|
CA
|
D:ASP1029
|
4.3
|
0.9
|
1.0
|
|
CA
|
D:ASP1027
|
4.3
|
1.0
|
1.0
|
|
CB
|
D:ASP988
|
4.4
|
0.6
|
1.0
|
|
C
|
D:SER1028
|
4.4
|
0.1
|
1.0
|
|
CG
|
D:GLU980
|
4.5
|
0.2
|
1.0
|
|
CB
|
D:ASP1027
|
4.5
|
0.5
|
1.0
|
|
N
|
D:SER1028
|
4.5
|
0.6
|
1.0
|
|
N
|
D:ALA1031
|
4.5
|
0.6
|
1.0
|
|
O
|
D:SER1028
|
4.7
|
0.6
|
1.0
|
|
CB
|
D:GLU980
|
4.7
|
0.5
|
1.0
|
|
CG
|
D:LEU1030
|
4.7
|
0.1
|
1.0
|
|
OH
|
D:TYR952
|
4.8
|
1.0
|
1.0
|
|
Calcium binding site 6 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 6 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca2015
b:60.4
occ:1.00
|
O
|
D:ASP1149
|
2.3
|
0.9
|
1.0
|
|
OE1
|
D:GLU1096
|
2.3
|
75.0
|
1.0
|
|
OD2
|
D:ASP1146
|
2.3
|
57.5
|
1.0
|
|
O
|
D:ILE1148
|
2.3
|
79.5
|
1.0
|
|
OD2
|
D:ASP1105
|
2.3
|
74.9
|
1.0
|
|
OD1
|
D:ASP1105
|
2.7
|
78.3
|
1.0
|
|
CG
|
D:ASP1105
|
2.9
|
76.6
|
1.0
|
|
C
|
D:ASP1149
|
3.3
|
0.2
|
1.0
|
|
C
|
D:ILE1148
|
3.4
|
79.7
|
1.0
|
|
CG
|
D:ASP1146
|
3.5
|
58.7
|
1.0
|
|
CD
|
D:GLU1096
|
3.5
|
73.7
|
1.0
|
|
CB
|
D:ASP1149
|
3.7
|
0.3
|
1.0
|
|
CA
|
D:ASP1149
|
3.8
|
0.9
|
1.0
|
|
N
|
D:ASP1149
|
3.9
|
0.1
|
1.0
|
|
O
|
D:ASP1146
|
3.9
|
75.5
|
1.0
|
|
NZ
|
C:LYS159
|
4.0
|
77.6
|
1.0
|
|
N
|
D:ASP1146
|
4.0
|
73.1
|
1.0
|
|
OD1
|
D:ASN1070
|
4.1
|
80.2
|
1.0
|
|
OD1
|
D:ASP1146
|
4.2
|
54.9
|
1.0
|
|
CB
|
D:GLU1096
|
4.3
|
76.4
|
1.0
|
|
CB
|
D:ASP1105
|
4.3
|
70.0
|
1.0
|
|
OE2
|
D:GLU1096
|
4.3
|
72.6
|
1.0
|
|
C
|
D:ASP1146
|
4.4
|
75.5
|
1.0
|
|
N
|
D:THR1150
|
4.5
|
78.3
|
1.0
|
|
N
|
D:ILE1148
|
4.5
|
85.3
|
1.0
|
|
CG
|
D:GLU1096
|
4.5
|
74.4
|
1.0
|
|
CA
|
D:ASP1146
|
4.5
|
73.4
|
1.0
|
|
CA
|
D:ILE1148
|
4.5
|
84.4
|
1.0
|
|
OH
|
D:TYR1068
|
4.6
|
58.9
|
1.0
|
|
CB
|
D:ASP1146
|
4.6
|
65.7
|
1.0
|
|
CB
|
D:SER1145
|
4.9
|
76.6
|
1.0
|
|
C
|
D:SER1145
|
5.0
|
74.0
|
1.0
|
|
CA
|
D:THR1150
|
5.0
|
83.5
|
1.0
|
|
Calcium binding site 7 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 7 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca2016
b:0.0
occ:1.00
|
OE2
|
D:GLU1213
|
2.3
|
0.8
|
1.0
|
|
OD1
|
D:ASP1262
|
2.3
|
0.9
|
1.0
|
|
O
|
D:GLY1264
|
2.3
|
0.7
|
1.0
|
|
OD1
|
D:ASP1221
|
2.3
|
0.5
|
1.0
|
|
O
|
D:GLN1265
|
2.3
|
0.2
|
1.0
|
|
O
|
D:ASP1262
|
2.3
|
0.9
|
1.0
|
|
OD2
|
D:ASP1221
|
2.7
|
0.1
|
1.0
|
|
CG
|
D:ASP1221
|
2.8
|
0.2
|
1.0
|
|
C
|
D:GLY1264
|
3.3
|
0.2
|
1.0
|
|
C
|
D:ASP1262
|
3.3
|
0.5
|
1.0
|
|
C
|
D:GLN1265
|
3.4
|
0.8
|
1.0
|
|
CG
|
D:ASP1262
|
3.4
|
0.9
|
1.0
|
|
CD
|
D:GLU1213
|
3.4
|
0.9
|
1.0
|
|
NE2
|
D:GLN1266
|
3.6
|
0.3
|
1.0
|
|
N
|
D:ASP1262
|
3.7
|
0.0
|
1.0
|
|
O
|
D:GLU1263
|
3.9
|
0.3
|
1.0
|
|
CA
|
D:GLN1265
|
3.9
|
0.7
|
1.0
|
|
CA
|
D:ASP1262
|
3.9
|
0.6
|
1.0
|
|
N
|
D:GLN1265
|
4.0
|
0.1
|
1.0
|
|
CB
|
D:GLN1265
|
4.0
|
0.1
|
1.0
|
|
C
|
D:GLU1263
|
4.1
|
0.1
|
1.0
|
|
OE1
|
D:GLU1213
|
4.1
|
0.7
|
1.0
|
|
OD2
|
D:ASP1262
|
4.2
|
0.5
|
1.0
|
|
CB
|
D:ASP1262
|
4.2
|
0.9
|
1.0
|
|
N
|
D:GLY1264
|
4.3
|
0.2
|
1.0
|
|
CA
|
D:GLY1264
|
4.3
|
0.1
|
1.0
|
|
CB
|
D:ASP1221
|
4.3
|
0.8
|
1.0
|
|
CG
|
D:GLU1213
|
4.4
|
0.4
|
1.0
|
|
CD
|
D:GLN1266
|
4.4
|
0.8
|
1.0
|
|
N
|
D:GLU1263
|
4.4
|
0.2
|
1.0
|
|
C
|
D:THR1261
|
4.5
|
0.5
|
1.0
|
|
N
|
D:GLN1266
|
4.5
|
0.2
|
1.0
|
|
CB
|
D:THR1261
|
4.7
|
0.0
|
1.0
|
|
CA
|
D:THR1261
|
4.8
|
0.6
|
1.0
|
|
CG
|
D:GLN1265
|
4.8
|
0.5
|
1.0
|
|
CA
|
D:GLU1263
|
4.8
|
0.7
|
1.0
|
|
OH
|
D:TYR1185
|
5.0
|
0.6
|
1.0
|
|
Calcium binding site 8 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 8 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca2017
b:79.7
occ:1.00
|
OE2
|
D:GLU1328
|
2.3
|
83.0
|
1.0
|
|
O
|
D:VAL1375
|
2.3
|
93.9
|
1.0
|
|
OD2
|
D:ASP1336
|
2.3
|
91.6
|
1.0
|
|
OD1
|
D:ASP1373
|
2.3
|
91.9
|
1.0
|
|
CG
|
D:ASP1336
|
3.2
|
91.9
|
1.0
|
|
CD
|
D:GLU1328
|
3.3
|
82.4
|
1.0
|
|
OD1
|
D:ASP1336
|
3.5
|
88.1
|
1.0
|
|
C
|
D:VAL1375
|
3.5
|
92.0
|
1.0
|
|
CG
|
D:ASP1373
|
3.6
|
86.6
|
1.0
|
|
CG
|
D:GLU1328
|
3.7
|
91.6
|
1.0
|
|
O
|
D:ASP1373
|
3.8
|
95.4
|
1.0
|
|
OG1
|
D:THR1372
|
3.9
|
0.5
|
1.0
|
|
N
|
D:VAL1375
|
4.0
|
93.8
|
1.0
|
|
CE1
|
D:TYR1300
|
4.1
|
63.8
|
1.0
|
|
OH
|
D:TYR1300
|
4.2
|
62.0
|
1.0
|
|
N
|
D:ASP1373
|
4.2
|
99.9
|
1.0
|
|
C
|
D:ASP1373
|
4.2
|
92.4
|
1.0
|
|
OD2
|
D:ASP1373
|
4.3
|
78.9
|
1.0
|
|
OE2
|
D:GLU1379
|
4.4
|
72.3
|
1.0
|
|
CA
|
D:VAL1375
|
4.4
|
90.0
|
1.0
|
|
N
|
D:GLY1376
|
4.4
|
93.7
|
1.0
|
|
CA
|
D:GLY1376
|
4.4
|
96.1
|
1.0
|
|
OE1
|
D:GLU1328
|
4.4
|
74.2
|
1.0
|
|
CB
|
D:ASP1336
|
4.5
|
97.4
|
1.0
|
|
CB
|
D:ASP1373
|
4.6
|
87.5
|
1.0
|
|
CA
|
D:ASP1373
|
4.6
|
93.1
|
1.0
|
|
CZ
|
D:TYR1300
|
4.6
|
66.8
|
1.0
|
|
CG2
|
D:VAL1375
|
4.8
|
85.7
|
1.0
|
|
NH1
|
C:ARG323
|
4.9
|
74.6
|
1.0
|
|
N
|
D:GLY1374
|
4.9
|
76.9
|
1.0
|
|
CB
|
D:GLU1328
|
5.0
|
90.1
|
1.0
|
|
Calcium binding site 9 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 9 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca2014
b:0.6
occ:1.00
|
O
|
F:ASP1029
|
2.3
|
0.3
|
1.0
|
|
OE1
|
F:GLU980
|
2.3
|
0.9
|
1.0
|
|
OD1
|
F:ASP988
|
2.3
|
0.3
|
1.0
|
|
OD1
|
F:ASP1027
|
2.3
|
0.6
|
1.0
|
|
O
|
F:LEU1030
|
2.3
|
0.9
|
1.0
|
|
O
|
F:ASP1027
|
3.1
|
0.2
|
1.0
|
|
C
|
F:ASP1029
|
3.2
|
0.6
|
1.0
|
|
C
|
F:LEU1030
|
3.3
|
0.5
|
1.0
|
|
CD
|
F:GLU980
|
3.4
|
0.2
|
1.0
|
|
CG
|
F:ASP988
|
3.5
|
0.6
|
1.0
|
|
CG
|
F:ASP1027
|
3.5
|
0.6
|
1.0
|
|
N
|
F:LEU1030
|
3.7
|
0.5
|
1.0
|
|
CA
|
F:LEU1030
|
3.7
|
0.2
|
1.0
|
|
C
|
F:ASP1027
|
3.8
|
0.9
|
1.0
|
|
CB
|
F:LEU1030
|
3.8
|
0.4
|
1.0
|
|
OE2
|
F:GLU980
|
4.1
|
0.8
|
1.0
|
|
N
|
F:ASP1027
|
4.1
|
0.4
|
1.0
|
|
N
|
F:ASP1029
|
4.2
|
0.1
|
1.0
|
|
OD2
|
F:ASP988
|
4.2
|
0.5
|
1.0
|
|
CA
|
F:ASP1029
|
4.3
|
0.6
|
1.0
|
|
OD2
|
F:ASP1027
|
4.3
|
0.0
|
1.0
|
|
CA
|
F:ASP1027
|
4.3
|
0.1
|
1.0
|
|
CB
|
F:ASP988
|
4.4
|
0.5
|
1.0
|
|
C
|
F:SER1028
|
4.4
|
0.4
|
1.0
|
|
CG
|
F:GLU980
|
4.5
|
0.5
|
1.0
|
|
CB
|
F:ASP1027
|
4.5
|
0.4
|
1.0
|
|
N
|
F:SER1028
|
4.5
|
0.0
|
1.0
|
|
N
|
F:ALA1031
|
4.5
|
1.0
|
1.0
|
|
O
|
F:SER1028
|
4.7
|
0.6
|
1.0
|
|
CB
|
F:GLU980
|
4.7
|
0.9
|
1.0
|
|
CG
|
F:LEU1030
|
4.7
|
0.5
|
1.0
|
|
OH
|
F:TYR952
|
4.8
|
0.9
|
1.0
|
|
Calcium binding site 10 out
of 12 in 3kq4
Go back to
Calcium Binding Sites List in 3kq4
Calcium binding site 10 out
of 12 in the Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure of Intrinsic Factor-Cobalamin Bound to Its Receptor Cubilin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca2015
b:58.4
occ:1.00
|
O
|
F:ASP1149
|
2.3
|
0.5
|
1.0
|
|
OE1
|
F:GLU1096
|
2.3
|
77.3
|
1.0
|
|
OD2
|
F:ASP1146
|
2.3
|
61.2
|
1.0
|
|
O
|
F:ILE1148
|
2.3
|
74.3
|
1.0
|
|
OD2
|
F:ASP1105
|
2.3
|
81.9
|
1.0
|
|
OD1
|
F:ASP1105
|
2.7
|
89.5
|
1.0
|
|
CG
|
F:ASP1105
|
2.9
|
84.4
|
1.0
|
|
C
|
F:ASP1149
|
3.3
|
0.2
|
1.0
|
|
C
|
F:ILE1148
|
3.4
|
75.4
|
1.0
|
|
CG
|
F:ASP1146
|
3.5
|
64.0
|
1.0
|
|
CD
|
F:GLU1096
|
3.5
|
73.4
|
1.0
|
|
CB
|
F:ASP1149
|
3.7
|
1.0
|
1.0
|
|
CA
|
F:ASP1149
|
3.8
|
0.7
|
1.0
|
|
N
|
F:ASP1149
|
3.9
|
0.6
|
1.0
|
|
O
|
F:ASP1146
|
3.9
|
87.0
|
1.0
|
|
NZ
|
E:LYS159
|
4.0
|
68.9
|
1.0
|
|
N
|
F:ASP1146
|
4.0
|
82.3
|
1.0
|
|
OD1
|
F:ASN1070
|
4.1
|
69.0
|
1.0
|
|
OD1
|
F:ASP1146
|
4.2
|
58.4
|
1.0
|
|
CB
|
F:GLU1096
|
4.3
|
71.4
|
1.0
|
|
CB
|
F:ASP1105
|
4.3
|
74.7
|
1.0
|
|
OE2
|
F:GLU1096
|
4.3
|
72.9
|
1.0
|
|
C
|
F:ASP1146
|
4.4
|
88.1
|
1.0
|
|
N
|
F:THR1150
|
4.5
|
78.4
|
1.0
|
|
N
|
F:ILE1148
|
4.5
|
86.9
|
1.0
|
|
CG
|
F:GLU1096
|
4.5
|
70.0
|
1.0
|
|
CA
|
F:ASP1146
|
4.5
|
85.1
|
1.0
|
|
CA
|
F:ILE1148
|
4.5
|
83.5
|
1.0
|
|
OH
|
F:TYR1068
|
4.6
|
54.2
|
1.0
|
|
CB
|
F:ASP1146
|
4.6
|
75.3
|
1.0
|
|
CB
|
F:SER1145
|
4.9
|
70.1
|
1.0
|
|
C
|
F:SER1145
|
5.0
|
71.7
|
1.0
|
|
CA
|
F:THR1150
|
5.0
|
83.2
|
1.0
|
|
Reference:
C.B.Andersen,
M.Madsen,
T.Storm,
S.K.Moestrup,
G.R.Andersen.
Structural Basis For Receptor Recognition of Vitamin-B(12)-Intrinsic Factor Complexes. Nature V. 464 445 2010.
ISSN: ISSN 0028-0836
PubMed: 20237569
DOI: 10.1038/NATURE08874
Page generated: Sat Jul 13 12:35:15 2024
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