Calcium in PDB 8em4: Cryo-Em Structure of LRP2 at pH 7.5
Calcium Binding Sites:
Calcium binding site 1 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 1 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4745
b:30.0
occ:1.00
|
OD2
|
A:ASP52
|
2.3
|
74.2
|
1.0
|
O
|
A:THR50
|
2.3
|
72.2
|
1.0
|
O
|
A:TRP45
|
2.3
|
77.3
|
1.0
|
OD1
|
A:ASP48
|
2.3
|
78.3
|
1.0
|
OD2
|
A:ASP58
|
2.4
|
80.8
|
1.0
|
OE2
|
A:GLU59
|
2.8
|
81.8
|
1.0
|
CG
|
A:ASP52
|
3.3
|
74.2
|
1.0
|
CG
|
A:ASP48
|
3.4
|
78.3
|
1.0
|
C
|
A:THR50
|
3.4
|
72.2
|
1.0
|
CD
|
A:GLU59
|
3.5
|
81.8
|
1.0
|
C
|
A:TRP45
|
3.5
|
77.3
|
1.0
|
O
|
A:ARG46
|
3.6
|
81.9
|
1.0
|
CG
|
A:ASP58
|
3.6
|
80.8
|
1.0
|
CG
|
A:GLU59
|
3.8
|
81.8
|
1.0
|
OD2
|
A:ASP48
|
3.9
|
78.3
|
1.0
|
OG1
|
A:THR50
|
3.9
|
72.2
|
1.0
|
NZ
|
B:LYS4337
|
4.0
|
65.7
|
1.0
|
N
|
A:ASP52
|
4.0
|
74.2
|
1.0
|
C
|
A:ARG46
|
4.0
|
81.9
|
1.0
|
N
|
A:ASP48
|
4.1
|
78.3
|
1.0
|
OD1
|
A:ASP52
|
4.1
|
74.2
|
1.0
|
N
|
A:THR50
|
4.1
|
72.2
|
1.0
|
CB
|
A:ASP52
|
4.2
|
74.2
|
1.0
|
CB
|
A:ASP58
|
4.3
|
80.8
|
1.0
|
CA
|
A:THR50
|
4.3
|
72.2
|
1.0
|
CA
|
A:TRP45
|
4.4
|
77.3
|
1.0
|
N
|
A:ARG51
|
4.4
|
71.3
|
1.0
|
OE1
|
A:GLU59
|
4.4
|
81.8
|
1.0
|
N
|
A:ARG46
|
4.5
|
81.9
|
1.0
|
CA
|
A:ARG51
|
4.5
|
71.3
|
1.0
|
CB
|
A:TRP45
|
4.5
|
77.3
|
1.0
|
CA
|
A:ARG46
|
4.5
|
81.9
|
1.0
|
CB
|
A:ASP48
|
4.6
|
78.3
|
1.0
|
OD1
|
A:ASP58
|
4.6
|
80.8
|
1.0
|
CB
|
A:THR50
|
4.6
|
72.2
|
1.0
|
N
|
A:CYS47
|
4.6
|
83.2
|
1.0
|
C
|
A:ARG51
|
4.7
|
71.3
|
1.0
|
CA
|
A:ASP48
|
4.7
|
78.3
|
1.0
|
CA
|
A:ASP52
|
4.8
|
74.2
|
1.0
|
CA
|
A:CYS47
|
4.9
|
83.2
|
1.0
|
N
|
A:GLY49
|
4.9
|
77.0
|
1.0
|
C
|
A:ASP48
|
4.9
|
78.3
|
1.0
|
C
|
A:CYS47
|
5.0
|
83.2
|
1.0
|
|
Calcium binding site 2 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 2 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4746
b:30.0
occ:1.00
|
O
|
A:ASP90
|
2.3
|
58.7
|
1.0
|
OD1
|
A:ASP88
|
2.3
|
64.3
|
1.0
|
O
|
A:TRP85
|
2.3
|
59.2
|
1.0
|
OD2
|
A:ASP92
|
2.3
|
59.0
|
1.0
|
OE2
|
A:GLU99
|
2.4
|
65.3
|
1.0
|
OD2
|
A:ASP98
|
2.7
|
63.0
|
1.0
|
OD1
|
A:ASP98
|
2.8
|
63.0
|
1.0
|
CG
|
A:ASP98
|
3.1
|
63.0
|
1.0
|
CG
|
A:ASP92
|
3.1
|
59.0
|
1.0
|
C
|
A:ASP90
|
3.4
|
58.7
|
1.0
|
CD
|
A:GLU99
|
3.5
|
65.3
|
1.0
|
CG
|
A:ASP88
|
3.5
|
64.3
|
1.0
|
C
|
A:TRP85
|
3.5
|
59.2
|
1.0
|
OD1
|
A:ASP92
|
3.7
|
59.0
|
1.0
|
N
|
A:ASP90
|
3.8
|
58.7
|
1.0
|
CA
|
A:ASP90
|
3.9
|
58.7
|
1.0
|
NZ
|
B:LYS4027
|
4.0
|
85.6
|
1.0
|
CG
|
A:GLU99
|
4.0
|
65.3
|
1.0
|
CB
|
A:ASP90
|
4.0
|
30.0
|
1.0
|
N
|
A:ASP92
|
4.0
|
59.0
|
1.0
|
CB
|
A:ASP92
|
4.0
|
59.0
|
1.0
|
N
|
A:ASP88
|
4.1
|
64.3
|
1.0
|
OD2
|
A:ASP88
|
4.1
|
64.3
|
1.0
|
CA
|
A:TRP85
|
4.2
|
59.2
|
1.0
|
CB
|
A:TRP85
|
4.4
|
59.2
|
1.0
|
C
|
A:VAL86
|
4.4
|
65.2
|
1.0
|
N
|
A:LYS91
|
4.5
|
59.8
|
1.0
|
OE1
|
A:GLU99
|
4.5
|
65.3
|
1.0
|
N
|
A:VAL86
|
4.5
|
65.2
|
1.0
|
O
|
A:VAL86
|
4.6
|
65.2
|
1.0
|
CB
|
A:ASP98
|
4.6
|
63.0
|
1.0
|
CB
|
A:ASP88
|
4.6
|
64.3
|
1.0
|
N
|
A:CYS87
|
4.6
|
71.9
|
1.0
|
CA
|
A:VAL86
|
4.6
|
65.2
|
1.0
|
CA
|
A:ASP88
|
4.7
|
64.3
|
1.0
|
C
|
A:ASP88
|
4.7
|
64.3
|
1.0
|
CA
|
A:ASP92
|
4.7
|
59.0
|
1.0
|
N
|
A:GLN89
|
4.8
|
63.5
|
1.0
|
CA
|
A:LYS91
|
4.9
|
59.8
|
1.0
|
N
|
A:GLU99
|
4.9
|
65.3
|
1.0
|
C
|
A:LYS91
|
4.9
|
59.8
|
1.0
|
CA
|
A:CYS87
|
5.0
|
71.9
|
1.0
|
C
|
A:CYS87
|
5.0
|
71.9
|
1.0
|
|
Calcium binding site 3 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 3 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4747
b:30.0
occ:1.00
|
O
|
A:ASP244
|
2.3
|
70.6
|
1.0
|
O
|
A:TRP239
|
2.3
|
66.9
|
1.0
|
OD1
|
A:ASP242
|
2.3
|
70.2
|
1.0
|
OD1
|
A:ASP246
|
2.5
|
70.2
|
1.0
|
OD2
|
A:ASP252
|
2.6
|
69.6
|
1.0
|
OE2
|
A:GLU253
|
2.6
|
70.0
|
1.0
|
CB
|
A:ASP252
|
3.2
|
69.6
|
1.0
|
C
|
A:ASP244
|
3.3
|
70.6
|
1.0
|
CG
|
A:ASP252
|
3.3
|
69.6
|
1.0
|
CG
|
A:ASP242
|
3.3
|
70.2
|
1.0
|
CG
|
A:ASP246
|
3.5
|
70.2
|
1.0
|
C
|
A:TRP239
|
3.5
|
66.9
|
1.0
|
N
|
A:ASP244
|
3.6
|
70.6
|
1.0
|
CD
|
A:GLU253
|
3.8
|
70.0
|
1.0
|
OD2
|
A:ASP242
|
3.8
|
70.2
|
1.0
|
CA
|
A:ASP244
|
3.8
|
70.6
|
1.0
|
N
|
A:ASP246
|
4.0
|
70.2
|
1.0
|
O
|
A:VAL240
|
4.1
|
64.8
|
1.0
|
N
|
A:ASP242
|
4.1
|
70.2
|
1.0
|
C
|
A:VAL240
|
4.1
|
64.8
|
1.0
|
CB
|
A:ASP244
|
4.1
|
70.6
|
1.0
|
CB
|
A:ASP246
|
4.1
|
70.2
|
1.0
|
CG
|
A:GLU253
|
4.2
|
70.0
|
1.0
|
N
|
A:ASP245
|
4.4
|
72.0
|
1.0
|
N
|
A:GLY243
|
4.4
|
70.5
|
1.0
|
N
|
A:VAL240
|
4.4
|
64.8
|
1.0
|
CA
|
A:TRP239
|
4.4
|
66.9
|
1.0
|
CA
|
A:VAL240
|
4.4
|
64.8
|
1.0
|
OD2
|
A:ASP246
|
4.5
|
70.2
|
1.0
|
N
|
A:CYS241
|
4.5
|
69.0
|
1.0
|
OD1
|
A:ASP252
|
4.5
|
69.6
|
1.0
|
CB
|
A:TRP239
|
4.6
|
66.9
|
1.0
|
CB
|
A:ASP242
|
4.6
|
70.2
|
1.0
|
CA
|
A:CA4778
|
4.7
|
30.0
|
1.0
|
CA
|
A:ASP252
|
4.7
|
69.6
|
1.0
|
CA
|
A:ASP246
|
4.7
|
70.2
|
1.0
|
CA
|
A:ASP242
|
4.7
|
70.2
|
1.0
|
C
|
A:GLY243
|
4.7
|
70.5
|
1.0
|
OE1
|
A:GLU253
|
4.8
|
70.0
|
1.0
|
CA
|
A:ASP245
|
4.8
|
72.0
|
1.0
|
C
|
A:ASP242
|
4.9
|
70.2
|
1.0
|
CA
|
A:CYS241
|
4.9
|
69.0
|
1.0
|
C
|
A:ASP245
|
4.9
|
72.0
|
1.0
|
C
|
A:CYS241
|
4.9
|
69.0
|
1.0
|
|
Calcium binding site 4 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 4 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4748
b:30.0
occ:1.00
|
OD2
|
A:ASP296
|
2.3
|
63.0
|
1.0
|
OD1
|
A:ASP286
|
2.3
|
64.3
|
1.0
|
O
|
A:LYS283
|
2.4
|
59.2
|
1.0
|
O
|
A:VAL288
|
2.4
|
58.7
|
1.0
|
OE2
|
A:GLU297
|
2.4
|
65.3
|
1.0
|
O
|
A:VAL284
|
2.5
|
65.2
|
1.0
|
OD2
|
A:ASP290
|
2.6
|
59.0
|
1.0
|
C
|
A:VAL284
|
3.2
|
65.2
|
1.0
|
CG
|
A:ASP286
|
3.4
|
64.3
|
1.0
|
CD
|
A:GLU297
|
3.4
|
65.3
|
1.0
|
CG
|
A:ASP290
|
3.4
|
59.0
|
1.0
|
CG
|
A:ASP296
|
3.5
|
63.0
|
1.0
|
C
|
A:LYS283
|
3.5
|
59.2
|
1.0
|
C
|
A:VAL288
|
3.5
|
58.7
|
1.0
|
N
|
A:ASP286
|
3.7
|
64.3
|
1.0
|
CA
|
A:VAL284
|
3.7
|
65.2
|
1.0
|
N
|
A:VAL288
|
3.8
|
58.7
|
1.0
|
CG
|
A:GLU297
|
3.8
|
65.3
|
1.0
|
N
|
A:ASP290
|
4.0
|
59.0
|
1.0
|
N
|
A:VAL284
|
4.1
|
65.2
|
1.0
|
OD2
|
A:ASP286
|
4.1
|
64.3
|
1.0
|
N
|
A:CYS285
|
4.1
|
71.9
|
1.0
|
N
|
A:GLY287
|
4.1
|
63.5
|
1.0
|
OD1
|
A:ASP290
|
4.1
|
59.0
|
1.0
|
CB
|
A:ASP290
|
4.2
|
59.0
|
1.0
|
CA
|
A:VAL288
|
4.2
|
58.7
|
1.0
|
CB
|
A:ASP296
|
4.3
|
63.0
|
1.0
|
CB
|
A:ASP286
|
4.3
|
64.3
|
1.0
|
OD1
|
A:ASP296
|
4.4
|
63.0
|
1.0
|
CA
|
A:ASP286
|
4.4
|
64.3
|
1.0
|
OE1
|
A:GLU297
|
4.5
|
65.3
|
1.0
|
N
|
A:PRO289
|
4.5
|
59.8
|
1.0
|
CA
|
A:CYS285
|
4.5
|
71.9
|
1.0
|
C
|
A:CYS285
|
4.5
|
71.9
|
1.0
|
CA
|
A:PRO289
|
4.6
|
59.8
|
1.0
|
C
|
A:ASP286
|
4.7
|
64.3
|
1.0
|
CA
|
A:LYS283
|
4.7
|
59.2
|
1.0
|
C
|
A:PRO289
|
4.7
|
59.8
|
1.0
|
CA
|
A:ASP290
|
4.8
|
59.0
|
1.0
|
C
|
A:GLY287
|
4.8
|
63.5
|
1.0
|
CB
|
A:VAL288
|
4.8
|
30.0
|
1.0
|
CA
|
A:GLY287
|
5.0
|
63.5
|
1.0
|
CB
|
A:LYS283
|
5.0
|
30.0
|
1.0
|
|
Calcium binding site 5 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 5 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4749
b:30.0
occ:1.00
|
OD2
|
A:ASP1055
|
2.2
|
67.7
|
1.0
|
OD1
|
A:ASP1045
|
2.2
|
71.6
|
1.0
|
O
|
A:PHE1042
|
2.3
|
65.6
|
1.0
|
O
|
A:VAL1047
|
2.3
|
69.6
|
1.0
|
OD2
|
A:ASP1049
|
2.3
|
66.5
|
1.0
|
OE2
|
A:GLU1056
|
2.4
|
69.4
|
1.0
|
CG
|
A:ASP1045
|
3.3
|
71.6
|
1.0
|
CG
|
A:ASP1055
|
3.4
|
67.7
|
1.0
|
CG
|
A:ASP1049
|
3.4
|
66.5
|
1.0
|
C
|
A:VAL1047
|
3.5
|
69.6
|
1.0
|
C
|
A:PHE1042
|
3.5
|
65.6
|
1.0
|
CD
|
A:GLU1056
|
3.5
|
69.4
|
1.0
|
N
|
A:VAL1047
|
3.8
|
69.6
|
1.0
|
N
|
A:ASP1045
|
3.8
|
71.6
|
1.0
|
OD2
|
A:ASP1045
|
3.9
|
71.6
|
1.0
|
N
|
A:ASP1049
|
3.9
|
66.5
|
1.0
|
CG
|
A:GLU1056
|
4.0
|
69.4
|
1.0
|
CB
|
A:ASP1049
|
4.0
|
66.5
|
1.0
|
O
|
A:ARG1043
|
4.0
|
69.2
|
1.0
|
OD1
|
A:ASP1055
|
4.1
|
67.7
|
1.0
|
C
|
A:ARG1043
|
4.2
|
69.2
|
1.0
|
CA
|
A:PHE1042
|
4.2
|
65.6
|
1.0
|
CA
|
A:VAL1047
|
4.2
|
69.6
|
1.0
|
N
|
A:GLY1046
|
4.3
|
71.8
|
1.0
|
CB
|
A:PHE1042
|
4.3
|
65.6
|
1.0
|
CB
|
A:ASP1055
|
4.3
|
67.7
|
1.0
|
CG2
|
A:VAL1047
|
4.3
|
69.6
|
1.0
|
CB
|
A:ASP1045
|
4.3
|
71.6
|
1.0
|
OD1
|
A:ASP1049
|
4.3
|
66.5
|
1.0
|
N
|
A:CYS1044
|
4.5
|
72.6
|
1.0
|
N
|
A:ARG1043
|
4.5
|
69.2
|
1.0
|
N
|
A:ASP1048
|
4.5
|
66.8
|
1.0
|
CA
|
A:ASP1045
|
4.5
|
71.6
|
1.0
|
OE1
|
A:GLU1056
|
4.6
|
69.4
|
1.0
|
CA
|
A:ASP1049
|
4.7
|
66.5
|
1.0
|
CA
|
A:CYS1044
|
4.7
|
72.6
|
1.0
|
CA
|
A:ARG1043
|
4.7
|
69.2
|
1.0
|
C
|
A:CYS1044
|
4.7
|
72.6
|
1.0
|
C
|
A:ASP1045
|
4.8
|
71.6
|
1.0
|
CA
|
A:ASP1048
|
4.8
|
66.8
|
1.0
|
C
|
A:GLY1046
|
4.9
|
71.8
|
1.0
|
C
|
A:ASP1048
|
4.9
|
66.8
|
1.0
|
CB
|
A:VAL1047
|
4.9
|
69.6
|
1.0
|
|
Calcium binding site 6 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 6 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4750
b:30.0
occ:1.00
|
OD2
|
A:ASP1091
|
2.2
|
79.2
|
1.0
|
OD1
|
A:ASP1087
|
2.2
|
79.2
|
1.0
|
OE2
|
A:GLU1098
|
2.3
|
88.4
|
1.0
|
OD2
|
A:ASP1097
|
2.3
|
85.3
|
1.0
|
O
|
A:GLN1089
|
2.3
|
77.1
|
1.0
|
O
|
A:TRP1084
|
2.6
|
76.0
|
1.0
|
CG
|
A:ASP1097
|
3.3
|
85.3
|
1.0
|
CG
|
A:ASP1091
|
3.3
|
79.2
|
1.0
|
CG
|
A:ASP1087
|
3.4
|
79.2
|
1.0
|
CD
|
A:GLU1098
|
3.4
|
88.4
|
1.0
|
C
|
A:GLN1089
|
3.4
|
77.1
|
1.0
|
CB
|
A:ASP1097
|
3.8
|
85.3
|
1.0
|
C
|
A:TRP1084
|
3.8
|
76.0
|
1.0
|
CG
|
A:GLU1098
|
3.9
|
88.4
|
1.0
|
N
|
A:ASP1087
|
3.9
|
79.2
|
1.0
|
OD2
|
A:ASP1087
|
3.9
|
79.2
|
1.0
|
N
|
A:ASP1091
|
4.0
|
79.2
|
1.0
|
O
|
A:ASP1087
|
4.1
|
79.2
|
1.0
|
CB
|
A:ASP1091
|
4.1
|
79.2
|
1.0
|
OD1
|
A:ASP1091
|
4.2
|
79.2
|
1.0
|
CA
|
A:GLN1089
|
4.3
|
77.1
|
1.0
|
OD1
|
A:ASP1097
|
4.4
|
85.3
|
1.0
|
N
|
A:ASN1090
|
4.4
|
79.7
|
1.0
|
N
|
A:GLN1089
|
4.4
|
77.1
|
1.0
|
CA
|
A:TRP1084
|
4.4
|
76.0
|
1.0
|
OE1
|
A:GLU1098
|
4.4
|
88.4
|
1.0
|
CB
|
A:GLN1089
|
4.4
|
77.1
|
1.0
|
C
|
A:ASP1087
|
4.4
|
79.2
|
1.0
|
CA
|
A:ASP1087
|
4.5
|
79.2
|
1.0
|
CB
|
A:TRP1084
|
4.5
|
76.0
|
1.0
|
C
|
A:ARG1085
|
4.5
|
81.8
|
1.0
|
CB
|
A:ASP1087
|
4.5
|
79.2
|
1.0
|
CA
|
A:ASN1090
|
4.5
|
79.7
|
1.0
|
NH1
|
A:ARG422
|
4.5
|
71.2
|
1.0
|
O
|
A:ARG1085
|
4.6
|
81.8
|
1.0
|
N
|
A:CYS1086
|
4.6
|
83.7
|
1.0
|
C
|
A:CYS1086
|
4.7
|
83.7
|
1.0
|
CA
|
A:ASP1091
|
4.7
|
79.2
|
1.0
|
CA
|
A:CYS1086
|
4.7
|
83.7
|
1.0
|
C
|
A:ASN1090
|
4.8
|
79.7
|
1.0
|
N
|
A:ARG1085
|
4.8
|
81.8
|
1.0
|
|
Calcium binding site 7 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 7 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4751
b:30.0
occ:1.00
|
OD1
|
A:ASP1130
|
2.2
|
76.8
|
1.0
|
OD2
|
A:ASP1140
|
2.2
|
78.1
|
1.0
|
OD2
|
A:ASP1134
|
2.3
|
81.5
|
1.0
|
OE2
|
A:GLU1141
|
2.4
|
79.0
|
1.0
|
O
|
A:TRP1127
|
2.5
|
83.8
|
1.0
|
O
|
A:ASP1132
|
2.5
|
74.1
|
1.0
|
O
|
A:VAL1128
|
2.6
|
83.5
|
1.0
|
CG
|
A:ASP1130
|
3.1
|
76.8
|
1.0
|
CG
|
A:ASP1134
|
3.3
|
81.5
|
1.0
|
CG
|
A:ASP1140
|
3.3
|
78.1
|
1.0
|
C
|
A:VAL1128
|
3.4
|
83.5
|
1.0
|
CD
|
A:GLU1141
|
3.5
|
79.0
|
1.0
|
C
|
A:TRP1127
|
3.6
|
83.8
|
1.0
|
OD2
|
A:ASP1130
|
3.7
|
76.8
|
1.0
|
C
|
A:ASP1132
|
3.7
|
74.1
|
1.0
|
N
|
A:ASP1130
|
3.8
|
76.8
|
1.0
|
CA
|
A:VAL1128
|
3.9
|
83.5
|
1.0
|
CG
|
A:GLU1141
|
4.0
|
79.0
|
1.0
|
CB
|
A:ASP1134
|
4.0
|
81.5
|
1.0
|
OD1
|
A:ASP1134
|
4.1
|
81.5
|
1.0
|
CB
|
A:ASP1130
|
4.1
|
76.8
|
1.0
|
CB
|
A:ASP1140
|
4.1
|
78.1
|
1.0
|
N
|
A:VAL1128
|
4.2
|
83.5
|
1.0
|
N
|
A:ASP1132
|
4.2
|
74.1
|
1.0
|
OD1
|
A:ASP1140
|
4.2
|
78.1
|
1.0
|
N
|
A:ASP1134
|
4.2
|
81.5
|
1.0
|
CA
|
A:ASP1130
|
4.4
|
76.8
|
1.0
|
N
|
A:CYS1129
|
4.4
|
80.5
|
1.0
|
CA
|
A:ASP1132
|
4.5
|
74.1
|
1.0
|
OE1
|
A:GLU1141
|
4.5
|
79.0
|
1.0
|
C
|
A:ASP1130
|
4.6
|
76.8
|
1.0
|
N
|
A:THR1131
|
4.6
|
70.8
|
1.0
|
CA
|
A:TRP1127
|
4.7
|
83.8
|
1.0
|
CB
|
A:TRP1127
|
4.7
|
83.8
|
1.0
|
N
|
A:ASN1133
|
4.8
|
76.0
|
1.0
|
C
|
A:CYS1129
|
4.8
|
80.5
|
1.0
|
CA
|
A:ASP1134
|
4.8
|
81.5
|
1.0
|
CA
|
A:CYS1129
|
4.8
|
80.5
|
1.0
|
CB
|
A:ASP1132
|
5.0
|
74.1
|
1.0
|
|
Calcium binding site 8 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 8 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4752
b:30.0
occ:1.00
|
OD2
|
A:ASP1174
|
2.3
|
73.5
|
1.0
|
O
|
A:ASP1172
|
2.3
|
76.5
|
1.0
|
OE2
|
A:GLU1181
|
2.4
|
84.0
|
1.0
|
O
|
A:TYR1167
|
2.4
|
79.9
|
1.0
|
OD2
|
A:ASP1170
|
2.4
|
78.8
|
1.0
|
OD2
|
A:ASP1180
|
2.6
|
79.5
|
1.0
|
OE1
|
A:GLU1181
|
2.6
|
84.0
|
1.0
|
CD
|
A:GLU1181
|
2.8
|
84.0
|
1.0
|
CG
|
A:ASP1170
|
3.3
|
78.8
|
1.0
|
CG
|
A:ASP1174
|
3.3
|
73.5
|
1.0
|
C
|
A:TYR1167
|
3.5
|
79.9
|
1.0
|
C
|
A:ASP1172
|
3.5
|
76.5
|
1.0
|
CG
|
A:ASP1180
|
3.6
|
79.5
|
1.0
|
OD1
|
A:ASP1170
|
3.6
|
78.8
|
1.0
|
CB
|
A:ASP1180
|
3.9
|
79.5
|
1.0
|
CB
|
A:ASP1174
|
4.0
|
73.5
|
1.0
|
N
|
A:ASP1172
|
4.1
|
76.5
|
1.0
|
N
|
A:ASP1170
|
4.1
|
78.8
|
1.0
|
N
|
A:ASP1174
|
4.1
|
73.5
|
1.0
|
CA
|
A:TYR1167
|
4.1
|
79.9
|
1.0
|
OD1
|
A:ASP1174
|
4.2
|
73.5
|
1.0
|
CA
|
A:ASP1172
|
4.2
|
76.5
|
1.0
|
CG
|
A:GLU1181
|
4.3
|
84.0
|
1.0
|
CB
|
A:TYR1167
|
4.4
|
79.9
|
1.0
|
CB
|
A:ASP1170
|
4.5
|
78.8
|
1.0
|
C
|
A:VAL1168
|
4.5
|
80.1
|
1.0
|
CB
|
A:ASP1172
|
4.5
|
76.5
|
1.0
|
N
|
A:GLY1171
|
4.5
|
77.9
|
1.0
|
O
|
A:VAL1168
|
4.5
|
80.1
|
1.0
|
N
|
A:LYS1173
|
4.6
|
74.5
|
1.0
|
N
|
A:VAL1168
|
4.6
|
80.1
|
1.0
|
N
|
A:CYS1169
|
4.6
|
80.0
|
1.0
|
OD1
|
A:ASP1180
|
4.7
|
79.5
|
1.0
|
CA
|
A:ASP1174
|
4.7
|
73.5
|
1.0
|
CA
|
A:CYS1169
|
4.7
|
80.0
|
1.0
|
CA
|
A:ASP1170
|
4.8
|
78.8
|
1.0
|
CA
|
A:LYS1173
|
4.8
|
74.5
|
1.0
|
C
|
A:CYS1169
|
4.9
|
80.0
|
1.0
|
C
|
A:LYS1173
|
4.9
|
74.5
|
1.0
|
CA
|
A:VAL1168
|
4.9
|
80.1
|
1.0
|
|
Calcium binding site 9 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 9 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4753
b:30.0
occ:1.00
|
OD2
|
A:ASP1213
|
2.2
|
70.5
|
1.0
|
OD1
|
A:ASP1209
|
2.2
|
66.7
|
1.0
|
OE2
|
A:GLU1220
|
2.2
|
76.0
|
1.0
|
OD2
|
A:ASP1219
|
2.2
|
72.4
|
1.0
|
O
|
A:VAL1211
|
2.3
|
62.4
|
1.0
|
O
|
A:TYR1206
|
2.3
|
70.4
|
1.0
|
CG
|
A:ASP1213
|
3.2
|
70.5
|
1.0
|
CG
|
A:ASP1209
|
3.2
|
66.7
|
1.0
|
CD
|
A:GLU1220
|
3.2
|
76.0
|
1.0
|
CG
|
A:ASP1219
|
3.4
|
72.4
|
1.0
|
C
|
A:VAL1211
|
3.5
|
62.4
|
1.0
|
C
|
A:TYR1206
|
3.5
|
70.4
|
1.0
|
OD2
|
A:ASP1209
|
3.6
|
66.7
|
1.0
|
CG
|
A:GLU1220
|
3.7
|
76.0
|
1.0
|
CB
|
A:ASP1213
|
3.9
|
70.5
|
1.0
|
OD1
|
A:ASP1213
|
4.0
|
70.5
|
1.0
|
N
|
A:ASP1213
|
4.0
|
70.5
|
1.0
|
N
|
A:VAL1211
|
4.1
|
62.4
|
1.0
|
CB
|
A:ASP1219
|
4.2
|
72.4
|
1.0
|
N
|
A:ASP1209
|
4.2
|
66.7
|
1.0
|
OE1
|
A:GLU1220
|
4.2
|
76.0
|
1.0
|
OD1
|
A:ASP1219
|
4.3
|
72.4
|
1.0
|
CA
|
A:VAL1211
|
4.3
|
62.4
|
1.0
|
CA
|
A:TYR1206
|
4.3
|
70.4
|
1.0
|
CB
|
A:ASP1209
|
4.4
|
66.7
|
1.0
|
N
|
A:ARG1207
|
4.4
|
73.0
|
1.0
|
N
|
A:CYS1208
|
4.4
|
72.4
|
1.0
|
CB
|
A:TYR1206
|
4.5
|
70.4
|
1.0
|
N
|
A:TYR1212
|
4.5
|
68.7
|
1.0
|
CA
|
A:ARG1207
|
4.5
|
73.0
|
1.0
|
NH2
|
A:ARG931
|
4.6
|
55.0
|
1.0
|
CA
|
A:ASP1213
|
4.6
|
70.5
|
1.0
|
CB
|
A:VAL1211
|
4.6
|
62.4
|
1.0
|
CA
|
A:ASP1209
|
4.7
|
66.7
|
1.0
|
O
|
A:ASP1219
|
4.7
|
72.4
|
1.0
|
CA
|
A:TYR1212
|
4.7
|
68.7
|
1.0
|
C
|
A:ARG1207
|
4.7
|
73.0
|
1.0
|
C
|
A:TYR1212
|
4.8
|
68.7
|
1.0
|
C
|
A:ASP1219
|
4.8
|
72.4
|
1.0
|
N
|
A:GLY1210
|
4.8
|
63.8
|
1.0
|
C
|
A:ASP1209
|
4.9
|
66.7
|
1.0
|
|
Calcium binding site 10 out
of 84 in 8em4
Go back to
Calcium Binding Sites List in 8em4
Calcium binding site 10 out
of 84 in the Cryo-Em Structure of LRP2 at pH 7.5
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Cryo-Em Structure of LRP2 at pH 7.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4754
b:30.0
occ:1.00
|
OE2
|
A:GLU1263
|
2.2
|
65.3
|
1.0
|
OD2
|
A:ASP1256
|
2.3
|
59.0
|
1.0
|
OD2
|
A:ASP1262
|
2.3
|
63.0
|
1.0
|
OD1
|
A:ASP1252
|
2.3
|
64.3
|
1.0
|
O
|
A:TRP1249
|
2.3
|
59.2
|
1.0
|
O
|
A:HIS1254
|
2.3
|
58.7
|
1.0
|
CG
|
A:ASP1256
|
3.4
|
59.0
|
1.0
|
CD
|
A:GLU1263
|
3.4
|
65.3
|
1.0
|
CG
|
A:ASP1252
|
3.4
|
64.3
|
1.0
|
CG
|
A:ASP1262
|
3.4
|
63.0
|
1.0
|
C
|
A:TRP1249
|
3.5
|
59.2
|
1.0
|
C
|
A:HIS1254
|
3.5
|
58.7
|
1.0
|
CG
|
A:GLU1263
|
3.9
|
65.3
|
1.0
|
N
|
A:ASP1252
|
3.9
|
64.3
|
1.0
|
NH2
|
A:ARG846
|
3.9
|
57.6
|
1.0
|
OD2
|
A:ASP1252
|
4.0
|
64.3
|
1.0
|
N
|
A:ASP1256
|
4.1
|
59.0
|
1.0
|
N
|
A:CYS1251
|
4.1
|
71.9
|
1.0
|
N
|
A:HIS1254
|
4.1
|
58.7
|
1.0
|
CB
|
A:ASP1262
|
4.1
|
63.0
|
1.0
|
OD1
|
A:ASP1256
|
4.1
|
59.0
|
1.0
|
CB
|
A:ASP1256
|
4.2
|
59.0
|
1.0
|
CA
|
A:HIS1254
|
4.3
|
58.7
|
1.0
|
CA
|
A:TRP1249
|
4.3
|
59.2
|
1.0
|
OD1
|
A:ASP1262
|
4.4
|
63.0
|
1.0
|
N
|
A:GLU1250
|
4.4
|
65.2
|
1.0
|
OE1
|
A:GLU1263
|
4.4
|
65.3
|
1.0
|
CB
|
A:TRP1249
|
4.5
|
59.2
|
1.0
|
CA
|
A:GLU1250
|
4.5
|
65.2
|
1.0
|
C
|
A:GLU1250
|
4.5
|
65.2
|
1.0
|
CB
|
A:HIS1254
|
4.5
|
58.7
|
1.0
|
N
|
A:PRO1255
|
4.5
|
59.8
|
1.0
|
CB
|
A:ASP1252
|
4.6
|
64.3
|
1.0
|
O
|
A:ASP1262
|
4.6
|
63.0
|
1.0
|
CA
|
A:ASP1252
|
4.6
|
64.3
|
1.0
|
CA
|
A:PRO1255
|
4.7
|
59.8
|
1.0
|
C
|
A:ASP1252
|
4.7
|
64.3
|
1.0
|
C
|
A:PRO1255
|
4.8
|
59.8
|
1.0
|
CA
|
A:CYS1251
|
4.8
|
71.9
|
1.0
|
C
|
A:ASP1262
|
4.8
|
63.0
|
1.0
|
CA
|
A:ASP1256
|
4.8
|
59.0
|
1.0
|
C
|
A:CYS1251
|
4.8
|
71.9
|
1.0
|
N
|
A:GLY1253
|
4.9
|
63.5
|
1.0
|
ND1
|
A:HIS1254
|
5.0
|
58.7
|
1.0
|
|
Reference:
A.Beenken,
G.Cerutti,
A.W.Fitzpatrick,
J.Barasch,
L.Shapiro.
Cryo-Em Structure of LRP2 Cell(Cambridge,Mass.) 2023.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2023.01.016
Page generated: Fri Jul 19 08:19:56 2024
|