Calcium in PDB 8em7: Cryo-Em Structure of LRP2 at pH 5.2
Calcium Binding Sites:
Calcium binding site 1 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 1 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4755
b:30.0
occ:1.00
|
OD1
|
A:ASN3575
|
2.2
|
72.0
|
1.0
|
OD2
|
A:ASP3585
|
2.2
|
74.1
|
1.0
|
O
|
A:ARG3577
|
2.3
|
74.7
|
1.0
|
OE1
|
A:GLU3586
|
2.3
|
73.2
|
1.0
|
O
|
A:ALA3572
|
2.3
|
72.7
|
1.0
|
OE2
|
A:GLU3586
|
2.4
|
73.2
|
1.0
|
OD1
|
A:ASP3585
|
2.6
|
74.1
|
1.0
|
CG
|
A:ASP3585
|
2.7
|
74.1
|
1.0
|
CD
|
A:GLU3586
|
2.7
|
73.2
|
1.0
|
OD2
|
A:ASP3579
|
2.8
|
75.7
|
1.0
|
CG
|
A:ASN3575
|
3.1
|
72.0
|
1.0
|
C
|
A:ALA3572
|
3.4
|
72.7
|
1.0
|
C
|
A:ARG3577
|
3.5
|
74.7
|
1.0
|
ND2
|
A:ASN3575
|
3.5
|
72.0
|
1.0
|
CG
|
A:ASP3579
|
3.7
|
75.7
|
1.0
|
N
|
A:ASP3579
|
3.8
|
75.7
|
1.0
|
N
|
A:ASN3575
|
3.9
|
72.0
|
1.0
|
CB
|
A:ALA3572
|
4.0
|
72.7
|
1.0
|
CA
|
A:ALA3572
|
4.0
|
72.7
|
1.0
|
N
|
A:ARG3577
|
4.0
|
74.7
|
1.0
|
CB
|
A:ASP3585
|
4.1
|
74.1
|
1.0
|
CG
|
A:GLU3586
|
4.2
|
73.2
|
1.0
|
CB
|
A:ASP3579
|
4.2
|
75.7
|
1.0
|
CB
|
A:ASN3575
|
4.3
|
72.0
|
1.0
|
C
|
A:LEU3573
|
4.3
|
71.0
|
1.0
|
CA
|
A:ARG3577
|
4.3
|
74.7
|
1.0
|
N
|
A:GLN3578
|
4.4
|
75.7
|
1.0
|
O
|
A:LEU3573
|
4.4
|
71.0
|
1.0
|
CA
|
A:GLN3578
|
4.4
|
75.7
|
1.0
|
N
|
A:LEU3573
|
4.4
|
71.0
|
1.0
|
CA
|
A:ASN3575
|
4.5
|
72.0
|
1.0
|
OD1
|
A:ASP3579
|
4.6
|
75.7
|
1.0
|
N
|
A:ALA3576
|
4.6
|
73.0
|
1.0
|
C
|
A:GLN3578
|
4.6
|
75.7
|
1.0
|
N
|
A:CYS3574
|
4.6
|
71.2
|
1.0
|
CA
|
A:ASP3579
|
4.7
|
75.7
|
1.0
|
CA
|
A:LEU3573
|
4.7
|
71.0
|
1.0
|
N
|
A:GLU3586
|
4.7
|
73.2
|
1.0
|
C
|
A:ASN3575
|
4.8
|
72.0
|
1.0
|
C
|
A:CYS3574
|
4.8
|
71.2
|
1.0
|
C
|
A:ASP3585
|
4.9
|
74.1
|
1.0
|
CA
|
A:ASP3585
|
4.9
|
74.1
|
1.0
|
CA
|
A:CYS3574
|
5.0
|
71.2
|
1.0
|
CB
|
A:ARG3577
|
5.0
|
30.0
|
1.0
|
|
Calcium binding site 2 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 2 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4756
b:30.0
occ:1.00
|
OD2
|
A:ASP92
|
2.2
|
59.0
|
1.0
|
OD1
|
A:ASP88
|
2.3
|
64.3
|
1.0
|
O
|
A:TRP85
|
2.4
|
59.2
|
1.0
|
O
|
A:ASP90
|
2.4
|
58.7
|
1.0
|
OE2
|
A:GLU99
|
2.5
|
65.3
|
1.0
|
O
|
A:VAL86
|
2.5
|
65.2
|
1.0
|
OD1
|
A:ASP98
|
2.6
|
63.0
|
1.0
|
CG
|
A:ASP92
|
2.9
|
59.0
|
1.0
|
OD1
|
A:ASP92
|
3.0
|
59.0
|
1.0
|
C
|
A:VAL86
|
3.3
|
65.2
|
1.0
|
CG
|
A:ASP88
|
3.3
|
64.3
|
1.0
|
CD
|
A:GLU99
|
3.5
|
65.3
|
1.0
|
CG
|
A:ASP98
|
3.5
|
63.0
|
1.0
|
C
|
A:ASP90
|
3.5
|
58.7
|
1.0
|
C
|
A:TRP85
|
3.5
|
59.2
|
1.0
|
N
|
A:ASP88
|
3.7
|
64.3
|
1.0
|
N
|
A:ASP90
|
3.8
|
58.7
|
1.0
|
CA
|
A:VAL86
|
3.9
|
65.2
|
1.0
|
CG
|
A:GLU99
|
4.0
|
65.3
|
1.0
|
OD2
|
A:ASP88
|
4.0
|
64.3
|
1.0
|
CB
|
A:ASP98
|
4.1
|
63.0
|
1.0
|
CA
|
A:ASP90
|
4.1
|
58.7
|
1.0
|
N
|
A:CYS87
|
4.1
|
71.9
|
1.0
|
N
|
A:VAL86
|
4.2
|
65.2
|
1.0
|
N
|
A:ASP92
|
4.2
|
59.0
|
1.0
|
CB
|
A:ASP92
|
4.2
|
59.0
|
1.0
|
N
|
A:GLN89
|
4.3
|
63.5
|
1.0
|
CB
|
A:ASP88
|
4.3
|
64.3
|
1.0
|
CA
|
A:CYS87
|
4.3
|
71.9
|
1.0
|
CA
|
A:ASP88
|
4.4
|
64.3
|
1.0
|
CB
|
A:ASP90
|
4.4
|
30.0
|
1.0
|
OD2
|
A:ASP98
|
4.4
|
63.0
|
1.0
|
C
|
A:CYS87
|
4.4
|
71.9
|
1.0
|
OE1
|
A:GLU99
|
4.5
|
65.3
|
1.0
|
C
|
A:ASP88
|
4.6
|
64.3
|
1.0
|
N
|
A:LYS91
|
4.7
|
59.8
|
1.0
|
CA
|
A:TRP85
|
4.7
|
59.2
|
1.0
|
C
|
A:GLN89
|
4.7
|
63.5
|
1.0
|
C
|
A:ASP98
|
4.9
|
63.0
|
1.0
|
CA
|
A:ASP92
|
4.9
|
59.0
|
1.0
|
NZ
|
A:LYS385
|
4.9
|
67.4
|
1.0
|
CA
|
A:LYS91
|
4.9
|
59.8
|
1.0
|
C
|
A:LYS91
|
4.9
|
59.8
|
1.0
|
N
|
A:GLU99
|
5.0
|
65.3
|
1.0
|
|
Calcium binding site 3 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 3 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4757
b:30.0
occ:1.00
|
O
|
A:VAL130
|
2.2
|
69.6
|
1.0
|
OD2
|
A:ASP132
|
2.3
|
66.5
|
1.0
|
OE2
|
A:GLU139
|
2.3
|
69.4
|
1.0
|
OD1
|
A:ASP128
|
2.3
|
71.6
|
1.0
|
O
|
A:TYR125
|
2.4
|
65.6
|
1.0
|
OD2
|
A:ASP138
|
2.6
|
67.7
|
1.0
|
CD
|
A:GLU139
|
3.3
|
69.4
|
1.0
|
C
|
A:VAL130
|
3.4
|
69.6
|
1.0
|
CG
|
A:ASP132
|
3.4
|
66.5
|
1.0
|
CG
|
A:ASP128
|
3.5
|
71.6
|
1.0
|
C
|
A:TYR125
|
3.5
|
65.6
|
1.0
|
CG
|
A:ASP138
|
3.7
|
67.7
|
1.0
|
N
|
A:VAL130
|
3.8
|
69.6
|
1.0
|
CG
|
A:GLU139
|
3.9
|
69.4
|
1.0
|
CA
|
A:VAL130
|
3.9
|
69.6
|
1.0
|
CB
|
A:VAL130
|
4.0
|
69.6
|
1.0
|
N
|
A:ASP128
|
4.0
|
71.6
|
1.0
|
CA
|
A:TYR125
|
4.0
|
65.6
|
1.0
|
N
|
A:ASP132
|
4.0
|
66.5
|
1.0
|
OD2
|
A:ASP128
|
4.1
|
71.6
|
1.0
|
CB
|
A:ASP132
|
4.1
|
66.5
|
1.0
|
CB
|
A:TYR125
|
4.1
|
30.0
|
1.0
|
NH1
|
A:ARG171
|
4.1
|
30.0
|
1.0
|
CB
|
A:ASP138
|
4.3
|
67.7
|
1.0
|
OE1
|
A:GLU139
|
4.4
|
69.4
|
1.0
|
OD1
|
A:ASP132
|
4.4
|
66.5
|
1.0
|
O
|
A:ARG126
|
4.5
|
69.2
|
1.0
|
C
|
A:ARG126
|
4.5
|
69.2
|
1.0
|
N
|
A:SER131
|
4.5
|
66.8
|
1.0
|
CG1
|
A:VAL130
|
4.6
|
69.6
|
1.0
|
CA
|
A:ASP128
|
4.6
|
71.6
|
1.0
|
CB
|
A:ASP128
|
4.6
|
71.6
|
1.0
|
N
|
A:ARG126
|
4.6
|
69.2
|
1.0
|
C
|
A:ASP128
|
4.6
|
71.6
|
1.0
|
OD1
|
A:ASP138
|
4.6
|
67.7
|
1.0
|
N
|
A:CYS127
|
4.7
|
72.6
|
1.0
|
CA
|
A:ASP132
|
4.7
|
66.5
|
1.0
|
N
|
A:HIS129
|
4.8
|
71.8
|
1.0
|
CA
|
A:SER131
|
4.8
|
66.8
|
1.0
|
CA
|
A:CYS127
|
4.9
|
72.6
|
1.0
|
C
|
A:CYS127
|
4.9
|
72.6
|
1.0
|
C
|
A:SER131
|
4.9
|
66.8
|
1.0
|
CA
|
A:ARG126
|
5.0
|
69.2
|
1.0
|
CG
|
A:TYR125
|
5.0
|
30.0
|
1.0
|
|
Calcium binding site 4 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 4 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4758
b:30.0
occ:1.00
|
OD1
|
A:ASP165
|
2.3
|
78.3
|
1.0
|
OE2
|
A:GLU176
|
2.3
|
81.8
|
1.0
|
O
|
A:LYS167
|
2.3
|
72.2
|
1.0
|
OD2
|
A:ASP169
|
2.4
|
74.2
|
1.0
|
O
|
A:GLN162
|
2.4
|
77.3
|
1.0
|
OD2
|
A:ASP175
|
2.4
|
80.8
|
1.0
|
CD
|
A:GLU176
|
3.3
|
81.8
|
1.0
|
CG
|
A:ASP165
|
3.3
|
78.3
|
1.0
|
C
|
A:LYS167
|
3.4
|
72.2
|
1.0
|
CG
|
A:ASP169
|
3.4
|
74.2
|
1.0
|
C
|
A:GLN162
|
3.6
|
77.3
|
1.0
|
CG
|
A:ASP175
|
3.6
|
80.8
|
1.0
|
CG
|
A:GLU176
|
3.6
|
81.8
|
1.0
|
O
|
A:LYS163
|
3.8
|
81.9
|
1.0
|
N
|
A:LYS167
|
3.8
|
72.2
|
1.0
|
OD2
|
A:ASP165
|
3.8
|
78.3
|
1.0
|
N
|
A:ASP169
|
3.9
|
74.2
|
1.0
|
N
|
A:ASP165
|
4.0
|
78.3
|
1.0
|
CB
|
A:ASP169
|
4.0
|
74.2
|
1.0
|
C
|
A:LYS163
|
4.1
|
81.9
|
1.0
|
CA
|
A:LYS167
|
4.1
|
72.2
|
1.0
|
N
|
A:HIS166
|
4.3
|
77.0
|
1.0
|
CB
|
A:ASP175
|
4.3
|
80.8
|
1.0
|
CA
|
A:GLN162
|
4.4
|
77.3
|
1.0
|
CB
|
A:LYS167
|
4.4
|
30.0
|
1.0
|
OD1
|
A:ASP169
|
4.4
|
74.2
|
1.0
|
OE1
|
A:GLU176
|
4.4
|
81.8
|
1.0
|
N
|
A:VAL168
|
4.4
|
71.3
|
1.0
|
OD1
|
A:ASP175
|
4.5
|
80.8
|
1.0
|
CB
|
A:ASP165
|
4.6
|
78.3
|
1.0
|
N
|
A:CYS164
|
4.6
|
83.2
|
1.0
|
N
|
A:LYS163
|
4.6
|
81.9
|
1.0
|
CA
|
A:VAL168
|
4.6
|
71.3
|
1.0
|
CA
|
A:ASP165
|
4.6
|
78.3
|
1.0
|
CA
|
A:ASP169
|
4.6
|
74.2
|
1.0
|
C
|
A:HIS166
|
4.7
|
77.0
|
1.0
|
CA
|
A:LYS163
|
4.7
|
81.9
|
1.0
|
C
|
A:VAL168
|
4.7
|
71.3
|
1.0
|
C
|
A:ASP165
|
4.7
|
78.3
|
1.0
|
CB
|
A:GLN162
|
4.7
|
30.0
|
1.0
|
CA
|
A:CYS164
|
4.8
|
83.2
|
1.0
|
N
|
A:GLU176
|
4.9
|
81.8
|
1.0
|
CA
|
A:HIS166
|
4.9
|
77.0
|
1.0
|
C
|
A:CYS164
|
4.9
|
83.2
|
1.0
|
CB
|
A:GLU176
|
5.0
|
81.8
|
1.0
|
|
Calcium binding site 5 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 5 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4759
b:30.0
occ:1.00
|
OD1
|
A:ASP203
|
2.2
|
69.2
|
1.0
|
OD1
|
A:ASP207
|
2.3
|
68.0
|
1.0
|
OD2
|
A:ASP213
|
2.3
|
67.6
|
1.0
|
O
|
A:TYR200
|
2.3
|
61.7
|
1.0
|
O
|
A:ASP205
|
2.4
|
71.1
|
1.0
|
OE2
|
A:GLU214
|
2.4
|
66.1
|
1.0
|
CG
|
A:ASP203
|
3.0
|
69.2
|
1.0
|
C
|
A:TYR200
|
3.4
|
61.7
|
1.0
|
CD
|
A:GLU214
|
3.4
|
66.1
|
1.0
|
CG
|
A:ASP207
|
3.4
|
68.0
|
1.0
|
CG
|
A:ASP213
|
3.5
|
67.6
|
1.0
|
C
|
A:ASP205
|
3.6
|
71.1
|
1.0
|
OD2
|
A:ASP203
|
3.6
|
69.2
|
1.0
|
N
|
A:ASP203
|
3.9
|
69.2
|
1.0
|
CG
|
A:GLU214
|
3.9
|
66.1
|
1.0
|
N
|
A:ASP207
|
4.0
|
68.0
|
1.0
|
CB
|
A:ASP207
|
4.0
|
68.0
|
1.0
|
CB
|
A:ASP203
|
4.1
|
69.2
|
1.0
|
CA
|
A:VAL201
|
4.1
|
63.9
|
1.0
|
N
|
A:CYS202
|
4.1
|
69.1
|
1.0
|
N
|
A:VAL201
|
4.1
|
63.9
|
1.0
|
N
|
A:ASP205
|
4.2
|
71.1
|
1.0
|
CB
|
A:ASP213
|
4.3
|
67.6
|
1.0
|
CA
|
A:TYR200
|
4.3
|
61.7
|
1.0
|
OD1
|
A:ASP213
|
4.3
|
67.6
|
1.0
|
C
|
A:VAL201
|
4.4
|
63.9
|
1.0
|
CB
|
A:TYR200
|
4.4
|
30.0
|
1.0
|
OE1
|
A:GLU214
|
4.4
|
66.1
|
1.0
|
CA
|
A:ASP205
|
4.4
|
71.1
|
1.0
|
OD2
|
A:ASP207
|
4.4
|
68.0
|
1.0
|
CA
|
A:ASP203
|
4.5
|
69.2
|
1.0
|
N
|
A:ASN206
|
4.5
|
68.8
|
1.0
|
NH1
|
A:ARG576
|
4.6
|
61.4
|
1.0
|
C
|
A:ASN206
|
4.7
|
68.8
|
1.0
|
CA
|
A:ASP207
|
4.7
|
68.0
|
1.0
|
CA
|
A:ASN206
|
4.7
|
68.8
|
1.0
|
O
|
A:ASP213
|
4.7
|
67.6
|
1.0
|
CB
|
A:ASP205
|
4.8
|
30.0
|
1.0
|
N
|
A:HIS204
|
4.8
|
72.2
|
1.0
|
C
|
A:ASP203
|
4.8
|
69.2
|
1.0
|
C
|
A:CYS202
|
4.9
|
69.1
|
1.0
|
CA
|
A:CYS202
|
5.0
|
69.1
|
1.0
|
C
|
A:ASP213
|
5.0
|
67.6
|
1.0
|
|
Calcium binding site 6 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 6 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4760
b:30.0
occ:1.00
|
O
|
A:ASP244
|
2.3
|
70.6
|
1.0
|
OD2
|
A:ASP246
|
2.3
|
70.2
|
1.0
|
OE2
|
A:GLU253
|
2.3
|
70.0
|
1.0
|
OD1
|
A:ASP242
|
2.3
|
70.2
|
1.0
|
O
|
A:TRP239
|
2.4
|
66.9
|
1.0
|
OD2
|
A:ASP252
|
2.5
|
69.6
|
1.0
|
C
|
A:ASP244
|
3.3
|
70.6
|
1.0
|
CG
|
A:ASP246
|
3.3
|
70.2
|
1.0
|
CD
|
A:GLU253
|
3.4
|
70.0
|
1.0
|
CG
|
A:ASP242
|
3.4
|
70.2
|
1.0
|
C
|
A:TRP239
|
3.5
|
66.9
|
1.0
|
N
|
A:ASP244
|
3.6
|
70.6
|
1.0
|
CB
|
A:ASP244
|
3.6
|
70.6
|
1.0
|
CG
|
A:ASP252
|
3.6
|
69.6
|
1.0
|
CA
|
A:ASP244
|
3.7
|
70.6
|
1.0
|
OD2
|
A:ASP242
|
3.9
|
70.2
|
1.0
|
CG
|
A:GLU253
|
3.9
|
70.0
|
1.0
|
NZ
|
A:LYS554
|
3.9
|
61.4
|
1.0
|
OD1
|
A:ASP246
|
4.1
|
70.2
|
1.0
|
CB
|
A:ASP246
|
4.1
|
70.2
|
1.0
|
N
|
A:ASP246
|
4.1
|
70.2
|
1.0
|
CA
|
A:TRP239
|
4.1
|
66.9
|
1.0
|
O
|
A:ASP252
|
4.2
|
69.6
|
1.0
|
N
|
A:ASP242
|
4.2
|
70.2
|
1.0
|
OD1
|
A:ASP252
|
4.3
|
69.6
|
1.0
|
CB
|
A:TRP239
|
4.4
|
66.9
|
1.0
|
OE1
|
A:GLU253
|
4.4
|
70.0
|
1.0
|
N
|
A:ASP245
|
4.4
|
72.0
|
1.0
|
N
|
A:VAL240
|
4.6
|
64.8
|
1.0
|
CB
|
A:ASP252
|
4.6
|
69.6
|
1.0
|
C
|
A:VAL240
|
4.7
|
64.8
|
1.0
|
CB
|
A:ASP242
|
4.7
|
70.2
|
1.0
|
N
|
A:CYS241
|
4.7
|
69.0
|
1.0
|
N
|
A:GLY243
|
4.7
|
70.5
|
1.0
|
CG
|
A:ASP244
|
4.7
|
70.6
|
1.0
|
CA
|
A:ASP242
|
4.8
|
70.2
|
1.0
|
CA
|
A:ASP246
|
4.8
|
70.2
|
1.0
|
CA
|
A:VAL240
|
4.8
|
64.8
|
1.0
|
C
|
A:ASP242
|
4.8
|
70.2
|
1.0
|
C
|
A:GLY243
|
4.8
|
70.5
|
1.0
|
C
|
A:ASP252
|
5.0
|
69.6
|
1.0
|
CA
|
A:ASP245
|
5.0
|
72.0
|
1.0
|
|
Calcium binding site 7 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 7 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4761
b:30.0
occ:1.00
|
OD1
|
A:ASP286
|
2.3
|
64.3
|
1.0
|
O
|
A:VAL288
|
2.4
|
58.7
|
1.0
|
O
|
A:ASP296
|
2.4
|
63.0
|
1.0
|
O
|
A:LYS283
|
2.5
|
59.2
|
1.0
|
OE1
|
A:GLU297
|
2.5
|
65.3
|
1.0
|
OD2
|
A:ASP296
|
2.6
|
63.0
|
1.0
|
OD2
|
A:ASP290
|
2.6
|
59.0
|
1.0
|
CG
|
A:ASP296
|
3.2
|
63.0
|
1.0
|
CG
|
A:ASP286
|
3.5
|
64.3
|
1.0
|
CG
|
A:ASP290
|
3.5
|
59.0
|
1.0
|
C
|
A:VAL288
|
3.5
|
58.7
|
1.0
|
C
|
A:ASP296
|
3.5
|
63.0
|
1.0
|
CD
|
A:GLU297
|
3.6
|
65.3
|
1.0
|
N
|
A:VAL288
|
3.6
|
58.7
|
1.0
|
C
|
A:LYS283
|
3.7
|
59.2
|
1.0
|
CB
|
A:ASP296
|
3.8
|
63.0
|
1.0
|
N
|
A:GLY287
|
3.8
|
63.5
|
1.0
|
N
|
A:ASP290
|
3.9
|
59.0
|
1.0
|
OD1
|
A:ASP296
|
4.0
|
63.0
|
1.0
|
OD2
|
A:ASP286
|
4.1
|
64.3
|
1.0
|
N
|
A:ASP286
|
4.2
|
64.3
|
1.0
|
OD1
|
A:ASP290
|
4.2
|
59.0
|
1.0
|
CB
|
A:ASP290
|
4.2
|
59.0
|
1.0
|
CA
|
A:VAL288
|
4.2
|
58.7
|
1.0
|
CA
|
A:LYS283
|
4.2
|
59.2
|
1.0
|
CA
|
A:ASP296
|
4.3
|
63.0
|
1.0
|
CG
|
A:GLU297
|
4.3
|
65.3
|
1.0
|
CA
|
A:PRO289
|
4.3
|
59.8
|
1.0
|
N
|
A:PRO289
|
4.4
|
59.8
|
1.0
|
N
|
A:GLU297
|
4.4
|
65.3
|
1.0
|
CA
|
A:GLU297
|
4.5
|
65.3
|
1.0
|
C
|
A:GLY287
|
4.5
|
63.5
|
1.0
|
OE2
|
A:GLU297
|
4.5
|
65.3
|
1.0
|
CA
|
A:GLY287
|
4.6
|
63.5
|
1.0
|
CB
|
A:ASP286
|
4.6
|
64.3
|
1.0
|
C
|
A:CYS285
|
4.6
|
71.9
|
1.0
|
C
|
A:PRO289
|
4.6
|
59.8
|
1.0
|
CB
|
A:LYS283
|
4.6
|
30.0
|
1.0
|
C
|
A:ASP286
|
4.6
|
64.3
|
1.0
|
C
|
A:VAL284
|
4.6
|
65.2
|
1.0
|
CA
|
A:ASP286
|
4.7
|
64.3
|
1.0
|
N
|
A:CYS285
|
4.7
|
71.9
|
1.0
|
CA
|
A:ASP290
|
4.7
|
59.0
|
1.0
|
N
|
A:VAL284
|
4.8
|
65.2
|
1.0
|
O
|
A:VAL284
|
4.9
|
65.2
|
1.0
|
CA
|
A:CYS285
|
4.9
|
71.9
|
1.0
|
CB
|
A:VAL288
|
5.0
|
30.0
|
1.0
|
CB
|
A:GLU297
|
5.0
|
65.3
|
1.0
|
|
Calcium binding site 8 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 8 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4762
b:30.0
occ:1.00
|
OD1
|
A:ASP1045
|
2.3
|
71.6
|
1.0
|
O
|
A:VAL1047
|
2.3
|
69.6
|
1.0
|
O
|
A:PHE1042
|
2.4
|
65.6
|
1.0
|
OD1
|
A:ASP1049
|
2.5
|
66.5
|
1.0
|
OE2
|
A:GLU1056
|
2.6
|
69.4
|
1.0
|
OD2
|
A:ASP1055
|
2.8
|
67.7
|
1.0
|
C
|
A:VAL1047
|
3.3
|
69.6
|
1.0
|
CG
|
A:ASP1045
|
3.3
|
71.6
|
1.0
|
C
|
A:PHE1042
|
3.4
|
65.6
|
1.0
|
N
|
A:ASP1049
|
3.5
|
66.5
|
1.0
|
CB
|
A:ASP1055
|
3.5
|
67.7
|
1.0
|
CG
|
A:ASP1055
|
3.6
|
67.7
|
1.0
|
CG
|
A:ASP1049
|
3.7
|
66.5
|
1.0
|
CA
|
A:ASP1048
|
3.7
|
66.8
|
1.0
|
OD2
|
A:ASP1045
|
3.7
|
71.6
|
1.0
|
CD
|
A:GLU1056
|
3.8
|
69.4
|
1.0
|
N
|
A:ASP1048
|
3.9
|
66.8
|
1.0
|
CB
|
A:PHE1042
|
4.0
|
65.6
|
1.0
|
C
|
A:ASP1048
|
4.0
|
66.8
|
1.0
|
CA
|
A:PHE1042
|
4.1
|
65.6
|
1.0
|
OE1
|
A:GLU1056
|
4.2
|
69.4
|
1.0
|
N
|
A:ASP1045
|
4.3
|
71.6
|
1.0
|
N
|
A:VAL1047
|
4.3
|
69.6
|
1.0
|
CB
|
A:ASP1049
|
4.3
|
66.5
|
1.0
|
N
|
A:ARG1043
|
4.4
|
69.2
|
1.0
|
CA
|
A:VAL1047
|
4.5
|
69.6
|
1.0
|
CA
|
A:ASP1049
|
4.5
|
66.5
|
1.0
|
C
|
A:ARG1043
|
4.5
|
69.2
|
1.0
|
CB
|
A:ASP1045
|
4.6
|
71.6
|
1.0
|
CA
|
A:ARG1043
|
4.6
|
69.2
|
1.0
|
OD2
|
A:ASP1049
|
4.6
|
66.5
|
1.0
|
O
|
A:ARG1043
|
4.7
|
69.2
|
1.0
|
NH2
|
A:ARG1409
|
4.8
|
83.7
|
1.0
|
CA
|
A:ASP1045
|
4.8
|
71.6
|
1.0
|
C
|
A:ASP1045
|
4.8
|
71.6
|
1.0
|
OD1
|
A:ASP1055
|
4.8
|
67.7
|
1.0
|
N
|
A:GLY1046
|
4.9
|
71.8
|
1.0
|
N
|
A:CYS1044
|
4.9
|
72.6
|
1.0
|
CB
|
A:ASP1048
|
5.0
|
66.8
|
1.0
|
CA
|
A:ASP1055
|
5.0
|
67.7
|
1.0
|
|
Calcium binding site 9 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 9 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4763
b:30.0
occ:1.00
|
OD2
|
A:ASP1097
|
2.1
|
85.3
|
1.0
|
OE2
|
A:GLU1098
|
2.2
|
88.4
|
1.0
|
OD2
|
A:ASP1091
|
2.3
|
79.2
|
1.0
|
O
|
A:GLN1089
|
2.3
|
77.1
|
1.0
|
OD1
|
A:ASP1087
|
2.3
|
79.2
|
1.0
|
O
|
A:TRP1084
|
2.3
|
76.0
|
1.0
|
CG
|
A:ASP1097
|
3.2
|
85.3
|
1.0
|
CD
|
A:GLU1098
|
3.3
|
88.4
|
1.0
|
CG
|
A:ASP1087
|
3.3
|
79.2
|
1.0
|
C
|
A:GLN1089
|
3.4
|
77.1
|
1.0
|
CG
|
A:ASP1091
|
3.4
|
79.2
|
1.0
|
C
|
A:TRP1084
|
3.5
|
76.0
|
1.0
|
CA
|
A:ASN1090
|
3.5
|
79.7
|
1.0
|
N
|
A:ASP1091
|
3.5
|
79.2
|
1.0
|
OD2
|
A:ASP1087
|
3.6
|
79.2
|
1.0
|
C
|
A:ASN1090
|
3.8
|
79.7
|
1.0
|
CB
|
A:ASP1097
|
3.8
|
85.3
|
1.0
|
N
|
A:ASN1090
|
3.9
|
79.7
|
1.0
|
CG
|
A:GLU1098
|
3.9
|
88.4
|
1.0
|
O
|
A:ASP1087
|
4.1
|
79.2
|
1.0
|
CB
|
A:ASP1091
|
4.1
|
79.2
|
1.0
|
CA
|
A:TRP1084
|
4.1
|
76.0
|
1.0
|
OD1
|
A:ASP1097
|
4.2
|
85.3
|
1.0
|
N
|
A:ASP1087
|
4.2
|
79.2
|
1.0
|
OE1
|
A:GLU1098
|
4.3
|
88.4
|
1.0
|
CB
|
A:TRP1084
|
4.4
|
76.0
|
1.0
|
OD1
|
A:ASP1091
|
4.4
|
79.2
|
1.0
|
CA
|
A:ASP1091
|
4.4
|
79.2
|
1.0
|
CB
|
A:ASP1087
|
4.6
|
79.2
|
1.0
|
N
|
A:ARG1085
|
4.6
|
81.8
|
1.0
|
C
|
A:ARG1085
|
4.6
|
81.8
|
1.0
|
NH1
|
A:ARG1413
|
4.6
|
71.3
|
1.0
|
CA
|
A:GLN1089
|
4.7
|
77.1
|
1.0
|
C
|
A:ASP1087
|
4.7
|
79.2
|
1.0
|
O
|
A:ASN1090
|
4.7
|
79.7
|
1.0
|
N
|
A:CYS1086
|
4.8
|
83.7
|
1.0
|
CB
|
A:ASN1090
|
4.8
|
79.7
|
1.0
|
CA
|
A:ASP1087
|
4.8
|
79.2
|
1.0
|
O
|
A:ARG1085
|
4.8
|
81.8
|
1.0
|
N
|
A:GLN1089
|
4.9
|
77.1
|
1.0
|
CA
|
A:ARG1085
|
4.9
|
81.8
|
1.0
|
|
Calcium binding site 10 out
of 88 in 8em7
Go back to
Calcium Binding Sites List in 8em7
Calcium binding site 10 out
of 88 in the Cryo-Em Structure of LRP2 at pH 5.2
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 5.2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4764
b:30.0
occ:1.00
|
OE2
|
A:GLU1141
|
2.2
|
79.0
|
1.0
|
OD2
|
A:ASP1134
|
2.2
|
81.5
|
1.0
|
O
|
A:TRP1127
|
2.3
|
83.8
|
1.0
|
OD1
|
A:ASP1130
|
2.3
|
76.8
|
1.0
|
O
|
A:ASP1132
|
2.4
|
74.1
|
1.0
|
OD2
|
A:ASP1130
|
2.5
|
76.8
|
1.0
|
CG
|
A:ASP1130
|
2.6
|
76.8
|
1.0
|
OD2
|
A:ASP1140
|
3.1
|
78.1
|
1.0
|
CG
|
A:ASP1134
|
3.3
|
81.5
|
1.0
|
CD
|
A:GLU1141
|
3.4
|
79.0
|
1.0
|
C
|
A:TRP1127
|
3.5
|
83.8
|
1.0
|
C
|
A:ASP1132
|
3.6
|
74.1
|
1.0
|
N
|
A:ASP1130
|
3.9
|
76.8
|
1.0
|
CB
|
A:ASP1130
|
4.0
|
76.8
|
1.0
|
CG
|
A:ASP1140
|
4.0
|
78.1
|
1.0
|
N
|
A:ASP1134
|
4.1
|
81.5
|
1.0
|
CB
|
A:ASP1134
|
4.2
|
81.5
|
1.0
|
CA
|
A:TRP1127
|
4.2
|
83.8
|
1.0
|
CG
|
A:GLU1141
|
4.2
|
79.0
|
1.0
|
OD1
|
A:ASP1134
|
4.2
|
81.5
|
1.0
|
N
|
A:ASP1132
|
4.2
|
74.1
|
1.0
|
CB
|
A:TRP1127
|
4.2
|
83.8
|
1.0
|
CA
|
A:ASP1132
|
4.3
|
74.1
|
1.0
|
OE1
|
A:GLU1141
|
4.3
|
79.0
|
1.0
|
CA
|
A:ASP1130
|
4.3
|
76.8
|
1.0
|
NZ
|
A:LYS1430
|
4.3
|
57.8
|
1.0
|
C
|
A:VAL1128
|
4.4
|
83.5
|
1.0
|
C
|
A:ASP1130
|
4.4
|
76.8
|
1.0
|
CB
|
A:ASP1132
|
4.4
|
74.1
|
1.0
|
O
|
A:ASP1130
|
4.4
|
76.8
|
1.0
|
O
|
A:VAL1128
|
4.5
|
83.5
|
1.0
|
N
|
A:CYS1129
|
4.5
|
80.5
|
1.0
|
CB
|
A:ASP1140
|
4.6
|
78.1
|
1.0
|
N
|
A:VAL1128
|
4.6
|
83.5
|
1.0
|
C
|
A:CYS1129
|
4.6
|
80.5
|
1.0
|
N
|
A:ASN1133
|
4.7
|
76.0
|
1.0
|
CA
|
A:ASP1134
|
4.8
|
81.5
|
1.0
|
CA
|
A:VAL1128
|
4.8
|
83.5
|
1.0
|
CA
|
A:ASN1133
|
4.8
|
76.0
|
1.0
|
CA
|
A:CYS1129
|
4.9
|
80.5
|
1.0
|
C
|
A:ASN1133
|
5.0
|
76.0
|
1.0
|
OD1
|
A:ASP1140
|
5.0
|
78.1
|
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 08:20:11 2024
|