Calcium in PDB 8dvn: Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10
Protein crystallography data
The structure of Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10, PDB code: 8dvn
was solved by
A.K.Thakur,
N.P.D.Liau,
J.Sudhamsu,
R.N.Hannoush,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.33 /
2.53
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.097,
116.783,
127.164,
90,
90,
90
|
R / Rfree (%)
|
20.9 /
24.6
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10
(pdb code 8dvn). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10, PDB code: 8dvn:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 8dvn
Go back to
Calcium Binding Sites List in 8dvn
Calcium binding site 1 out
of 4 in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10
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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1302
b:81.6
occ:1.00
|
O
|
A:ILE879
|
2.6
|
68.7
|
1.0
|
O
|
A:LEU838
|
2.6
|
67.6
|
1.0
|
OD1
|
A:ASP878
|
3.1
|
70.7
|
1.0
|
C
|
A:ILE879
|
3.8
|
67.0
|
1.0
|
C
|
A:LEU838
|
3.8
|
69.3
|
1.0
|
CG
|
A:ASP878
|
3.9
|
66.0
|
1.0
|
OD2
|
A:ASP878
|
4.0
|
64.3
|
1.0
|
OG1
|
A:THR797
|
4.1
|
62.9
|
1.0
|
CB
|
A:THR839
|
4.1
|
69.5
|
1.0
|
OG1
|
A:THR839
|
4.2
|
73.3
|
1.0
|
CA
|
A:THR839
|
4.4
|
62.7
|
1.0
|
N
|
A:ILE879
|
4.5
|
61.5
|
1.0
|
N
|
A:THR839
|
4.5
|
68.3
|
1.0
|
CA
|
A:LEU880
|
4.6
|
69.2
|
1.0
|
N
|
A:LEU880
|
4.7
|
71.6
|
1.0
|
N
|
A:LEU838
|
4.7
|
66.9
|
1.0
|
CA
|
A:ILE879
|
4.8
|
68.1
|
1.0
|
CB
|
A:LEU880
|
4.8
|
72.9
|
1.0
|
CD1
|
A:LEU880
|
4.8
|
79.1
|
1.0
|
CG1
|
A:ILE879
|
4.9
|
70.5
|
1.0
|
CA
|
A:LEU838
|
4.9
|
65.1
|
1.0
|
CA
|
A:GLY795
|
5.0
|
58.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 8dvn
Go back to
Calcium Binding Sites List in 8dvn
Calcium binding site 2 out
of 4 in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10
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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1303
b:72.2
occ:1.00
|
O
|
A:THR724
|
2.7
|
66.4
|
1.0
|
OD1
|
A:ASN727
|
2.8
|
71.4
|
1.0
|
OG
|
A:SER749
|
2.8
|
63.3
|
1.0
|
CG
|
A:ASN727
|
3.5
|
73.1
|
1.0
|
ND2
|
A:ASN727
|
3.5
|
66.5
|
1.0
|
CB
|
A:SER749
|
3.8
|
69.8
|
1.0
|
O
|
A:GLY725
|
3.9
|
72.4
|
1.0
|
C
|
A:THR724
|
4.0
|
60.2
|
1.0
|
CA
|
A:SER749
|
4.0
|
67.8
|
1.0
|
N
|
A:SER749
|
4.1
|
61.2
|
1.0
|
OD1
|
A:ASP748
|
4.1
|
73.6
|
1.0
|
C
|
A:GLY725
|
4.4
|
66.0
|
1.0
|
CA
|
A:GLY725
|
4.4
|
59.8
|
1.0
|
N
|
A:GLY725
|
4.7
|
67.1
|
1.0
|
CB
|
A:ASN727
|
4.9
|
65.0
|
1.0
|
CG2
|
A:THR724
|
4.9
|
59.6
|
1.0
|
|
Calcium binding site 3 out
of 4 in 8dvn
Go back to
Calcium Binding Sites List in 8dvn
Calcium binding site 3 out
of 4 in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10
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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1304
b:91.0
occ:1.00
|
O
|
A:ILE1062
|
2.6
|
71.7
|
1.0
|
OD2
|
A:ASP1018
|
2.8
|
62.8
|
1.0
|
O
|
A:LEU1019
|
3.1
|
64.3
|
1.0
|
OD1
|
A:ASP1018
|
3.2
|
69.3
|
1.0
|
CG
|
A:ASP1018
|
3.4
|
68.5
|
1.0
|
C
|
A:ILE1062
|
3.8
|
68.1
|
1.0
|
C
|
A:LEU1019
|
4.1
|
68.1
|
1.0
|
N
|
A:ILE1062
|
4.5
|
70.5
|
1.0
|
CB
|
A:SER1020
|
4.6
|
73.1
|
1.0
|
O
|
A:LEU1107
|
4.6
|
83.8
|
1.0
|
N
|
A:LEU1019
|
4.6
|
66.0
|
1.0
|
CB
|
A:VAL1063
|
4.6
|
68.1
|
1.0
|
N
|
A:VAL1063
|
4.7
|
70.1
|
1.0
|
CA
|
A:VAL1063
|
4.7
|
72.8
|
1.0
|
OG
|
A:SER1020
|
4.7
|
75.9
|
1.0
|
CB
|
A:ASP1018
|
4.8
|
57.5
|
1.0
|
CA
|
A:ILE1062
|
4.8
|
71.4
|
1.0
|
CA
|
A:CA1305
|
4.8
|
81.2
|
1.0
|
CG2
|
A:ILE1062
|
4.9
|
66.1
|
1.0
|
CA
|
A:SER1020
|
4.9
|
75.6
|
1.0
|
N
|
A:SER1020
|
4.9
|
64.2
|
1.0
|
|
Calcium binding site 4 out
of 4 in 8dvn
Go back to
Calcium Binding Sites List in 8dvn
Calcium binding site 4 out
of 4 in the Crystal Structure of LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10
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 LRP6 E3E4 in Complex with Disulfide Constrained Peptide E3.10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1305
b:81.2
occ:1.00
|
O
|
A:ILE1191
|
2.6
|
75.3
|
1.0
|
OD1
|
A:ASP1190
|
3.0
|
87.2
|
1.0
|
O
|
A:LEU1150
|
3.0
|
64.5
|
1.0
|
C
|
A:ILE1191
|
3.8
|
71.5
|
1.0
|
CG
|
A:ASP1190
|
3.9
|
73.6
|
1.0
|
C
|
A:LEU1150
|
4.1
|
64.4
|
1.0
|
OD2
|
A:ASP1190
|
4.1
|
68.5
|
1.0
|
CD2
|
A:HIS1192
|
4.4
|
69.9
|
1.0
|
O
|
A:LEU1107
|
4.4
|
83.8
|
1.0
|
CA
|
A:HIS1192
|
4.4
|
69.2
|
1.0
|
N
|
A:ILE1191
|
4.4
|
64.4
|
1.0
|
CB
|
A:HIS1192
|
4.5
|
62.2
|
1.0
|
OG1
|
A:THR1151
|
4.5
|
62.9
|
1.0
|
CB
|
A:THR1151
|
4.6
|
63.5
|
1.0
|
N
|
A:HIS1192
|
4.6
|
66.4
|
1.0
|
N
|
A:LEU1150
|
4.6
|
56.3
|
1.0
|
CG
|
A:HIS1192
|
4.8
|
64.0
|
1.0
|
CA
|
A:ILE1191
|
4.8
|
60.8
|
1.0
|
CA
|
A:CA1304
|
4.8
|
91.0
|
1.0
|
CA
|
A:THR1151
|
4.9
|
74.7
|
1.0
|
N
|
A:THR1151
|
4.9
|
63.0
|
1.0
|
CG2
|
A:ILE1191
|
4.9
|
57.3
|
1.0
|
CA
|
A:LEU1150
|
5.0
|
66.2
|
1.0
|
|
Reference:
A.K.Thakur,
S.E.Miller,
N.P.D.Liau,
S.Hwang,
S.Hansen,
F.De Sousa E Melo,
J.Sudhamsu,
R.N.Hannoush.
Synthetic Multivalent Disulfide-Constrained Peptide Agonists Potentiate WNT1/ Beta-Catenin Signaling Via LRP6 Coreceptor Clustering. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 36893429
DOI: 10.1021/ACSCHEMBIO.2C00753
Page generated: Tue Apr 11 12:44:07 2023
|