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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: Fri Jul 19 08:01:53 2024

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