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Calcium in PDB 7ndg: Cryo-Em Structure of the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B (pdb code 7ndg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cryo-Em Structure of the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B, PDB code: 7ndg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7ndg

Go back to Calcium Binding Sites List in 7ndg
Calcium binding site 1 out of 3 in the Cryo-Em Structure of the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B


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 the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:111.0
occ:1.00
 OD1 A:ASP110 2.5 148.0 1.0
O A:SER277 2.5 123.6 1.0
O A:THR118 2.6 136.8 1.0
O A:PHE107 2.8 129.1 1.0
OG1 A:THR118 2.8 148.5 1.0
CG A:ASP110 3.5 150.0 1.0
C A:SER277 3.6 122.0 1.0
C A:THR118 3.6 140.2 1.0
CB A:THR118 3.9 150.3 1.0
OD2 A:ASP110 3.9 157.3 1.0
C A:PHE107 4.0 130.4 1.0
O A:ASP110 4.0 136.3 1.0
CA A:THR118 4.1 140.6 1.0
N A:THR118 4.1 140.5 1.0
O A:LEU111 4.2 142.8 1.0
CA A:SER277 4.2 119.6 1.0
CA A:ASN112 4.4 133.2 1.0
OD1 A:ASN112 4.5 154.5 1.0
CB A:SER277 4.5 124.0 1.0
C A:ASP110 4.5 138.9 1.0
O A:LEU108 4.5 124.7 1.0
C A:LEU111 4.6 140.6 1.0
N A:ASN112 4.7 133.9 1.0
N A:ASP278 4.7 115.3 1.0
CA A:PHE107 4.8 130.4 1.0
CB A:ASP110 4.8 140.8 1.0
N A:CYS119 4.8 136.6 1.0
C A:LEU108 4.9 126.4 1.0
CB A:ASN112 4.9 131.9 1.0
N A:LEU108 4.9 124.7 1.0
OD1 A:ASP278 4.9 134.2 1.0
N A:ASP110 4.9 132.8 1.0
CA A:ASP278 5.0 113.4 1.0
CA A:ASP110 5.0 135.6 1.0
CA A:LEU108 5.0 121.1 1.0

Calcium binding site 2 out of 3 in 7ndg

Go back to Calcium Binding Sites List in 7ndg
Calcium binding site 2 out of 3 in the Cryo-Em Structure of the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B


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 the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca501

b:111.0
occ:1.00
 OD1 G:ASP110 2.5 148.0 1.0
O G:SER277 2.5 123.6 1.0
O G:THR118 2.6 136.8 1.0
O G:PHE107 2.8 129.1 1.0
OG1 G:THR118 2.8 148.5 1.0
CG G:ASP110 3.5 150.0 1.0
C G:SER277 3.6 122.0 1.0
C G:THR118 3.6 140.2 1.0
CB G:THR118 3.9 150.3 1.0
OD2 G:ASP110 3.9 157.3 1.0
C G:PHE107 4.0 130.4 1.0
O G:ASP110 4.0 136.3 1.0
CA G:THR118 4.1 140.6 1.0
N G:THR118 4.1 140.5 1.0
O G:LEU111 4.2 142.8 1.0
CA G:SER277 4.2 119.6 1.0
CA G:ASN112 4.4 133.2 1.0
OD1 G:ASN112 4.5 154.5 1.0
CB G:SER277 4.5 124.0 1.0
C G:ASP110 4.5 138.9 1.0
O G:LEU108 4.5 124.7 1.0
C G:LEU111 4.6 140.6 1.0
N G:ASN112 4.7 133.9 1.0
N G:ASP278 4.7 115.3 1.0
CA G:PHE107 4.8 130.4 1.0
CB G:ASP110 4.8 140.8 1.0
N G:CYS119 4.8 136.6 1.0
CB G:ASN112 4.9 131.9 1.0
C G:LEU108 4.9 126.4 1.0
N G:LEU108 4.9 124.7 1.0
OD1 G:ASP278 4.9 134.2 1.0
N G:ASP110 4.9 132.8 1.0
CA G:ASP278 5.0 113.4 1.0
CA G:ASP110 5.0 135.6 1.0
CA G:LEU108 5.0 121.1 1.0

Calcium binding site 3 out of 3 in 7ndg

Go back to Calcium Binding Sites List in 7ndg
Calcium binding site 3 out of 3 in the Cryo-Em Structure of the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B


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 the Ternary Complex Between Netrin-1, Neogenin and Repulsive Guidance Molecule B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:111.0
occ:1.00
 OD1 D:ASP110 2.5 148.0 1.0
O D:SER277 2.5 123.6 1.0
O D:THR118 2.6 136.8 1.0
O D:PHE107 2.8 129.1 1.0
OG1 D:THR118 2.8 148.5 1.0
CG D:ASP110 3.5 150.0 1.0
C D:SER277 3.6 122.0 1.0
C D:THR118 3.6 140.2 1.0
CB D:THR118 3.9 150.3 1.0
OD2 D:ASP110 3.9 157.3 1.0
C D:PHE107 4.0 130.4 1.0
O D:ASP110 4.0 136.3 1.0
CA D:THR118 4.1 140.6 1.0
N D:THR118 4.1 140.5 1.0
O D:LEU111 4.2 142.8 1.0
CA D:SER277 4.2 119.6 1.0
CA D:ASN112 4.4 133.2 1.0
OD1 D:ASN112 4.5 154.5 1.0
CB D:SER277 4.5 124.0 1.0
C D:ASP110 4.5 138.9 1.0
O D:LEU108 4.5 124.7 1.0
C D:LEU111 4.6 140.6 1.0
N D:ASN112 4.7 133.9 1.0
N D:ASP278 4.7 115.3 1.0
CA D:PHE107 4.8 130.4 1.0
CB D:ASP110 4.8 140.8 1.0
N D:CYS119 4.8 136.6 1.0
C D:LEU108 4.9 126.4 1.0
CB D:ASN112 4.9 131.9 1.0
N D:LEU108 4.9 124.7 1.0
OD1 D:ASP278 4.9 134.2 1.0
N D:ASP110 4.9 132.8 1.0
CA D:ASP278 5.0 113.4 1.0
CA D:ASP110 5.0 135.6 1.0
CA D:LEU108 5.0 121.1 1.0

Reference:

R.A.Robinson, S.C.Griffiths, L.L.Van De Haar, T.Malinauskas, E.Y.Van Battum, P.Zelina, R.A.Schwab, D.Karia, L.Malinauskaite, S.Brignani, M.H.Van Den Munkhof, O.Dudukcu, A.A.De Ruiter, D.M.A.Van Den Heuvel, B.Bishop, J.Elegheert, A.R.Aricescu, R.J.Pasterkamp, C.Siebold. Simultaneous Binding of Guidance Cues NET1 and Rgm Blocks Extracellular NEO1 Signaling. Cell 2021.
PubMed: 33740419
DOI: 10.1016/J.CELL.2021.02.045
Page generated: Wed Jul 9 23:36:41 2025

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