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Calcium in PDB 3biw: Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex

Protein crystallography data

The structure of Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex, PDB code: 3biw was solved by D.Arac, A.A.Boucard, E.Ozkan, P.Strop, E.Newell, T.C.Sudhof, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 229.830, 148.796, 123.602, 90.00, 90.38, 90.00
R / Rfree (%) 24.6 / 27.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex (pdb code 3biw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex, PDB code: 3biw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3biw

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Calcium binding site 1 out of 6 in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex


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 the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:89.2
occ:1.00
 OD1 E:ASN238 2.1 92.2 1.0
O E:VAL154 2.3 0.3 1.0
OD2 E:ASP137 2.3 96.8 1.0
O E:ILE236 2.4 91.4 1.0
OD1 E:ASP137 3.0 98.9 1.0
CG E:ASP137 3.0 98.6 1.0
CG E:ASN238 3.4 90.8 1.0
C E:VAL154 3.4 0.6 1.0
C E:ILE236 3.7 92.0 1.0
ND2 E:ASN238 4.1 92.2 1.0
N E:ASN238 4.2 88.7 1.0
CA E:VAL154 4.2 0.5 1.0
N E:GLY155 4.3 0.8 1.0
CA E:GLY155 4.3 0.7 1.0
O A:GLN395 4.4 92.8 1.0
CB E:ASN238 4.4 89.1 1.0
CB E:ASP137 4.5 99.0 1.0
CB E:VAL154 4.5 0.2 1.0
CA E:ILE236 4.6 94.0 1.0
N E:PHE237 4.6 89.7 1.0
OE2 A:GLU397 4.6 93.5 1.0
CA E:PHE237 4.7 88.1 1.0
N E:ILE236 4.8 96.9 1.0
CB E:ILE236 4.9 93.8 1.0
CA E:ASN238 5.0 89.2 1.0
C E:PHE237 5.0 88.1 1.0

Calcium binding site 2 out of 6 in 3biw

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Calcium binding site 2 out of 6 in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex


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 the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:96.3
occ:1.00
 OD2 E:ASP104 3.2 99.1 1.0
O E:ASN103 3.3 95.5 1.0
OD2 A:ASP402 3.9 93.5 1.0
CG E:ASP104 4.3 98.9 1.0
OD1 A:ASP402 4.3 92.0 1.0
C E:ASN103 4.4 95.6 1.0
CB E:ASN103 4.5 95.4 1.0
O A:THR569 4.5 76.6 1.0
CG A:ASP402 4.5 91.7 1.0
OD1 E:ASP104 4.7 0.6 1.0
NH1 A:ARG311 4.9 80.1 1.0

Calcium binding site 3 out of 6 in 3biw

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Calcium binding site 3 out of 6 in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex


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 the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:76.8
occ:1.00
 OD1 F:ASN238 2.2 80.6 1.0
O F:VAL154 2.2 97.0 1.0
O F:ILE236 2.5 79.9 1.0
OD2 F:ASP137 2.5 90.9 1.0
OD1 F:ASP137 3.1 88.9 1.0
CG F:ASP137 3.2 89.6 1.0
C F:VAL154 3.4 97.7 1.0
CG F:ASN238 3.4 81.9 1.0
C F:ILE236 3.7 79.8 1.0
O B:GLN395 3.9 96.3 1.0
ND2 F:ASN238 4.1 83.6 1.0
CA F:VAL154 4.3 96.2 1.0
N F:GLY155 4.3 99.3 1.0
CA F:GLY155 4.3 0.1 1.0
N F:ASN238 4.3 81.2 1.0
OE2 B:GLU397 4.3 96.5 1.0
CB F:ASN238 4.5 81.4 1.0
CA F:ILE236 4.5 79.0 1.0
CB F:VAL154 4.6 96.0 1.0
CB F:ASP137 4.6 88.5 1.0
N F:PHE237 4.7 79.9 1.0
N F:ILE236 4.7 79.3 1.0
CA F:PHE237 4.8 79.6 1.0
O B:GLY396 4.9 91.8 1.0
CB F:ILE236 4.9 78.3 1.0
CD1 F:LEU234 5.0 73.8 1.0

Calcium binding site 4 out of 6 in 3biw

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Calcium binding site 4 out of 6 in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex


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 the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca402

b:96.8
occ:1.00
 OD2 F:ASP104 3.4 91.3 1.0
O F:ASN103 3.4 88.2 1.0
OD2 B:ASP402 4.0 83.9 1.0
OD1 B:ASP402 4.4 81.8 1.0
CG F:ASP104 4.4 90.4 1.0
C F:ASN103 4.5 88.0 1.0
CB F:ASN103 4.5 91.0 1.0
CG B:ASP402 4.6 83.0 1.0
O B:THR569 4.7 72.4 1.0
OD1 F:ASP104 4.9 90.6 1.0
NH1 B:ARG311 4.9 79.5 1.0

Calcium binding site 5 out of 6 in 3biw

Go back to Calcium Binding Sites List in 3biw
Calcium binding site 5 out of 6 in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:79.5
occ:1.00
 O G:VAL154 2.2 82.9 1.0
OD1 G:ASN238 2.2 87.8 1.0
OD2 G:ASP137 2.4 90.6 1.0
O G:ILE236 2.4 84.0 1.0
OD1 G:ASP137 3.0 92.0 1.0
CG G:ASP137 3.0 91.3 1.0
C G:VAL154 3.3 83.8 1.0
CG G:ASN238 3.4 86.8 1.0
C G:ILE236 3.7 83.5 1.0
CA G:VAL154 4.2 83.9 1.0
ND2 G:ASN238 4.2 87.0 1.0
N G:GLY155 4.2 83.7 1.0
N G:ASN238 4.3 84.7 1.0
CA G:GLY155 4.3 84.4 1.0
CB G:VAL154 4.5 84.5 1.0
CB G:ASP137 4.5 90.8 1.0
CB G:ASN238 4.5 85.8 1.0
CA G:ILE236 4.6 83.3 1.0
O C:GLN395 4.6 85.3 1.0
N G:PHE237 4.6 83.7 1.0
CA G:PHE237 4.8 84.4 1.0
N G:ILE236 4.8 83.0 1.0
CB G:ILE236 5.0 83.1 1.0

Calcium binding site 6 out of 6 in 3biw

Go back to Calcium Binding Sites List in 3biw
Calcium binding site 6 out of 6 in the Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Neuroligin-1/Neurexin-1BETA Synaptic Adhesion Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca402

b:0.7
occ:1.00
 OD2 G:ASP104 3.2 0.6 1.0
O G:ASN103 3.3 0.6 1.0
OD2 C:ASP402 3.7 84.3 1.0
OD1 C:ASP402 4.0 81.8 1.0
O C:THR569 4.2 0.4 1.0
CG C:ASP402 4.3 82.5 1.0
CG G:ASP104 4.3 0.4 1.0
C G:ASN103 4.4 0.9 1.0
CB G:ASN103 4.5 0.5 1.0
NH1 C:ARG311 4.7 97.0 1.0
OD1 G:ASP104 4.7 0.4 1.0

Reference:

D.Arac, A.A.Boucard, E.Ozkan, P.Strop, E.Newell, T.C.Sudhof, A.T.Brunger. Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1BETA Complex Reveal Specific Protein-Protein and Protein-Ca(2+) Interactions. Neuron V. 56 992 2007.
ISSN: ISSN 0896-6273
PubMed: 18093522
DOI: 10.1016/J.NEURON.2007.12.002
Page generated: Sat Jul 13 08:18:27 2024

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