Calcium in PDB 3hn8: Crystal Structure of Synaptotagmin

The structure of Crystal Structure of Synaptotagmin, PDB code: 3hn8 was solved by P.Strop, M.Vrljic, J.Ernst, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 3.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	205.675, 205.675, 143.125, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 25.9

The structure of Crystal Structure of Synaptotagmin also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Synaptotagmin (pdb code 3hn8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Synaptotagmin, PDB code: 3hn8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca600 b:58.3 occ:1.00 O A:PHE387 2.6 73.1 1.0 OD2 A:ASP328 2.8 73.6 1.0 OD1 A:ASP328 2.9 82.1 1.0 OD2 A:ASP388 2.9 0.9 1.0 OD1 A:ASP334 3.0 0.4 1.0 CG A:ASP328 3.0 74.1 1.0 OD2 A:ASP386 3.1 62.7 1.0 OD1 A:ASP386 3.3 64.6 1.0 CG A:ASP334 3.4 98.5 1.0 CG A:ASP386 3.6 63.5 1.0 CG A:ASP388 3.7 0.7 1.0 CA A:CA606 3.8 57.1 1.0 C A:PHE387 3.8 69.3 1.0 OD2 A:ASP334 3.9 95.1 1.0 CB A:ASP334 4.0 78.5 1.0 OD1 A:ASP388 4.2 76.6 1.0 CA A:ASP388 4.2 98.0 1.0 ND2 B:ASN511 4.2 68.8 1.0 CB A:ASP328 4.3 79.0 1.0 N A:ASP334 4.3 95.3 1.0 N A:ASP388 4.5 78.0 1.0 CB A:ASP388 4.6 0.4 1.0 CA A:ASP334 4.8 85.9 1.0 N A:PHE387 4.9 71.6 1.0 CA A:PHE387 4.9 69.6 1.0

Calcium binding site 2 out of 18 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:50.0 occ:1.00 OG A:SER391 2.8 89.3 1.0 OD2 A:ASP394 2.8 89.9 1.0 OE2 B:GLU476 2.9 0.0 1.0 OD1 A:ASP388 2.9 76.6 1.0 OD1 A:ASP394 2.9 71.3 1.0 O A:ARG392 2.9 87.3 1.0 CG A:ASP394 3.1 81.9 1.0 CB A:SER391 3.2 69.2 1.0 OE1 B:GLU476 3.3 71.4 1.0 CD B:GLU476 3.3 96.0 1.0 CG A:ASP388 3.6 0.7 1.0 CA A:CA606 3.8 57.1 1.0 C A:ARG392 4.1 87.0 1.0 C A:SER391 4.1 71.3 1.0 CB A:ASP388 4.2 0.4 1.0 OD2 A:ASP388 4.2 0.9 1.0 CA A:SER391 4.3 72.1 1.0 N A:ARG392 4.3 0.0 1.0 O A:SER391 4.4 72.0 1.0 CB A:ASP394 4.4 79.8 1.0 CG B:GLU476 4.6 90.8 1.0 N A:ASP394 4.6 73.6 1.0 CA A:ARG392 4.8 0.8 1.0 CB B:GLU476 4.9 75.7 1.0 C A:HIS393 5.0 69.6 1.0 CA A:ASP394 5.0 72.6 1.0

Calcium binding site 3 out of 18 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:51.1 occ:1.00 OD1 A:ASP520 2.5 70.7 1.0 OD2 A:ASP460 2.6 73.0 1.0 OD2 A:ASP522 2.6 64.8 1.0 OD1 A:ASP522 2.8 81.7 1.0 OE2 A:GLU528 2.9 0.7 1.0 O A:MET459 2.9 76.9 1.0 CG A:ASP522 3.1 75.1 1.0 CD A:GLU528 3.1 91.1 1.0 CG A:ASP460 3.5 71.7 1.0 C A:MET459 3.5 76.9 1.0 OE1 A:GLU528 3.6 77.2 1.0 CG A:GLU528 3.7 76.2 1.0 CG A:ASP520 3.7 88.4 1.0 CA A:ASP460 3.9 77.5 1.0 N A:ASP460 3.9 69.2 1.0 CB A:MET459 4.2 68.2 1.0 CB A:ASP460 4.2 94.0 1.0 OD1 A:ASP460 4.3 67.5 1.0 CA A:CA605 4.3 55.5 1.0 OD2 A:ASP520 4.4 88.7 1.0 CA A:MET459 4.5 69.7 1.0 O A:TYR521 4.5 81.1 1.0 CB A:ASP522 4.6 76.5 1.0 CB A:ASP520 4.7 89.9 1.0

Calcium binding site 4 out of 18 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:79.1 occ:1.00 OD2 A:ASP466 2.8 0.9 1.0 OD1 A:ASN490 2.8 0.6 1.0 OD1 A:ASP466 2.9 0.5 1.0 CG A:ASP466 3.2 0.5 1.0 CG A:ASN490 3.8 0.4 1.0 CA A:CA605 3.9 55.5 1.0 OD1 A:ASP460 4.0 67.5 1.0 ND2 A:ASN490 4.0 0.4 1.0 OG1 A:THR462 4.3 97.8 1.0 CG A:ASP460 4.4 71.7 1.0 CG2 A:THR462 4.4 0.9 1.0 CB A:ASP466 4.7 78.4 1.0 OD2 A:ASP460 4.8 73.0 1.0 CB A:ASP460 4.9 94.0 1.0 CB A:THR462 4.9 0.7 1.0

Calcium binding site 5 out of 18 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:55.5 occ:1.00 O A:TYR521 2.5 81.1 1.0 OD2 A:ASP460 2.7 73.0 1.0 OD1 A:ASP460 2.8 67.5 1.0 OD2 A:ASP522 2.9 64.8 1.0 OD2 A:ASP520 3.0 88.7 1.0 CG A:ASP460 3.1 71.7 1.0 CG A:ASP466 3.4 0.5 1.0 OD1 A:ASP466 3.4 0.5 1.0 C A:TYR521 3.5 71.5 1.0 OD1 A:ASP520 3.5 70.7 1.0 CG A:ASP520 3.6 88.4 1.0 CB A:ASP466 3.7 78.4 1.0 OD2 A:ASP466 3.8 0.9 1.0 CA A:CA603 3.9 79.1 1.0 CA A:ASP522 4.0 65.8 1.0 CG A:ASP522 4.0 75.1 1.0 N A:ASP466 4.0 85.4 1.0 N A:ASP522 4.2 61.9 1.0 CA A:CA602 4.3 51.1 1.0 CA A:ASP466 4.5 72.7 1.0 CB A:ASP460 4.5 94.0 1.0 CA A:TYR521 4.5 64.1 1.0 N A:TYR521 4.6 71.0 1.0 CB A:ASP522 4.6 76.5 1.0 CD2 A:TYR521 4.8 85.5 1.0 CB A:TYR521 4.9 69.8 1.0 C A:SER465 4.9 78.8 1.0 OD1 A:ASP522 5.0 81.7 1.0 C A:ASP520 5.0 86.2 1.0

Calcium binding site 6 out of 18 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:57.1 occ:1.00 OD1 A:ASP386 2.6 64.6 1.0 OD1 A:ASP388 2.6 76.6 1.0 OD2 A:ASP328 2.7 73.6 1.0 OD1 A:ASP394 2.8 71.3 1.0 O A:LYS327 2.9 0.7 1.0 OD2 A:ASP388 3.0 0.9 1.0 OE2 B:GLU476 3.0 0.0 1.0 CG A:ASP388 3.2 0.7 1.0 C A:LYS327 3.3 0.5 1.0 ND2 B:ASN511 3.4 68.8 1.0 CD B:GLU476 3.6 96.0 1.0 CG A:ASP386 3.6 63.5 1.0 N A:ASP328 3.6 72.5 1.0 OE1 B:GLU476 3.6 71.4 1.0 CA A:ASP328 3.7 79.9 1.0 CG A:ASP328 3.8 74.1 1.0 CA A:CA600 3.8 58.3 1.0 CA A:CA601 3.8 50.0 1.0 CG A:ASP394 3.9 81.9 1.0 CB A:LYS327 3.9 71.4 1.0 CA A:LYS327 4.2 86.0 1.0 OD2 A:ASP386 4.2 62.7 1.0 CB A:ASP328 4.3 79.0 1.0 CB A:ASP394 4.5 79.8 1.0 CG B:ASN511 4.6 74.0 1.0 CB A:ASP388 4.6 0.4 1.0 CB A:ASP386 4.6 61.2 1.0 OD2 A:ASP394 4.8 89.9 1.0 OD1 A:ASP328 4.8 82.1 1.0 CG B:GLU476 4.9 90.8 1.0

Calcium binding site 7 out of 18 in the Crystal Structure of Synaptotagmin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca600 b:53.6 occ:1.00 O B:PHE387 2.5 68.8 1.0 OD2 B:ASP328 2.8 80.4 1.0 OD2 B:ASP388 2.9 0.2 1.0 OD2 B:ASP386 2.9 63.5 1.0 OD1 B:ASP328 3.0 0.9 1.0 OD1 B:ASP334 3.0 0.7 1.0 OD1 B:ASP386 3.1 63.9 1.0 CG B:ASP328 3.1 1.0 1.0 CG B:ASP334 3.4 94.7 1.0 CG B:ASP386 3.4 62.1 1.0 CG B:ASP388 3.6 84.7 1.0 C B:PHE387 3.6 69.9 1.0 CB B:ASP334 3.9 85.0 1.0 OD2 B:ASP334 3.9 92.4 1.0 CA B:CA606 3.9 57.2 1.0 OD1 B:ASP388 4.1 69.6 1.0 CA B:ASP388 4.1 81.7 1.0 N B:ASP334 4.3 91.8 1.0 N B:ASP388 4.3 77.6 1.0 CB B:ASP388 4.5 78.5 1.0 CB B:ASP328 4.5 0.4 1.0 N B:PHE387 4.7 70.1 1.0 CA B:ASP334 4.7 84.8 1.0 CA B:PHE387 4.8 67.9 1.0 CB B:ASP386 4.9 60.1 1.0

Calcium binding site 8 out of 18 in the Crystal Structure of Synaptotagmin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:51.0 occ:1.00 O B:ARG392 2.6 72.1 1.0 OD2 B:ASP394 2.7 89.4 1.0 OG B:SER391 2.7 82.9 1.0 OD1 B:ASP388 2.8 69.6 1.0 OD1 B:ASP394 3.0 76.7 1.0 CG B:ASP394 3.1 83.4 1.0 CB B:SER391 3.1 69.7 1.0 CG B:ASP388 3.5 84.7 1.0 C B:ARG392 3.8 72.2 1.0 CA B:CA606 3.8 57.2 1.0 C B:SER391 3.9 73.8 1.0 CB B:ASP388 4.1 78.5 1.0 N B:ARG392 4.1 93.8 1.0 CA B:SER391 4.2 75.1 1.0 O B:SER391 4.2 70.4 1.0 OD2 B:ASP388 4.3 0.2 1.0 N B:ASP394 4.3 79.2 1.0 CB B:ASP394 4.4 84.0 1.0 CA B:ARG392 4.5 92.7 1.0 C B:HIS393 4.7 67.7 1.0 N B:HIS393 4.7 75.9 1.0 CA B:ASP394 4.8 77.1 1.0 CA B:HIS393 4.8 72.3 1.0

Calcium binding site 9 out of 18 in the Crystal Structure of Synaptotagmin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:52.0 occ:1.00 OD1 B:ASP522 2.7 83.8 1.0 OD2 B:ASP522 2.7 66.1 1.0 OD2 B:ASP460 2.7 66.1 1.0 OD1 B:ASP520 2.8 56.3 1.0 OE2 B:GLU528 2.8 0.1 1.0 O B:MET459 2.9 80.3 1.0 CD B:GLU528 3.0 89.7 1.0 CG B:ASP522 3.1 77.2 1.0 OE1 B:GLU528 3.4 76.1 1.0 C B:MET459 3.6 87.3 1.0 CG B:ASP460 3.7 84.7 1.0 CG B:GLU528 3.7 76.0 1.0 CA B:ASP460 3.9 83.4 1.0 CG B:ASP520 4.0 74.2 1.0 N B:ASP460 4.0 74.8 1.0 CB B:MET459 4.3 74.5 1.0 CB B:ASP460 4.4 0.3 1.0 OD1 B:ASP460 4.5 83.1 1.0 CB B:ASP522 4.6 79.6 1.0 CA B:MET459 4.6 76.8 1.0 CA B:CA605 4.7 51.1 1.0 O B:TYR521 4.7 73.6 1.0 OD2 B:ASP520 4.7 73.8 1.0 CB B:ASP520 5.0 76.7 1.0

Calcium binding site 10 out of 18 in the Crystal Structure of Synaptotagmin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Synaptotagmin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:76.4 occ:1.00 OD1 B:ASN490 2.8 99.5 1.0 OD1 B:ASP466 3.0 0.6 1.0 OD2 B:ASP466 3.2 0.3 1.0 CG B:ASP466 3.4 0.5 1.0 OD1 B:ASP460 3.8 83.1 1.0 CG B:ASN490 3.9 95.7 1.0 CA B:CA605 3.9 51.1 1.0 OG1 B:THR462 3.9 0.1 1.0 CG2 B:THR462 4.0 0.1 1.0 CG B:ASP460 4.1 84.7 1.0 ND2 B:ASN490 4.2 0.5 1.0 CB B:THR462 4.5 0.0 1.0 CB B:ASP460 4.6 0.3 1.0 OD2 B:ASP460 4.6 66.1 1.0 CB B:ASP466 4.9 74.2 1.0

M.Vrljic, P.Strop, J.A.Ernst, R.B.Sutton, S.Chu, A.T.Brunger. Molecular Mechanism of the Synaptotagmin-Snare Interaction in CA2+-Triggered Vesicle Fusion. Nat.Struct.Mol.Biol. V. 17 325 2010.
ISSN: ISSN 1545-9993
PubMed: 20173762
DOI: 10.1038/NSMB.1764