Magnesium in PDB 1dqv: Crystal Structure of Synaptotagmin III C2A/C2B

The structure of Crystal Structure of Synaptotagmin III C2A/C2B, PDB code: 1dqv was solved by R.B.Sutton, J.A.Ernst, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.20
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	125.959, 125.959, 118.438, 90.00, 90.00, 120.00
R / Rfree (%)	29.3 / 34.8

The binding sites of Magnesium atom in the Crystal Structure of Synaptotagmin III C2A/C2B (pdb code 1dqv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Synaptotagmin III C2A/C2B, PDB code: 1dqv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Synaptotagmin III C2A/C2B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Synaptotagmin III C2A/C2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg590 b:69.6 occ:1.00 OD2 A:ASP328 2.8 81.0 1.0 MG A:MG591 2.9 63.8 1.0 CG A:ASP328 3.5 80.5 1.0 OD2 A:ASP388 3.6 59.7 1.0 OD2 A:ASP386 3.7 51.1 1.0 CB A:ASP328 3.9 76.7 1.0 MG A:MG592 4.1 66.3 1.0 CA A:ASP328 4.2 72.7 1.0 OD1 A:ASP328 4.4 81.8 1.0 O A:PHE387 4.4 40.0 1.0 CG A:ASP386 4.5 45.7 1.0 OD1 A:ASP386 4.5 46.4 1.0 CG A:ASP388 4.6 53.5 1.0 CB A:ASP388 4.7 51.1 1.0 N A:ASP328 4.8 70.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Synaptotagmin III C2A/C2B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Synaptotagmin III C2A/C2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg591 b:63.8 occ:1.00 OD2 A:ASP328 2.8 81.0 1.0 MG A:MG590 2.9 69.6 1.0 OD1 A:ASP334 3.4 56.1 1.0 O A:PHE387 3.6 40.0 1.0 CG A:ASP334 4.0 51.5 1.0 CG A:ASP328 4.1 80.5 1.0 OD2 A:ASP388 4.3 59.7 1.0 OD2 A:ASP334 4.4 53.4 1.0 CA A:ASP388 4.7 48.7 1.0 CB A:ASP328 4.8 76.7 1.0 C A:PHE387 4.8 39.5 1.0 CB A:ASP334 4.8 47.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Synaptotagmin III C2A/C2B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Synaptotagmin III C2A/C2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg592 b:66.3 occ:1.00 OD2 A:ASP388 3.2 59.7 1.0 CB A:ASP388 3.4 51.1 1.0 CG A:ASP388 3.4 53.5 1.0 CB A:SER391 3.5 59.0 1.0 OG A:SER391 3.6 59.1 1.0 O A:ARG392 3.7 52.4 1.0 OD1 A:ASP394 3.9 52.2 1.0 MG A:MG590 4.1 69.6 1.0 OD2 A:ASP386 4.1 51.1 1.0 OD1 A:ASP388 4.2 54.2 1.0 CA A:SER391 4.7 56.1 1.0 CA A:ASP388 4.8 48.7 1.0 C A:SER391 4.8 56.4 1.0 C A:ARG392 4.8 52.2 1.0 CG A:ASP394 4.9 53.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Synaptotagmin III C2A/C2B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Synaptotagmin III C2A/C2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg593 b:34.3 occ:1.00 OD2 A:ASP460 2.8 51.3 1.0 OD1 A:ASP460 2.9 51.3 1.0 CG A:ASP460 3.2 51.3 1.0 OD1 A:ASP466 3.7 52.2 1.0 CG A:ASP466 4.1 52.2 1.0 OD2 A:ASP522 4.2 79.7 1.0 O A:TYR521 4.2 47.1 1.0 OD2 A:ASP466 4.3 52.2 1.0 CB A:ASP460 4.6 51.3 1.0 CA A:ASP522 4.6 0.3 1.0 CG A:ASP522 4.7 79.7 1.0 CB A:ASP522 4.8 79.7 1.0 OD1 A:ASP520 4.8 36.6 1.0

R.B.Sutton, J.A.Ernst, A.T.Brunger. Crystal Structure of the Cytosolic C2A-C2B Domains of Synaptotagmin III. Implications For Ca(+2)-Independent Snare Complex Interaction. J.Cell Biol. V. 147 589 1999.
ISSN: ISSN 0021-9525
PubMed: 10545502
DOI: 10.1083/JCB.147.3.589