Calcium in PDB 6nyt: MUNC13-1 C2B-Domain, Calcium Bound

The structure of MUNC13-1 C2B-Domain, Calcium Bound, PDB code: 6nyt was solved by D.R.Tomchick, J.Rizo, M.Machius, J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.37
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.943, 56.943, 89.983, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 16.9

The structure of MUNC13-1 C2B-Domain, Calcium Bound also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the MUNC13-1 C2B-Domain, Calcium Bound (pdb code 6nyt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the MUNC13-1 C2B-Domain, Calcium Bound, PDB code: 6nyt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the MUNC13-1 C2B-Domain, Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MUNC13-1 C2B-Domain, Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:8.3 occ:1.00 OD1 A:ASP759 2.3 9.2 1.0 O A:GLU758 2.4 8.0 1.0 O A:HOH1114 2.4 12.4 1.0 OD1 A:ASP757 2.4 7.3 1.0 OD2 A:ASP705 2.4 9.3 1.0 OD2 A:ASP711 2.4 8.8 1.0 OD1 A:ASP705 2.6 8.8 1.0 CG A:ASP705 2.8 8.5 1.0 CG A:ASP757 3.2 7.4 1.0 HA A:ASP759 3.4 12.1 1.0 HB2 A:ASP711 3.4 10.5 1.0 C A:GLU758 3.4 8.2 1.0 CG A:ASP711 3.4 8.3 1.0 OD2 A:ASP757 3.4 8.8 1.0 CG A:ASP759 3.6 10.4 1.0 H A:ASP711 3.7 8.4 1.0 CA A:CA902 3.8 8.3 1.0 CB A:ASP711 3.9 8.7 1.0 CA A:ASP759 4.1 10.1 1.0 HA A:SER710 4.1 8.9 1.0 N A:ASP759 4.1 8.8 1.0 O A:HOH1068 4.1 20.4 1.0 N A:ASP711 4.2 7.0 1.0 C A:ASP757 4.3 8.4 1.0 O A:ASP757 4.3 8.3 1.0 O A:HOH1046 4.3 17.6 1.0 N A:GLU758 4.3 8.5 1.0 CB A:ASP705 4.4 8.4 1.0 CB A:ASP759 4.4 11.1 1.0 OD1 A:ASP711 4.4 9.2 1.0 O A:HOH1125 4.4 32.1 1.0 OD2 A:ASP759 4.4 15.0 1.0 O A:HOH1027 4.5 13.4 1.0 CA A:GLU758 4.5 8.4 1.0 CB A:ASP757 4.6 7.6 1.0 H A:GLU758 4.6 10.2 1.0 HB3 A:ASP705 4.7 10.1 1.0 HB3 A:ASP711 4.7 10.5 1.0 CA A:ASP711 4.7 8.0 1.0 HB2 A:ASP705 4.7 10.1 1.0 HB3 A:GLU758 4.7 11.3 1.0 O A:HOH1087 4.8 25.6 1.0 HB3 A:ASP759 4.8 13.3 1.0 C A:SER710 4.9 7.9 1.0 CA A:SER710 4.9 7.4 1.0 CA A:ASP757 4.9 7.3 1.0 H A:ASP759 4.9 10.6 1.0 HA A:ASP757 4.9 8.7 1.0

Calcium binding site 2 out of 2 in the MUNC13-1 C2B-Domain, Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MUNC13-1 C2B-Domain, Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:8.3 occ:1.00 OD2 A:ASP757 2.3 8.8 1.0 OD2 A:ASP776 2.3 10.4 1.0 O A:LYS704 2.4 7.8 1.0 OD1 A:ASP705 2.4 8.8 1.0 O A:HOH1116 2.4 14.0 1.0 OD2 A:ASP759 2.4 15.0 1.0 OD1 A:ASP759 2.5 9.2 1.0 CG A:ASP759 2.8 10.4 1.0 C A:LYS704 3.3 8.2 1.0 CG A:ASP757 3.4 7.4 1.0 CG A:ASP776 3.4 9.2 1.0 HA A:ASP705 3.5 9.7 1.0 CG A:ASP705 3.6 8.5 1.0 HB2 A:ASP776 3.6 10.5 1.0 HB3 A:LYS704 3.8 9.9 1.0 CA A:CA901 3.8 8.3 1.0 HB2 A:LYS704 4.0 9.9 1.0 OD1 A:ASP757 4.0 7.3 1.0 N A:ASP705 4.0 7.8 1.0 CB A:ASP776 4.1 8.8 1.0 CA A:ASP705 4.1 8.1 1.0 CB A:LYS704 4.2 8.3 1.0 H A:ASP776 4.2 10.1 1.0 CB A:ASP759 4.3 11.1 1.0 CA A:LYS704 4.3 8.2 1.0 O A:HOH1046 4.3 17.6 1.0 HB3 A:ASP757 4.3 9.2 1.0 OD2 A:ASP705 4.4 9.3 1.0 OD1 A:ASP776 4.4 10.8 1.0 CB A:ASP705 4.4 8.4 1.0 CB A:ASP757 4.5 7.6 1.0 HB3 A:ASP759 4.6 13.3 1.0 O A:HOH1010 4.6 20.1 1.0 O A:HOH1005 4.6 20.4 1.0 O A:HOH1078 4.6 10.6 1.0 O A:ASP757 4.7 8.3 1.0 HB3 A:ASP776 4.7 10.5 1.0 HZ1 A:LYS771 4.7 24.7 1.0 H A:ASP705 4.7 9.3 1.0 HB2 A:ASP759 4.7 13.3 1.0 HZ2 A:LYS771 4.8 24.7 1.0 O A:HOH1114 4.9 12.4 1.0 HA A:LYS704 4.9 9.9 1.0 HB3 A:ASP705 4.9 10.1 1.0 N A:ASP776 4.9 8.4 1.0

O.H.Shin, J.Lu, J.S.Rhee, D.R.Tomchick, Z.P.Pang, S.M.Wojcik, M.Camacho-Perez, N.Brose, M.Machius, J.Rizo, C.Rosenmund, T.C.Sudhof. MUNC13 C2B Domain Is An Activity-Dependent CA2+ Regulator of Synaptic Exocytosis. Nat. Struct. Mol. Biol. V. 17 280 2010.
ISSN: ESSN 1545-9985
PubMed: 20154707
DOI: 10.1038/NSMB.1758