Chlorine 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:

Calcium

(Ca)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of MUNC13-1 C2B-Domain, Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl903 b:17.1 occ:1.00 H A:ALA806 2.5 17.8 1.0 HA A:SER805 2.9 23.1 1.0 HZ3 A:LYS704 3.0 11.3 1.0 HZ1 A:LYS704 3.1 11.3 1.0 HD2 A:PHE777 3.1 12.9 1.0 O A:HOH1029 3.1 21.2 1.0 HZ2 A:LYS704 3.1 11.3 1.0 O A:HOH1105 3.3 30.8 1.0 NZ A:LYS704 3.3 9.4 1.0 HB3 A:PHE777 3.3 12.0 1.0 N A:ALA806 3.3 14.9 1.0 O A:HOH1065 3.5 25.2 1.0 HB3 A:SER805 3.6 21.2 1.0 CA A:SER805 3.7 19.2 1.0 HG A:SER805 3.8 23.0 1.0 HB3 A:ALA806 3.9 17.2 1.0 CD2 A:PHE777 4.0 10.7 1.0 O A:ALA806 4.0 10.8 1.0 C A:SER805 4.0 17.4 1.0 CB A:SER805 4.1 17.6 1.0 O A:PHE777 4.2 9.5 1.0 CB A:PHE777 4.3 10.0 1.0 CA A:ALA806 4.3 12.8 1.0 OG A:SER805 4.4 19.2 1.0 HG23 A:VAL807 4.5 14.2 1.0 C A:ALA806 4.5 10.6 1.0 HH21 A:ARG801 4.5 30.3 1.0 CB A:ALA806 4.5 14.4 1.0 CG A:PHE777 4.6 9.4 1.0 H A:PHE777 4.7 10.9 1.0 CE A:LYS704 4.7 8.0 1.0 HB2 A:PHE777 4.8 12.0 1.0 HB2 A:ALA806 4.8 17.2 1.0 O A:LYS804 4.8 25.9 1.0 N A:SER805 4.8 22.8 1.0 C A:PHE777 4.9 9.0 1.0 HE2 A:PHE777 5.0 13.1 1.0 HB2 A:SER805 5.0 21.2 1.0 HG22 A:VAL807 5.0 14.2 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of MUNC13-1 C2B-Domain, Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl904 b:29.6 occ:1.00 HZ3 A:LYS723 2.2 32.6 0.6 H A:HIS741 2.3 17.9 1.0 HA A:PHE740 2.7 15.3 1.0 HZ2 A:LYS723 2.8 32.6 0.6 NZ A:LYS723 2.9 27.2 0.6 HE3 A:LYS723 2.9 28.3 0.4 N A:HIS741 3.1 14.9 1.0 HD3 A:LYS723 3.2 24.3 0.4 HD3 A:LYS723 3.2 24.2 0.6 HB2 A:HIS741 3.4 23.7 1.0 HZ1 A:LYS723 3.4 32.6 0.6 CA A:PHE740 3.6 12.7 1.0 CE A:LYS723 3.7 23.6 0.4 HD1 A:PHE740 3.7 17.6 1.0 CD A:LYS723 3.7 20.2 0.4 CD A:LYS723 3.7 20.2 0.6 HD2 A:LYS723 3.7 24.2 0.6 HZ2 A:LYS723 3.8 32.7 0.4 HD2 A:LYS723 3.8 24.3 0.4 HB3 A:PHE740 3.8 16.4 1.0 CE A:LYS723 3.8 23.5 0.6 C A:PHE740 3.8 15.0 1.0 O A:HIS741 4.0 18.0 1.0 CA A:HIS741 4.0 17.0 1.0 CB A:HIS741 4.1 19.8 1.0 HE2 A:LYS723 4.2 28.2 0.6 NZ A:LYS723 4.2 27.2 0.4 CB A:PHE740 4.2 13.6 1.0 O A:ASN739 4.4 16.0 1.0 CD1 A:PHE740 4.5 14.7 1.0 HE2 A:LYS723 4.5 28.3 0.4 HZ1 A:LYS723 4.5 32.7 0.4 C A:HIS741 4.5 17.1 1.0 CG A:HIS741 4.6 22.9 1.0 HE3 A:LYS723 4.6 28.2 0.6 N A:PHE740 4.7 12.4 1.0 O A:HOH1017 4.7 31.3 1.0 CG A:PHE740 4.8 14.5 1.0 HA A:HIS741 4.9 20.4 1.0 HB3 A:HIS741 4.9 23.7 1.0 HZ3 A:LYS723 5.0 32.7 0.4 O A:HOH1039 5.0 26.6 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