Lead in PDB 5vfe: Synaptotagmin 1 C2A Domain, Lead-Bound

The structure of Synaptotagmin 1 C2A Domain, Lead-Bound, PDB code: 5vfe was solved by A.B.Taylor, P.J.Hart, T.I.Igumenova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 1.38
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	55.040, 55.040, 77.160, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 17.8

The binding sites of Lead atom in the Synaptotagmin 1 C2A Domain, Lead-Bound (pdb code 5vfe). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 2 binding sites of Lead where determined in the Synaptotagmin 1 C2A Domain, Lead-Bound, PDB code: 5vfe:
Jump to Lead binding site number: 1; 2;

Lead binding site 1 out of 2 in the Synaptotagmin 1 C2A Domain, Lead-Bound


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Synaptotagmin 1 C2A Domain, Lead-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb301 b:15.4 occ:0.91 OD2 A:ASP172 2.5 17.7 1.0 OD1 A:ASP172 2.5 17.3 1.0 OD2 A:ASP230 2.5 17.2 1.0 OD1 A:ASP230 2.7 15.4 1.0 O A:HOH442 2.7 21.5 1.0 O A:HOH525 2.7 29.3 1.0 CG A:ASP172 2.8 15.9 1.0 O A:PHE231 2.8 15.7 1.0 OD2 A:ASP178 2.9 16.3 1.0 CG A:ASP230 2.9 15.8 1.0 O A:HOH419 3.7 46.9 1.0 CG A:ASP178 3.8 13.5 1.0 O A:HOH451 3.9 23.9 1.0 C A:PHE231 4.0 12.7 1.0 CB A:ASP178 4.1 12.3 1.0 CB A:ASP172 4.3 17.4 1.0 O A:HOH519 4.4 28.4 1.0 N A:ASP178 4.4 11.9 1.0 CB A:ASP230 4.4 15.1 1.0 O A:HOH467 4.6 27.7 1.0 OD2 A:ASP232 4.7 19.6 1.0 O A:HOH440 4.7 18.6 1.0 O A:HOH450 4.7 26.9 1.0 N A:PHE231 4.7 12.8 1.0 O A:HOH475 4.7 18.9 1.0 C A:ASP230 4.7 13.7 1.0 OD1 A:ASP178 4.8 13.6 1.0 CA A:ASP232 4.8 14.6 1.0 N A:ASP232 4.9 14.0 1.0 CA A:ASP178 4.9 12.0 1.0 CA A:PHE231 5.0 12.4 1.0

Lead binding site 2 out of 2 in the Synaptotagmin 1 C2A Domain, Lead-Bound


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Synaptotagmin 1 C2A Domain, Lead-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Pb301 b:14.5 occ:0.85 OD2 B:ASP172 2.5 17.1 1.0 OD1 B:ASP172 2.5 18.3 1.0 OD2 B:ASP230 2.6 17.0 1.0 OD1 B:ASP230 2.7 15.3 1.0 OD2 B:ASP178 2.7 16.1 1.0 O B:HOH540 2.8 32.0 1.0 O B:HOH467 2.8 24.3 1.0 CG B:ASP172 2.8 15.4 1.0 O B:PHE231 2.9 17.1 1.0 CG B:ASP230 3.0 15.9 1.0 CG B:ASP178 3.7 14.2 1.0 O B:HOH496 4.0 24.3 1.0 C B:PHE231 4.1 16.2 1.0 CB B:ASP178 4.1 14.2 1.0 CB B:ASP172 4.3 16.0 1.0 N B:ASP178 4.4 13.0 1.0 CB B:ASP230 4.5 16.8 1.0 O B:HOH457 4.5 16.3 1.0 O B:HOH423 4.6 17.4 1.0 O B:HOH477 4.7 20.2 1.0 O B:HOH431 4.7 28.2 1.0 N B:PHE231 4.7 13.3 1.0 C B:ASP230 4.8 14.5 1.0 OD1 B:ASP178 4.8 17.0 1.0 OD1 B:ASP232 4.8 21.8 1.0 CA B:ASP232 4.9 15.9 1.0 N B:ASP232 4.9 15.4 1.0 CA B:ASP178 4.9 12.1 1.0

S.Katti, B.Her, A.K.Srivastava, A.B.Taylor, S.W.Lockless, T.I.Igumenova. High Affinity Interactions of PB2+with Synaptotagmin I. Metallomics V. 10 1211 2018.
ISSN: ESSN 1756-591X
PubMed: 30063057
DOI: 10.1039/C8MT00135A