Calcium in PDB 4m5e: TSE3 Structure

The structure of TSE3 Structure, PDB code: 4m5e was solved by Y.Qian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.60 / 1.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.995, 70.128, 41.940, 90.00, 90.52, 90.00
R / Rfree (%)	18.1 / 19.9

The structure of TSE3 Structure also contains other interesting chemical elements:

Cadmium

(Cd)

1 atom

The binding sites of Calcium atom in the TSE3 Structure (pdb code 4m5e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the TSE3 Structure, PDB code: 4m5e:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the TSE3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of TSE3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:17.6 occ:1.00 O A:ASN384 2.3 20.3 1.0 O A:ARG379 2.4 20.0 0.5 O A:ARG379 2.4 20.0 0.5 O A:HOH618 2.5 20.6 1.0 OG A:SER378 2.5 19.3 1.0 OD1 A:ASP382 2.5 18.3 1.0 OE2 A:GLU375 2.5 17.4 1.0 OE1 A:GLU375 2.6 16.5 1.0 CD A:GLU375 2.9 15.4 1.0 CG A:ASP382 3.4 19.1 1.0 C A:ASN384 3.5 18.3 1.0 C A:ARG379 3.5 20.6 0.5 C A:ARG379 3.5 20.6 0.5 CB A:SER378 3.6 19.5 1.0 OD2 A:ASP382 3.7 23.4 1.0 N A:ARG379 3.9 19.1 0.5 N A:ARG379 3.9 19.1 0.5 C A:SER378 4.0 20.4 1.0 N A:ASN384 4.2 20.4 1.0 CA A:ASN384 4.2 21.4 1.0 CA A:ARG379 4.3 21.6 0.5 CA A:ARG379 4.3 21.6 0.5 CB A:ASN384 4.4 22.8 1.0 CG A:GLU375 4.4 16.6 1.0 O A:SER378 4.4 21.2 1.0 CA A:SER378 4.4 18.6 1.0 N A:LEU385 4.5 17.7 1.0 N A:TRP381 4.5 17.0 1.0 N A:ASP382 4.5 17.4 1.0 OG A:SER374 4.6 16.4 1.0 N A:PRO380 4.6 18.0 1.0 O A:SER374 4.6 17.0 1.0 O A:HOH857 4.6 33.7 1.0 CA A:PRO380 4.7 17.5 1.0 CA A:LEU385 4.7 19.6 1.0 CB A:ARG379 4.7 25.0 0.5 CB A:ARG379 4.7 25.0 0.5 CA A:GLU375 4.7 15.8 1.0 O A:HOH607 4.8 17.1 1.0 CB A:ASP382 4.8 22.1 1.0 C A:PRO380 4.9 18.4 1.0 CB A:GLU375 4.9 14.3 1.0

Calcium binding site 2 out of 4 in the TSE3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of TSE3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:17.7 occ:1.00 O A:ASP253 2.4 19.3 1.0 OE1 A:GLN254 2.4 17.3 1.0 OD1 A:ASN181 2.5 31.8 1.0 O A:HOH611 2.5 19.2 1.0 OE2 A:GLU258 2.5 24.0 1.0 O A:HOH604 2.5 18.0 1.0 OE1 A:GLU258 2.7 21.4 1.0 CD A:GLU258 2.9 20.1 1.0 CD A:GLN254 3.5 18.4 1.0 C A:ASP253 3.6 17.5 1.0 CG A:ASN181 3.6 27.4 1.0 NE2 A:GLN280 3.9 15.0 1.0 CA A:GLN254 4.0 19.5 1.0 NE2 A:GLN254 4.2 18.3 1.0 N A:GLN254 4.2 17.4 1.0 CB A:GLN254 4.2 17.5 1.0 CG A:GLU258 4.3 20.0 1.0 O A:GLU250 4.4 17.1 1.0 CA A:ASN181 4.4 23.9 1.0 O A:HOH623 4.4 27.7 1.0 CD A:GLN280 4.4 18.9 1.0 CG A:GLN254 4.5 18.5 1.0 CB A:ASN181 4.5 24.5 1.0 ND2 A:ASN181 4.5 19.6 1.0 CG A:GLN280 4.6 17.3 1.0 CB A:ASP253 4.6 21.2 1.0 CG A:ASP253 4.7 22.0 1.0 CA A:ASP253 4.7 15.2 1.0 O A:HOH943 4.7 36.3 1.0 CD A:PRO182 4.8 23.3 1.0 N A:ASN181 4.8 24.2 1.0 OE2 A:GLU250 5.0 18.5 1.0 OD1 A:ASP253 5.0 19.5 1.0 OD2 A:ASP253 5.0 21.7 1.0

Calcium binding site 3 out of 4 in the TSE3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of TSE3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:17.3 occ:1.00 OD1 A:ASP117 2.3 22.3 1.0 OD2 A:ASP117 2.5 21.4 1.0 O A:HOH636 2.5 26.5 1.0 O A:HOH880 2.5 35.4 1.0 O A:HOH721 2.6 27.4 1.0 O A:HOH668 2.6 30.0 1.0 CG A:ASP117 2.7 22.2 1.0 O A:HOH843 4.2 36.6 1.0 CB A:ASP117 4.2 16.7 1.0 N A:GLY297 4.2 20.1 1.0 CA A:GLY297 4.3 20.5 1.0 CG2 A:VAL300 4.5 24.0 1.0 O A:HOH1057 4.6 44.7 1.0 O A:ASP113 4.7 17.9 1.0 O A:HOH816 4.8 36.6 1.0 CA A:ASP117 4.9 17.1 1.0

Calcium binding site 4 out of 4 in the TSE3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of TSE3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:18.7 occ:1.00 O A:HOH648 2.5 20.6 1.0 O A:HOH672 2.6 23.6 1.0 O A:HOH610 2.8 19.2 1.0 CG A:LEU403 4.1 35.8 1.0 CD2 A:LEU403 4.2 33.2 1.0 CA A:GLU404 4.3 35.1 1.0 N A:GLU404 4.4 35.4 1.0 NE2 A:GLN241 4.5 24.4 1.0 C A:LEU403 4.7 34.8 1.0 O A:LEU403 4.7 40.4 1.0 CB A:GLU404 4.8 37.1 1.0 CB A:LEU403 5.0 32.6 1.0

D.Lu, G.Shang, H.Zhang, Q.Yu, X.Cong, J.Yuan, F.He, C.Zhu, Y.Zhao, K.Yin, Y.Chen, J.Hu, X.Zhang, Z.Yuan, S.Xu, W.Hu, H.Cang, L.Gu. Structural Insights Into the T6SS Effector Protein TSE3 and the TSE3-TSI3 Complex From Pseudomonas Aeruginosa Reveal A Calcium-Dependent Membrane-Binding Mechanism Mol.Microbiol. V. 92 1092 2014.
ISSN: ISSN 0950-382X
PubMed: 24724564
DOI: 10.1111/MMI.12616