Calcium in PDB 4n88: Crystal Structure of TSE3-TSI3 Complex with Calcium Ion

The structure of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion, PDB code: 4n88 was solved by G.J.Shang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.38 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.236, 95.317, 160.762, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.9

The binding sites of Calcium atom in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion (pdb code 4n88). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion, PDB code: 4n88:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:81.5 occ:1.00 O A:GLN20 2.6 67.8 1.0 O A:HOH639 2.7 67.7 1.0 OD1 A:ASP18 2.8 77.9 1.0 OE1 A:GLU25 2.8 61.1 1.0 OD2 A:ASP18 2.9 82.4 1.0 O A:HOH640 2.9 75.4 1.0 OE2 A:GLU25 3.2 63.1 1.0 CG A:ASP18 3.2 82.8 1.0 CD A:GLU25 3.4 66.8 1.0 C A:GLN20 3.8 71.5 1.0 CA A:VAL21 4.4 68.9 1.0 O A:SER13 4.5 63.8 1.0 N A:VAL21 4.6 67.5 1.0 N A:GLN20 4.6 69.1 1.0 CB A:ASP18 4.7 74.2 1.0 N A:THR22 4.8 64.8 1.0 O A:LEU11 4.8 62.5 1.0 CA A:GLN20 4.9 76.5 1.0 CG A:GLU25 4.9 67.1 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:57.2 occ:1.00 O A:ASN384 2.5 56.7 1.0 O A:ARG379 2.5 47.1 1.0 OD1 A:ASP382 2.6 52.3 1.0 OE2 A:GLU375 2.6 49.9 1.0 OG A:SER378 2.6 44.0 1.0 OE1 A:GLU375 2.9 48.0 1.0 CD A:GLU375 3.1 48.1 1.0 O B:HOH201 3.1 67.7 1.0 CG A:ASP382 3.3 50.9 1.0 OD2 A:ASP382 3.4 54.1 1.0 C A:ARG379 3.6 47.9 1.0 C A:ASN384 3.6 53.7 1.0 CB A:SER378 3.6 41.2 1.0 N A:ARG379 3.8 50.5 1.0 CA A:ARG379 4.1 51.0 1.0 C A:SER378 4.1 50.5 1.0 CB A:ARG379 4.3 57.0 1.0 N A:ASN384 4.3 53.1 1.0 CA A:ASN384 4.4 53.2 1.0 CB A:ASN384 4.5 53.1 1.0 O A:SER374 4.5 40.7 1.0 CA A:SER378 4.5 47.9 1.0 N A:LEU385 4.6 49.1 1.0 CG A:GLU375 4.6 40.2 1.0 N A:ASP382 4.6 47.1 1.0 N A:TRP381 4.6 48.9 1.0 O A:SER378 4.6 48.8 1.0 CA A:LEU385 4.7 49.6 1.0 CB A:ASP382 4.7 44.3 1.0 N A:PRO380 4.7 47.6 1.0 CA A:GLU375 4.8 45.6 1.0 O A:HOH608 4.8 47.7 1.0 CD2 A:LEU385 4.9 42.1 1.0 OG A:SER374 4.9 45.2 1.0 OE2 B:GLU103 4.9 54.3 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:39.2 occ:1.00 OE2 B:GLU126 2.4 48.5 1.0 OE2 A:GLU258 2.5 39.8 1.0 OE1 A:GLN280 2.6 39.3 1.0 O A:SER275 2.6 35.3 1.0 OD1 A:ASP262 2.6 43.1 1.0 OE1 B:GLU126 2.6 54.4 1.0 CD B:GLU126 2.7 51.0 1.0 OD2 A:ASP262 2.7 36.9 1.0 OG A:SER275 2.9 37.4 1.0 CG A:ASP262 3.0 40.3 1.0 CD A:GLN280 3.4 36.1 1.0 C A:SER275 3.5 34.4 1.0 CB A:SER275 3.6 39.4 1.0 CD A:GLU258 3.7 44.5 1.0 NE2 A:GLN280 3.7 34.7 1.0 CA A:SER275 3.8 41.7 1.0 N A:SER275 3.9 42.6 1.0 O B:HOH202 4.0 44.1 1.0 CG B:GLU126 4.0 49.7 1.0 CA A:CA504 4.2 40.1 1.0 OE1 A:GLN254 4.3 27.4 1.0 CB A:ASP262 4.4 43.0 1.0 CG A:GLU258 4.4 42.0 1.0 NZ A:LYS261 4.5 47.6 1.0 NE2 A:GLN254 4.6 39.0 1.0 OE1 A:GLU258 4.6 40.5 1.0 N A:ILE276 4.7 32.8 1.0 CG A:GLN280 4.8 33.5 1.0 CD A:GLN254 4.9 34.2 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:40.1 occ:1.00 OE1 A:GLN254 2.4 27.4 1.0 OD1 A:ASN181 2.4 36.2 1.0 O A:ASP253 2.5 35.5 1.0 OE1 A:GLU258 2.6 40.5 1.0 O A:HOH601 2.7 31.1 1.0 OE2 A:GLU258 2.9 39.8 1.0 O B:HOH202 2.9 44.1 1.0 OE1 A:GLN280 3.0 39.3 1.0 CD A:GLU258 3.1 44.5 1.0 CD A:GLN254 3.5 34.2 1.0 CG A:ASN181 3.6 35.4 1.0 C A:ASP253 3.7 33.2 1.0 CD A:GLN280 3.8 36.1 1.0 NH1 B:ARG60 4.0 32.1 1.0 CA A:GLN254 4.1 31.3 1.0 CB A:GLN254 4.2 32.6 1.0 CA A:CA503 4.2 39.2 1.0 NE2 A:GLN254 4.3 39.0 1.0 N A:GLN254 4.3 30.8 1.0 CG A:GLN280 4.3 33.5 1.0 ND2 A:ASN181 4.4 33.3 1.0 CG A:GLN254 4.4 36.9 1.0 O A:GLU250 4.5 32.9 1.0 CB A:ASP253 4.6 32.9 1.0 CG A:GLU258 4.6 42.0 1.0 OE1 A:GLU250 4.6 29.7 1.0 CA A:ASN181 4.6 39.0 1.0 CB A:ASN181 4.6 35.4 1.0 NE2 A:GLN280 4.7 34.7 1.0 OE2 B:GLU126 4.7 48.5 1.0 CA A:ASP253 4.8 33.0 1.0 N A:ASN181 4.9 40.5 1.0 CG A:ASP253 4.9 35.3 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:65.0 occ:1.00 OD1 C:ASP18 2.6 73.9 1.0 OE1 C:GLU25 2.7 64.0 1.0 OD2 C:ASP18 2.7 67.5 1.0 OE2 C:GLU25 2.7 62.1 1.0 O C:HOH644 2.7 58.5 1.0 O C:HOH608 2.7 58.2 1.0 O C:GLN20 2.7 66.0 1.0 CG C:ASP18 3.0 72.8 1.0 CD C:GLU25 3.0 63.1 1.0 O C:LEU11 3.9 57.9 1.0 C C:GLN20 3.9 63.3 1.0 CA C:VAL21 4.1 60.3 1.0 N C:VAL21 4.4 61.0 1.0 CB C:ASP18 4.4 67.5 1.0 CG C:GLU25 4.5 62.7 1.0 O C:SER13 4.6 55.1 1.0 N C:THR22 4.6 60.5 1.0 O C:HOH628 4.7 61.0 1.0 N C:GLN20 4.9 68.3 1.0 C C:LEU11 4.9 55.1 1.0 C C:VAL21 5.0 62.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:53.7 occ:1.00 O C:ASN384 2.4 53.7 1.0 OG C:SER378 2.5 40.0 1.0 O C:ARG379 2.5 46.9 1.0 OD1 C:ASP382 2.6 51.2 1.0 OE2 C:GLU375 2.6 45.4 1.0 OE1 C:GLU375 2.8 43.1 1.0 O D:HOH211 3.1 49.4 1.0 CD C:GLU375 3.1 48.0 1.0 CG C:ASP382 3.4 51.8 1.0 OD2 C:ASP382 3.4 51.0 1.0 N C:ARG379 3.5 44.7 1.0 C C:ARG379 3.5 44.1 1.0 C C:ASN384 3.6 54.9 1.0 CB C:SER378 3.7 42.1 1.0 C C:SER378 3.9 44.5 1.0 CA C:ARG379 3.9 46.1 1.0 CB C:ARG379 4.3 54.4 1.0 OE2 D:GLU103 4.3 56.6 1.0 CB C:ASN384 4.3 52.0 1.0 CA C:ASN384 4.4 51.2 1.0 O C:SER378 4.4 46.5 1.0 CA C:SER378 4.4 43.5 1.0 N C:ASN384 4.5 50.5 1.0 N C:LEU385 4.5 55.8 1.0 OG C:SER374 4.6 44.7 1.0 CG C:GLU375 4.6 44.8 1.0 O C:SER374 4.6 44.7 1.0 CA C:LEU385 4.6 45.5 1.0 N C:PRO380 4.7 46.5 1.0 CA C:GLU375 4.7 42.4 1.0 CB C:ASP382 4.8 51.3 1.0 N C:ASP382 4.8 51.2 1.0 N C:TRP381 4.8 49.7 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:38.3 occ:1.00 OE1 C:GLN280 2.4 42.3 1.0 OE2 C:GLU258 2.5 40.0 1.0 OE1 D:GLU126 2.6 48.3 1.0 OE2 D:GLU126 2.6 50.0 1.0 OD1 C:ASP262 2.7 39.2 1.0 O C:SER275 2.7 35.7 1.0 OG C:SER275 2.8 42.8 1.0 CD D:GLU126 2.8 50.6 1.0 OD2 C:ASP262 2.9 47.1 1.0 CG C:ASP262 3.1 44.5 1.0 CD C:GLN280 3.4 37.2 1.0 CD C:GLU258 3.7 43.2 1.0 NE2 C:GLN280 3.7 35.0 1.0 C C:SER275 3.7 40.3 1.0 CA C:CA504 3.9 50.0 1.0 CB C:SER275 3.9 44.3 1.0 O C:HOH645 3.9 43.4 1.0 CG D:GLU126 4.1 46.6 1.0 CA C:SER275 4.2 41.0 1.0 NE2 C:GLN254 4.2 43.9 1.0 N C:SER275 4.2 42.9 1.0 OE1 C:GLN254 4.2 38.0 1.0 NZ C:LYS261 4.4 45.0 1.0 CG C:GLU258 4.5 42.6 1.0 OE1 C:GLU258 4.5 48.2 1.0 CB C:ASP262 4.5 47.0 1.0 CD C:GLN254 4.7 39.8 1.0 CG C:GLN280 4.7 39.4 1.0 N C:ILE276 4.8 37.6 1.0 O D:SER99 4.9 38.0 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of TSE3-TSI3 Complex with Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of TSE3-TSI3 Complex with Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:50.0 occ:1.00 OE1 C:GLN254 2.3 38.0 1.0 OD1 C:ASN181 2.4 41.1 1.0 O C:ASP253 2.6 41.7 1.0 O C:HOH645 2.6 43.4 1.0 OE1 C:GLU258 2.7 48.2 1.0 O C:HOH602 2.7 36.5 1.0 OE2 C:GLU258 2.8 40.0 1.0 OE1 C:GLN280 3.0 42.3 1.0 CD C:GLU258 3.1 43.2 1.0 CD C:GLN254 3.4 39.8 1.0 CG C:ASN181 3.5 39.2 1.0 CD C:GLN280 3.7 37.2 1.0 C C:ASP253 3.8 43.8 1.0 CA C:CA503 3.9 38.3 1.0 ND2 C:ASN181 4.1 31.1 1.0 NE2 C:GLN254 4.2 43.9 1.0 NH1 D:ARG60 4.2 31.7 1.0 CA C:GLN254 4.2 37.6 1.0 CG C:GLN280 4.3 39.4 1.0 CB C:GLN254 4.3 37.8 1.0 O C:GLU250 4.4 37.3 1.0 NE2 C:GLN280 4.5 35.0 1.0 N C:GLN254 4.5 41.5 1.0 CG C:GLN254 4.5 39.3 1.0 CG C:GLU258 4.6 42.6 1.0 OE1 C:GLU250 4.7 33.6 1.0 CB C:ASN181 4.7 45.0 1.0 CB C:ASP253 4.7 32.9 1.0 CA C:ASN181 4.8 47.7 1.0 CA C:ASP253 4.9 35.3 1.0 OE1 D:GLU126 5.0 48.3 1.0 CG C:ASP253 5.0 40.1 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