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Calcium in PDB 4m5f: Complex Structure of TSE3-TSI3

Protein crystallography data

The structure of Complex Structure of TSE3-TSI3, PDB code: 4m5f was solved by L.C.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.34 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.242, 92.242, 169.765, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex Structure of TSE3-TSI3 (pdb code 4m5f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex Structure of TSE3-TSI3, PDB code: 4m5f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4m5f

Go back to Calcium Binding Sites List in 4m5f
Calcium binding site 1 out of 3 in the Complex Structure of TSE3-TSI3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex Structure of TSE3-TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:35.2
occ:1.00
OD1 A:ASN181 2.5 35.3 1.0
OE1 A:GLN254 2.5 33.8 1.0
O A:HOH604 2.7 21.9 1.0
O A:ASP253 2.8 25.8 1.0
O B:HOH309 2.8 29.0 1.0
OE1 A:GLU258 2.9 40.9 1.0
OE1 A:GLN280 3.0 22.5 1.0
OE2 A:GLU258 3.4 37.0 1.0
CD A:GLU258 3.5 41.5 1.0
CG A:ASN181 3.5 38.6 1.0
CD A:GLN254 3.7 27.8 1.0
CD A:GLN280 3.8 25.0 1.0
C A:ASP253 3.9 24.4 1.0
ND2 A:ASN181 4.0 38.9 1.0
NH1 B:ARG60 4.1 21.5 1.0
CA A:CA503 4.1 44.1 1.0
CA A:GLN254 4.3 24.6 1.0
CG A:GLN280 4.3 21.3 1.0
CB A:GLN254 4.4 23.6 1.0
O A:GLU250 4.5 20.9 1.0
N A:GLN254 4.5 23.2 1.0
NE2 A:GLN254 4.6 23.4 1.0
CG A:GLN254 4.7 19.1 1.0
OE1 A:GLU250 4.7 22.0 1.0
CB A:ASN181 4.8 30.9 1.0
NE2 A:GLN280 4.8 21.1 1.0
CG A:GLU258 4.9 32.6 1.0
OE1 B:GLU126 4.9 37.7 1.0
CB A:ASP253 4.9 25.3 1.0
CG A:ASP253 5.0 29.5 1.0
CZ B:ARG60 5.0 23.4 1.0

Calcium binding site 2 out of 3 in 4m5f

Go back to Calcium Binding Sites List in 4m5f
Calcium binding site 2 out of 3 in the Complex Structure of TSE3-TSI3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex Structure of TSE3-TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:29.4
occ:1.00
O A:ARG379 2.4 26.4 1.0
O A:ASN384 2.5 36.8 1.0
O A:HOH740 2.6 35.7 1.0
OE2 A:GLU375 2.6 25.5 1.0
OG A:SER378 2.7 30.0 1.0
OD1 A:ASP382 2.7 31.9 1.0
OE1 A:GLU375 2.8 26.2 1.0
CD A:GLU375 3.0 27.9 1.0
C A:ARG379 3.5 26.2 1.0
C A:ASN384 3.6 33.7 1.0
CB A:SER378 3.6 29.6 1.0
CG A:ASP382 3.6 34.0 1.0
N A:ARG379 3.9 28.3 1.0
OD2 A:ASP382 3.9 37.9 1.0
C A:SER378 4.1 27.4 1.0
CA A:ARG379 4.1 29.7 1.0
N A:ASN384 4.2 36.0 1.0
CA A:ASN384 4.3 36.0 1.0
CG A:GLU375 4.4 25.3 1.0
CB A:ARG379 4.4 30.8 1.0
CA A:SER378 4.5 27.2 1.0
N A:TRP381 4.5 28.3 1.0
CB A:ASN384 4.6 38.5 1.0
O A:SER378 4.6 26.3 1.0
N A:PRO380 4.6 25.8 1.0
CA A:GLU375 4.6 22.5 1.0
O A:SER374 4.6 27.4 1.0
N A:LEU385 4.6 33.6 1.0
N A:ASP382 4.6 33.0 1.0
OG A:SER374 4.7 27.6 1.0
CA A:PRO380 4.7 24.3 1.0
CA A:LEU385 4.8 34.3 1.0
O A:HOH674 4.8 32.7 1.0
CB A:GLU375 4.9 25.2 1.0
CB A:ASP382 4.9 27.7 1.0
C A:PRO380 5.0 30.6 1.0

Calcium binding site 3 out of 3 in 4m5f

Go back to Calcium Binding Sites List in 4m5f
Calcium binding site 3 out of 3 in the Complex Structure of TSE3-TSI3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex Structure of TSE3-TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:44.1
occ:1.00
OE1 A:GLN280 2.4 22.5 1.0
OE2 B:GLU126 2.6 36.5 1.0
OE1 B:GLU126 2.6 37.7 1.0
OD2 A:ASP262 2.7 26.0 1.0
O A:SER275 2.7 24.8 1.0
OD1 A:ASP262 2.7 29.6 1.0
CD B:GLU126 2.8 37.5 1.0
CG A:ASP262 2.9 28.7 1.0
OE1 A:GLU258 3.0 40.9 1.0
OG A:SER275 3.0 28.6 1.0
CD A:GLN280 3.4 25.0 1.0
C A:SER275 3.7 25.7 1.0
NE2 A:GLN280 3.8 21.1 1.0
O B:HOH309 3.9 29.0 1.0
CB A:SER275 4.1 23.6 1.0
CA A:CA501 4.1 35.2 1.0
CD A:GLU258 4.1 41.5 1.0
N A:SER275 4.1 24.5 1.0
CA A:SER275 4.2 22.9 1.0
CG B:GLU126 4.2 32.1 1.0
OE1 A:GLN254 4.2 33.8 1.0
CB A:ASP262 4.3 24.7 1.0
NZ A:LYS261 4.4 38.9 1.0
NE2 A:GLN254 4.5 23.4 1.0
CG A:GLU258 4.6 32.6 1.0
CG A:GLN280 4.7 21.3 1.0
CD A:GLN254 4.8 27.8 1.0
N A:ILE276 4.9 24.3 1.0

Reference:

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
Page generated: Sun Jul 14 10:05:23 2024

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