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Calcium in PDB 4luq: Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3

Protein crystallography data

The structure of Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3, PDB code: 4luq was solved by T.Wang, L.Li, W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.52 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.333, 81.288, 111.414, 90.00, 93.64, 90.00
R / Rfree (%) 13.9 / 18.8

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 4luq

Go back to Calcium Binding Sites List in 4luq
Calcium binding site 1 out of 6 in the Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3


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 Virulence Effector TSE3 in Complex with Neutralizer TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:13.3
occ:1.00
 O A:ARG379 2.3 13.5 1.0
O A:ASN384 2.3 14.9 1.0
OD1 A:ASP382 2.4 14.2 1.0
OG A:SER378 2.5 11.1 1.0
O A:HOH606 2.5 14.4 1.0
OE1 A:GLU375 2.5 13.1 1.0
OE2 A:GLU375 2.5 15.1 1.0
CD A:GLU375 2.8 14.5 1.0
CG A:ASP382 3.4 16.4 1.0
C A:ARG379 3.5 13.6 1.0
C A:ASN384 3.5 15.5 1.0
CB A:SER378 3.6 12.7 1.0
OD2 A:ASP382 3.7 16.3 1.0
N A:ARG379 3.9 13.8 1.0
C A:SER378 4.2 12.5 1.0
N A:ASN384 4.2 16.9 1.0
CA A:ARG379 4.3 13.2 1.0
CA A:ASN384 4.3 17.7 1.0
CG A:GLU375 4.3 13.6 1.0
O A:HOH834 4.4 35.1 1.0
CB A:ASN384 4.5 19.6 1.0
CA A:SER378 4.5 11.9 1.0
N A:LEU385 4.5 15.2 1.0
N A:TRP381 4.5 14.3 1.0
O A:SER378 4.5 12.3 1.0
CB A:ARG379 4.5 15.6 1.0
N A:ASP382 4.6 15.2 1.0
N A:PRO380 4.6 12.9 1.0
O A:SER374 4.6 11.4 1.0
OG A:SER374 4.6 13.8 1.0
CA A:LEU385 4.6 15.5 1.0
CA A:PRO380 4.6 13.9 1.0
O A:HOH607 4.7 13.5 1.0
CB A:ASP382 4.7 16.7 1.0
CA A:GLU375 4.8 11.4 1.0
C A:PRO380 4.9 14.1 1.0
CB A:GLU375 4.9 12.8 1.0

Calcium binding site 2 out of 6 in 4luq

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Calcium binding site 2 out of 6 in the Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3


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 Virulence Effector TSE3 in Complex with Neutralizer TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:13.7
occ:1.00
 OE1 A:GLN280 2.4 10.8 1.0
OE2 A:GLU258 2.4 13.3 1.0
O A:SER275 2.5 10.1 1.0
OD1 A:ASP262 2.5 11.1 1.0
OD2 A:ASP262 2.6 10.3 1.0
OG A:SER275 2.7 12.5 1.0
CG A:ASP262 2.8 12.1 1.0
CD A:GLN280 3.4 9.3 1.0
C A:SER275 3.5 10.4 1.0
CD A:GLU258 3.6 14.7 1.0
O A:HOH609 3.7 15.4 1.0
CB A:SER275 3.7 11.8 1.0
NE2 A:GLN280 3.8 11.2 1.0
CA A:SER275 4.0 10.3 1.0
N A:SER275 4.0 10.5 1.0
CG A:GLU258 4.1 12.5 1.0
O A:HOH719 4.2 27.0 1.0
CB A:ASP262 4.2 12.0 1.0
NZ A:LYS261 4.3 18.3 1.0
CA A:CA503 4.3 12.7 1.0
NE2 A:GLN254 4.4 10.7 1.0
OE1 A:GLN254 4.5 11.6 1.0
N A:ILE276 4.6 9.6 1.0
CG A:GLN280 4.7 8.9 1.0
OE1 A:GLU258 4.7 13.7 1.0
CD A:GLN254 4.9 12.8 1.0

Calcium binding site 3 out of 6 in 4luq

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Calcium binding site 3 out of 6 in the Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3


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 Virulence Effector TSE3 in Complex with Neutralizer TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:12.7
occ:1.00
 OD1 A:ASN181 2.3 12.4 1.0
OE1 A:GLN254 2.4 11.6 1.0
O A:HOH609 2.4 15.4 1.0
O A:ASP253 2.4 11.2 1.0
O A:HOH897 2.5 9.7 1.0
OE1 A:GLU258 2.5 13.7 1.0
OE2 A:GLU258 2.6 13.3 1.0
CD A:GLU258 2.9 14.7 1.0
OE1 A:GLN280 3.4 10.8 1.0
CD A:GLN254 3.5 12.8 1.0
CG A:ASN181 3.5 14.8 1.0
C A:ASP253 3.6 11.0 1.0
CD A:GLN280 4.0 9.3 1.0
CA A:GLN254 4.1 10.5 1.0
NE2 A:GLN254 4.1 10.7 1.0
CA A:CA502 4.3 13.7 1.0
CG A:GLN280 4.3 8.9 1.0
N A:GLN254 4.3 11.5 1.0
ND2 A:ASN181 4.3 18.6 1.0
O A:GLU250 4.4 10.3 1.0
CG A:GLU258 4.4 12.5 1.0
CB A:GLN254 4.4 11.3 1.0
CB A:ASN181 4.5 12.5 1.0
CG A:GLN254 4.5 11.4 1.0
CA A:ASN181 4.5 13.6 1.0
CB A:ASP253 4.7 11.9 1.0
CA A:ASP253 4.8 11.1 1.0
OE1 A:GLU250 4.8 11.7 1.0
CG A:ASP253 4.8 12.8 1.0
NE2 A:GLN280 4.9 11.2 1.0

Calcium binding site 4 out of 6 in 4luq

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Calcium binding site 4 out of 6 in the Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3


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 Virulence Effector TSE3 in Complex with Neutralizer TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:16.1
occ:1.00
 O B:ASN384 2.3 18.0 1.0
O B:ARG379 2.3 16.1 1.0
OG B:SER378 2.4 14.3 1.0
OD1 B:ASP382 2.4 16.5 1.0
O B:HOH614 2.5 15.8 1.0
OE1 B:GLU375 2.5 15.2 1.0
OE2 B:GLU375 2.6 17.2 1.0
CD B:GLU375 2.9 15.9 1.0
CG B:ASP382 3.4 19.2 1.0
C B:ARG379 3.5 16.1 1.0
C B:ASN384 3.5 18.4 1.0
CB B:SER378 3.6 14.9 1.0
OD2 B:ASP382 3.7 21.5 1.0
N B:ARG379 3.9 15.2 1.0
C B:SER378 4.1 15.4 1.0
CA B:ARG379 4.2 15.9 1.0
N B:ASN384 4.2 18.5 1.0
O B:HOH724 4.3 31.8 1.0
CA B:ASN384 4.3 18.3 1.0
CG B:GLU375 4.4 14.8 1.0
CB B:ASN384 4.4 21.9 1.0
CA B:SER378 4.5 14.1 1.0
N B:LEU385 4.5 18.5 1.0
CB B:ARG379 4.5 17.4 1.0
O B:SER378 4.5 16.0 1.0
OG B:SER374 4.6 16.2 1.0
N B:PRO380 4.6 16.1 1.0
N B:ASP382 4.6 18.6 1.0
CA B:LEU385 4.6 18.0 1.0
O B:SER374 4.6 14.4 1.0
N B:TRP381 4.6 17.4 1.0
CA B:PRO380 4.7 16.3 1.0
CB B:ASP382 4.7 18.9 1.0
CA B:GLU375 4.8 14.1 1.0
O B:HOH616 4.8 17.7 1.0
C B:PRO380 5.0 16.4 1.0
CB B:GLU375 5.0 15.7 1.0

Calcium binding site 5 out of 6 in 4luq

Go back to Calcium Binding Sites List in 4luq
Calcium binding site 5 out of 6 in the Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3


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 Virulence Effector TSE3 in Complex with Neutralizer TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:14.8
occ:1.00
 OD1 B:ASN181 2.2 15.3 1.0
OE1 B:GLN254 2.4 13.0 1.0
O B:HOH601 2.4 11.7 1.0
O B:ASP253 2.5 13.3 1.0
O B:HOH620 2.5 17.3 1.0
OE1 B:GLU258 2.5 16.0 1.0
OE2 B:GLU258 2.5 16.6 1.0
CD B:GLU258 2.8 15.9 1.0
OE1 B:GLN280 3.4 12.2 1.0
CG B:ASN181 3.5 15.4 1.0
CD B:GLN254 3.5 14.0 1.0
C B:ASP253 3.6 13.1 1.0
CD B:GLN280 4.0 11.7 1.0
CA B:GLN254 4.1 11.9 1.0
NE2 B:GLN254 4.2 12.8 1.0
CG B:GLN280 4.3 11.3 1.0
ND2 B:ASN181 4.3 20.1 1.0
O B:GLU250 4.3 10.8 1.0
N B:GLN254 4.3 13.1 1.0
CA B:CA503 4.3 16.6 1.0
CB B:GLN254 4.4 11.5 1.0
CG B:GLU258 4.4 15.3 1.0
CB B:ASN181 4.5 15.6 1.0
CA B:ASN181 4.5 14.9 1.0
CG B:GLN254 4.5 13.4 1.0
CB B:ASP253 4.7 13.6 1.0
OE1 B:GLU250 4.8 14.1 1.0
CA B:ASP253 4.8 13.0 1.0
CG B:ASP253 4.9 15.7 1.0
NE2 B:GLN280 4.9 13.6 1.0
N B:ASN181 5.0 14.8 1.0

Calcium binding site 6 out of 6 in 4luq

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Calcium binding site 6 out of 6 in the Crystal Structure of Virulence Effector TSE3 in Complex with Neutralizer TSI3


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 Virulence Effector TSE3 in Complex with Neutralizer TSI3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:16.6
occ:1.00
 OE1 B:GLN280 2.4 12.2 1.0
OD1 B:ASP262 2.5 14.3 1.0
OE2 B:GLU258 2.5 16.6 1.0
O B:SER275 2.6 13.1 1.0
OD2 B:ASP262 2.6 11.8 1.0
OG B:SER275 2.6 13.7 1.0
CG B:ASP262 2.8 12.3 1.0
CD B:GLN280 3.4 11.7 1.0
C B:SER275 3.5 11.6 1.0
CD B:GLU258 3.6 15.9 1.0
CB B:SER275 3.7 15.2 1.0
O B:HOH620 3.8 17.3 1.0
NE2 B:GLN280 3.8 13.6 1.0
CA B:SER275 4.0 13.3 1.0
N B:SER275 4.0 13.7 1.0
CG B:GLU258 4.1 15.3 1.0
CB B:ASP262 4.2 13.1 1.0
NZ B:LYS261 4.2 21.1 1.0
CA B:CA502 4.3 14.8 1.0
NE2 B:GLN254 4.4 12.8 1.0
OE1 B:GLN254 4.5 13.0 1.0
N B:ILE276 4.7 11.4 1.0
CG B:GLN280 4.7 11.3 1.0
OE1 B:GLU258 4.7 16.0 1.0
CD B:GLN254 4.9 14.0 1.0

Reference:

L.Li, W.Zhang, Q.Liu, Y.Gao, Y.Gao, Y.Wang, D.Z.Wang, Z.Li, T.Wang. Structural Insights on the Bacteriolytic and Self-Protection Mechanism of Muramidase Effector TSE3 in Pseudomonas Aeruginosa J.Biol.Chem. V. 288 30607 2013.
ISSN: ISSN 0021-9258
PubMed: 24025333
DOI: 10.1074/JBC.C113.506097
Page generated: Sun Jul 14 09:46:52 2024

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