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

Protein crystallography data

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

Calcium Binding Sites:

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 4n88

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


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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 4n88

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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 4n88

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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 4n88

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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 4n88

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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 4n88

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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 4n88

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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 4n88

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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

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: Sat Dec 12 05:00:35 2020

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