Calcium in PDB 8boz: Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex

Protein crystallography data

The structure of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex, PDB code: 8boz was solved by C.Cambillau, A.Roussel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.74 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.86, 449.07, 116.23, 90, 93.18, 90
R / Rfree (%) 23.3 / 26.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex (pdb code 8boz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex, PDB code: 8boz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8boz

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Calcium binding site 1 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:83.3
occ:1.00
 OD2 A:ASP573 2.3 89.1 1.0
OD2 A:ASP444 2.3 70.1 1.0
O A:GLN485 2.4 86.1 1.0
N A:GLN485 2.7 85.3 1.0
C A:GLN485 2.7 87.5 1.0
OD1 A:ASP484 3.0 78.1 1.0
CA A:GLN485 3.0 86.3 1.0
CG A:ASP573 3.0 82.6 1.0
OD1 A:ASP573 3.1 81.4 1.0
CB A:GLN485 3.3 84.2 1.0
CG A:ASP444 3.5 86.3 1.0
C A:ASP484 3.6 87.7 1.0
N A:ASP486 3.7 85.0 1.0
O A:PRO571 3.9 89.2 1.0
CG A:ASP484 4.0 82.4 1.0
CG A:GLN485 4.2 76.7 1.0
CA A:ASP484 4.2 81.2 1.0
CB A:ASP444 4.3 88.0 1.0
O A:ASP484 4.3 94.2 1.0
CA A:ASP486 4.4 92.5 1.0
CB A:ASP573 4.4 75.3 1.0
OD1 A:ASP444 4.5 93.7 1.0
CB A:PRO571 4.5 81.8 1.0
C A:PRO571 4.6 83.0 1.0
N A:ASP573 4.6 69.1 1.0
CB A:ASP484 4.7 79.6 1.0
OD2 A:ASP484 4.8 81.7 1.0

Calcium binding site 2 out of 8 in 8boz

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Calcium binding site 2 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:72.9
occ:1.00
 OD2 C:ASP444 2.3 60.2 1.0
OD1 C:ASP484 2.4 69.5 1.0
OD2 C:ASP573 2.4 73.9 1.0
CG C:ASP444 2.7 78.1 1.0
OD1 C:ASP444 2.8 87.6 1.0
CG C:ASP484 3.3 73.7 1.0
OD2 C:ASP484 3.6 78.0 1.0
O C:GLN485 3.6 78.5 1.0
CG C:ASP573 3.7 71.3 1.0
O C:HIS376 3.7 70.3 1.0
CD C:ARG378 3.7 71.6 1.0
NH1 C:ARG378 3.9 82.1 1.0
CB C:ASP444 3.9 80.9 1.0
CB C:HIS376 4.0 61.7 1.0
CG C:ARG378 4.3 73.5 1.0
CB C:ASP573 4.4 67.2 1.0
NE C:ARG378 4.5 71.6 1.0
CZ C:ARG378 4.6 81.4 1.0
C C:HIS376 4.6 60.7 1.0
OD1 C:ASP573 4.6 68.7 1.0
CG C:HIS376 4.6 64.0 1.0
N C:ASP444 4.6 76.3 1.0
CB C:ASP484 4.6 71.1 1.0
CA C:HIS376 4.6 59.8 1.0
C C:GLN485 4.7 77.2 1.0
O C:PRO571 4.7 71.8 1.0
N C:GLN485 4.8 63.9 1.0
CA C:ASP444 4.9 81.1 1.0
N C:ASP573 4.9 58.6 1.0
CA C:ASP484 4.9 74.9 1.0
ND1 C:HIS376 5.0 66.8 1.0
C C:ASP484 5.0 74.5 1.0

Calcium binding site 3 out of 8 in 8boz

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Calcium binding site 3 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:76.5
occ:1.00
 OD1 E:ASP573 2.4 82.8 1.0
OD2 E:ASP444 2.5 88.5 1.0
O E:GLN485 2.7 92.8 1.0
OD1 E:ASP484 2.8 87.4 1.0
OD1 E:ASP444 2.9 91.3 1.0
CG E:ASP444 3.1 88.5 1.0
CG E:ASP573 3.6 85.7 1.0
O E:PRO571 3.6 80.2 1.0
NH1 E:ARG378 3.7 90.9 1.0
C E:GLN485 3.9 86.0 1.0
CG E:ASP484 3.9 88.0 1.0
CD E:ARG378 4.0 86.6 1.0
OD2 E:ASP573 4.1 88.5 1.0
CG E:ARG378 4.3 79.4 1.0
O E:HIS376 4.3 88.9 1.0
N E:GLN485 4.4 90.7 1.0
OD2 E:ASP484 4.5 90.2 1.0
CB E:ASP444 4.6 87.4 1.0
C E:PRO571 4.6 82.5 1.0
N E:ASP573 4.6 88.3 1.0
C E:ASP484 4.7 94.8 1.0
CB E:HIS376 4.7 89.0 1.0
OD1 E:ASP486 4.7 98.2 1.0
CZ E:ARG378 4.7 81.2 1.0
CA E:GLN485 4.8 86.4 1.0
CB E:ASP573 4.8 85.3 1.0
N E:ASP486 4.8 83.5 1.0
NE E:ARG378 4.8 84.9 1.0
CA E:ASP486 4.9 92.9 1.0

Calcium binding site 4 out of 8 in 8boz

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Calcium binding site 4 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca701

b:83.3
occ:1.00
 OD1 G:ASP573 2.3 77.1 1.0
OD2 G:ASP444 2.3 82.5 1.0
OD1 G:ASP484 2.5 86.7 1.0
OD1 G:ASP444 2.6 96.7 1.0
CG G:ASP444 2.7 91.0 1.0
O G:GLN485 3.4 90.4 1.0
CG G:ASP573 3.5 80.5 1.0
CG G:ASP484 3.5 83.1 1.0
NE G:ARG378 3.8 81.6 1.0
O G:HIS376 3.9 72.7 1.0
OD2 G:ASP484 3.9 85.0 1.0
CB G:HIS376 4.0 71.8 1.0
CG G:ARG378 4.1 71.7 1.0
CB G:ASP444 4.1 90.0 1.0
OD2 G:ASP573 4.2 89.0 1.0
CD G:ARG378 4.4 77.9 1.0
O G:PRO571 4.4 77.6 1.0
CB G:ASP573 4.4 74.5 1.0
CZ G:ARG378 4.5 83.7 1.0
C G:GLN485 4.5 93.8 1.0
NH2 G:ARG378 4.6 85.9 1.0
CA G:HIS376 4.7 67.2 1.0
C G:HIS376 4.7 66.1 1.0
N G:ASP573 4.8 67.5 1.0
CG G:HIS376 4.8 79.6 1.0
N G:ASP444 4.8 86.7 1.0
N G:GLN485 4.8 93.1 1.0
CB G:ASP484 4.9 79.8 1.0
C G:ASP484 4.9 94.2 1.0

Calcium binding site 5 out of 8 in 8boz

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Calcium binding site 5 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca701

b:70.8
occ:1.00
 OD1 I:ASP573 2.4 79.8 1.0
OD2 I:ASP444 2.4 74.7 1.0
OD1 I:ASP484 2.5 83.2 1.0
OD1 I:ASP444 2.8 88.8 1.0
CG I:ASP444 2.9 82.1 1.0
O I:GLN485 3.0 77.2 1.0
CG I:ASP573 3.5 80.5 1.0
CG I:ASP484 3.6 85.4 1.0
O I:HIS376 4.0 71.8 1.0
NE I:ARG378 4.0 86.5 1.0
C I:GLN485 4.1 76.2 1.0
CB I:HIS376 4.1 79.5 1.0
OD2 I:ASP484 4.2 84.1 1.0
O I:PRO571 4.2 85.3 1.0
OD2 I:ASP573 4.2 72.8 1.0
NH2 I:ARG378 4.4 89.5 1.0
CB I:ASP444 4.4 79.1 1.0
CB I:ASP573 4.4 85.6 1.0
N I:GLN485 4.6 86.8 1.0
CZ I:ARG378 4.7 85.0 1.0
C I:ASP484 4.7 86.8 1.0
CG I:ARG378 4.7 82.8 1.0
N I:ASP573 4.8 83.9 1.0
CB I:ASP484 4.8 85.4 1.0
CA I:ASP484 4.9 81.0 1.0
C I:HIS376 4.9 83.0 1.0
CD I:ARG378 4.9 83.1 1.0
CA I:HIS376 5.0 86.8 1.0
CA I:GLN485 5.0 82.1 1.0

Calcium binding site 6 out of 8 in 8boz

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Calcium binding site 6 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca701

b:81.8
occ:1.00
 OD2 K:ASP444 2.3 73.6 1.0
OD2 K:ASP573 2.3 85.5 1.0
O K:GLN485 2.7 88.6 1.0
O K:PRO571 2.9 84.7 1.0
CG K:ASP573 3.0 86.1 1.0
CG K:ASP444 3.2 82.4 1.0
OD1 K:ASP573 3.2 84.6 1.0
OD1 K:ASP444 3.4 86.7 1.0
OD1 K:ASP484 3.4 91.5 1.0
C K:GLN485 3.9 83.4 1.0
N K:ASP573 4.0 75.2 1.0
C K:PRO571 4.1 82.0 1.0
CB K:ASP573 4.2 84.5 1.0
N K:GLN485 4.5 89.0 1.0
NE K:ARG378 4.5 82.3 1.0
CG K:ARG378 4.5 74.2 1.0
O K:HIS376 4.5 78.0 1.0
CB K:ASP444 4.6 86.0 1.0
CG K:ASP484 4.6 91.9 1.0
CA K:GLN485 4.7 82.9 1.0
CA K:ASP573 4.7 73.9 1.0
CA K:THR572 4.7 78.6 1.0
N K:ASP486 4.8 82.9 1.0
C K:THR572 4.8 81.1 1.0
N K:THR572 4.8 71.6 1.0
CB K:PRO571 4.9 82.7 1.0
CA K:ASP486 4.9 87.8 1.0
CG K:PRO571 4.9 86.3 1.0

Calcium binding site 7 out of 8 in 8boz

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Calcium binding site 7 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca701

b:91.8
occ:1.00
 OD2 M:ASP444 2.4 103.8 1.0
OD2 M:ASP573 2.5 106.2 1.0
OD1 M:ASP484 2.6 96.2 1.0
OD1 M:ASP444 2.7 119.2 1.0
CG M:ASP444 2.8 114.6 1.0
O M:GLN485 3.2 107.2 1.0
CG M:ASP573 3.7 105.6 1.0
O M:HIS376 3.7 97.1 1.0
CG M:ASP484 3.8 100.6 1.0
NE M:ARG378 3.8 95.6 1.0
O M:PRO571 4.0 96.0 1.0
CB M:HIS376 4.0 96.3 1.0
CG M:ARG378 4.1 98.1 1.0
CB M:ASP444 4.2 111.5 1.0
OD2 M:ASP484 4.3 104.6 1.0
C M:GLN485 4.3 116.3 1.0
CB M:ASP573 4.4 99.7 1.0
N M:GLN485 4.5 109.9 1.0
NH2 M:ARG378 4.5 115.7 1.0
CD M:ARG378 4.6 93.4 1.0
N M:ASP573 4.6 95.1 1.0
CZ M:ARG378 4.6 109.0 1.0
C M:HIS376 4.6 92.7 1.0
OD1 M:ASP573 4.7 109.3 1.0
CA M:HIS376 4.8 92.1 1.0
C M:ASP484 4.9 109.1 1.0
N M:ASP444 4.9 108.3 1.0
CG M:HIS376 4.9 95.8 1.0

Calcium binding site 8 out of 8 in 8boz

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Calcium binding site 8 out of 8 in the Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca701

b:106.2
occ:1.00
 OD2 O:ASP573 2.4 116.1 1.0
OD2 O:ASP444 2.5 122.2 1.0
OD1 O:ASP444 2.5 130.8 1.0
OD1 O:ASP484 2.8 115.2 1.0
CG O:ASP444 2.8 130.4 1.0
O O:GLN485 3.1 118.2 1.0
NE O:ARG378 3.4 114.0 1.0
CG O:ASP573 3.6 118.5 1.0
CG O:ASP484 3.9 114.9 1.0
CD O:ARG378 4.0 116.4 1.0
CG O:ARG378 4.1 111.3 1.0
OD1 O:ASP573 4.1 121.5 1.0
O O:HIS376 4.2 115.2 1.0
CZ O:ARG378 4.2 115.0 1.0
NH2 O:ARG378 4.3 124.1 1.0
C O:GLN485 4.3 124.4 1.0
CB O:HIS376 4.3 114.1 1.0
CB O:ASP444 4.3 130.3 1.0
OD2 O:ASP484 4.4 122.0 1.0
O O:PRO571 4.5 118.9 1.0
CB O:ASP573 4.7 120.1 1.0
N O:GLN485 4.7 118.2 1.0
N O:ASP573 4.8 121.2 1.0
C O:ASP484 4.8 118.0 1.0
N O:ASP444 4.9 113.4 1.0
OD1 O:ASP486 4.9 121.8 1.0

Reference:

T.T.H.Le, C.Kellenberger, M.Boyer, P.Santucci, N.Flaugnatti, E.Cascales, A.Roussel, S.Canaan, L.Journet, C.Cambillau. Activity and Crystal Structure of the Adherent-Invasive Escherichia Coli TLE3/TLI3 T6SS Effector/Immunity Complex Determined Using An ALPHAFOLD2 Predicted Model. Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
PubMed: 36675258
DOI: 10.3390/IJMS24021740
Page generated: Tue Apr 4 19:30:05 2023

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