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Cadmium in PDB 8b4b: Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna

Protein crystallography data

The structure of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna, PDB code: 8b4b was solved by A.Canals, S.Pieretti, M.Muriel, N.El Yaman, M.Fabrega-Ferrer, R.Perez-Luque, E.S.Krukonis, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.63 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.343, 60.975, 61.329, 87.52, 89.99, 62.96
R / Rfree (%) 19.9 / 23.5

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Cadmium atom in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna (pdb code 8b4b). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 24 binding sites of Cadmium where determined in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna, PDB code: 8b4b:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 24 in 8b4b

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Cadmium binding site 1 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd101

b:37.9
occ:0.25
 CD L:CD102 2.7 35.9 0.3
N Z:NH4206 2.8 26.6 1.0
O Z:SER75 2.9 23.8 1.0
C7 L:DT-40 3.4 25.4 1.0
N Z:ALA79 3.7 24.0 1.0
C Z:SER75 3.8 23.5 1.0
CA Z:SER75 3.8 20.6 1.0
CB Z:ALA79 3.8 24.4 1.0
CB Z:GLN78 3.9 23.1 1.0
CB Z:SER75 4.0 21.8 1.0
CG Z:GLN78 4.0 22.8 1.0
CA Z:ALA79 4.0 27.8 1.0
CZ2 Z:TRP64 4.1 27.2 1.0
ND2 Z:ASN38 4.1 27.2 1.0
OG Z:SER75 4.2 23.9 1.0
C Z:GLN78 4.2 27.4 1.0
C5 L:DT-40 4.4 23.0 1.0
C7 L:DT-39 4.4 25.0 1.0
C6 L:DT-40 4.6 22.4 1.0
CH2 Z:TRP64 4.6 24.4 1.0
CA Z:GLN78 4.7 26.1 1.0
OP2 L:DT-40 4.7 23.4 1.0
OE2 Z:GLU39 4.8 34.1 1.0
O Z:GLN78 5.0 22.3 1.0

Cadmium binding site 2 out of 24 in 8b4b

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Cadmium binding site 2 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd102

b:35.9
occ:0.26
 CD L:CD101 2.7 37.9 0.2
OP2 L:DT-40 2.8 23.4 1.0
OG Z:SER75 2.8 23.9 1.0
O5' L:DT-40 3.2 28.1 1.0
C6 L:DT-40 3.3 22.4 1.0
CB Z:SER75 3.4 21.8 1.0
P L:DT-40 3.6 25.6 1.0
C7 L:DT-40 3.7 25.4 1.0
C2' L:DT-41 3.8 27.6 1.0
C2' L:DT-40 3.9 24.3 1.0
C5 L:DT-40 3.9 23.0 1.0
ND2 Z:ASN38 4.0 27.2 1.0
CA Z:SER75 4.1 20.6 1.0
CZ2 Z:TRP64 4.2 27.2 1.0
C3' L:DT-40 4.2 24.5 1.0
NE1 Z:TRP64 4.3 27.0 1.0
N1 L:DT-40 4.3 22.2 1.0
O4' L:DT-40 4.3 24.9 1.0
C7 L:DT-39 4.3 25.0 1.0
C5' L:DT-40 4.4 24.3 1.0
C1' L:DT-40 4.4 23.3 1.0
N Z:NH4206 4.4 26.6 1.0
O3' L:DT-41 4.5 25.1 1.0
C3' L:DT-41 4.5 25.7 1.0
C4' L:DT-40 4.5 24.9 1.0
CE2 Z:TRP64 4.5 24.5 1.0
O Z:SER75 4.6 23.8 1.0
CG1 Z:VAL71 4.7 27.5 1.0
C Z:SER75 4.8 23.5 1.0
OP1 L:DT-40 4.9 33.0 1.0
C1' L:DT-41 4.9 24.6 1.0
O Z:HOH319 4.9 28.3 1.0

Cadmium binding site 3 out of 24 in 8b4b

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Cadmium binding site 3 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd103

b:55.0
occ:0.26
 CD L:CD104 2.8 59.5 0.3
O M:HOH255 2.8 52.9 1.0
NE2 W:GLN78 2.9 31.8 1.0
N6 L:DA-42 3.1 24.8 1.0
N7 L:DA-42 3.7 26.2 1.0
C5 L:DC-43 3.9 26.6 1.0
CD W:GLN78 4.1 24.4 1.0
C6 L:DA-42 4.1 27.3 1.0
O L:HOH212 4.2 33.4 1.0
C5 L:DA-42 4.3 25.6 1.0
O L:HOH205 4.3 42.0 1.0
C4 L:DC-43 4.3 28.0 1.0
O M:HOH253 4.3 37.6 1.0
C6 L:DC-43 4.4 25.5 1.0
N4 L:DC-43 4.5 22.6 1.0
OE1 W:GLN78 4.5 25.1 1.0
O W:HOH326 4.5 41.1 1.0
N6 M:DA41 4.6 28.1 1.0
O W:HOH329 4.8 33.7 1.0
C8 L:DA-42 5.0 25.0 1.0
N3 L:DC-43 5.0 24.5 1.0

Cadmium binding site 4 out of 24 in 8b4b

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Cadmium binding site 4 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd104

b:59.5
occ:0.28
 CD L:CD103 2.8 55.0 0.3
N7 L:DA-42 2.9 26.2 1.0
C8 L:DA-42 3.5 25.0 1.0
O L:HOH212 3.6 33.4 1.0
O L:HOH205 3.9 42.0 1.0
C2' L:DC-43 4.1 29.1 1.0
C5 L:DA-42 4.2 25.6 1.0
O L:HOH253 4.3 43.8 1.0
C6 L:DC-43 4.4 25.5 1.0
N6 L:DA-42 4.6 24.8 1.0
N1 L:DC-43 4.6 26.2 1.0
C5 L:DC-43 4.8 26.6 1.0
O M:HOH255 4.8 52.9 1.0
C6 L:DA-42 4.8 27.3 1.0
N9 L:DA-42 4.8 25.1 1.0
C1' L:DC-43 4.9 25.8 1.0
O4 L:DT-41 5.0 31.6 1.0
C7 L:DT-41 5.0 27.7 1.0

Cadmium binding site 5 out of 24 in 8b4b

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Cadmium binding site 5 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd101

b:32.7
occ:0.33
 OG W:SER74 2.5 40.0 1.0
N7 M:DG43 2.6 27.1 1.0
O M:HOH246 2.7 38.8 1.0
O M:HOH211 2.8 40.4 1.0
CB W:SER74 3.1 34.2 1.0
C8 M:DG43 3.5 28.5 1.0
C5 M:DG43 3.7 25.7 1.0
O6 M:DG43 3.9 26.6 1.0
O W:HOH308 3.9 45.4 1.0
O M:HOH231 4.2 34.1 1.0
C6 M:DG43 4.2 29.4 1.0
C6 M:DT42 4.2 25.7 1.0
C2' M:DT42 4.3 31.4 1.0
O W:HOH388 4.4 54.7 1.0
O L:HOH208 4.4 33.6 1.0
C5 M:DT42 4.4 20.9 1.0
N6 M:DA44 4.5 23.9 1.0
CA W:SER74 4.5 29.8 1.0
N1 M:DT42 4.6 26.7 1.0
N9 M:DG43 4.7 24.4 1.0
C7 M:DT42 4.7 25.8 1.0
C W:SER74 4.8 26.3 1.0
O W:HOH322 4.8 27.9 1.0
C4 M:DG43 4.8 28.6 1.0
O W:HOH360 4.9 42.0 1.0
C4 M:DT42 4.9 25.1 1.0
O W:SER74 5.0 30.1 1.0

Cadmium binding site 6 out of 24 in 8b4b

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Cadmium binding site 6 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd102

b:33.8
occ:0.25
 CD Z:CD203 2.7 37.6 0.2
O Z:THR77 2.8 24.6 1.0
OP2 M:DG36 2.8 25.5 1.0
O5' M:DG36 3.3 22.4 1.0
CG2 Z:THR77 3.4 23.8 1.0
C2' M:DG36 3.5 23.2 1.0
N Z:SER81 3.5 21.3 1.0
P M:DG36 3.6 22.9 1.0
CB Z:SER81 3.7 24.3 1.0
C Z:THR77 3.7 23.0 1.0
CG2 Z:ILE80 3.8 23.0 1.0
CA Z:SER81 3.8 23.3 1.0
CB Z:ILE80 3.9 23.4 1.0
C3' M:DG36 3.9 26.9 1.0
CA Z:THR77 4.1 26.9 1.0
C Z:ILE80 4.2 26.2 1.0
C7 M:DT37 4.3 23.6 1.0
OP1 M:DG36 4.3 26.5 1.0
OP2 M:DT37 4.3 26.8 1.0
CB Z:THR77 4.4 25.4 1.0
NH1 Z:ARG84 4.4 26.0 1.0
OG Z:SER81 4.5 24.6 1.0
OH Z:TYR105 4.5 26.0 1.0
C5' M:DG36 4.5 22.8 1.0
CA Z:ILE80 4.6 23.2 1.0
C8 M:DG36 4.6 24.6 1.0
C4' M:DG36 4.7 24.9 1.0
C1' M:DG36 4.7 25.8 1.0
N Z:GLN78 4.9 26.5 1.0
O Z:ILE80 4.9 22.6 1.0
O3' M:DA35 5.0 28.1 1.0
N Z:ILE80 5.0 21.9 1.0

Cadmium binding site 7 out of 24 in 8b4b

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Cadmium binding site 7 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd103

b:35.6
occ:0.25
 OP2 M:DA41 2.8 24.6 1.0
OG W:SER75 2.8 23.5 1.0
CD W:CD203 2.9 35.1 0.2
O5' M:DA41 3.2 26.4 1.0
CB W:SER75 3.4 22.6 1.0
C8 M:DA41 3.4 23.0 1.0
P M:DA41 3.7 25.7 1.0
C2' M:DA41 3.8 25.4 1.0
C2' M:DA40 3.8 25.2 1.0
ND2 W:ASN38 4.1 29.4 1.0
C7 M:DT42 4.1 25.8 1.0
CA W:SER75 4.2 23.3 1.0
N9 M:DA41 4.3 22.7 1.0
N7 M:DA41 4.3 25.6 1.0
C3' M:DA41 4.3 26.0 1.0
O W:HOH343 4.3 33.9 1.0
CZ2 W:TRP64 4.3 26.1 1.0
O4' M:DA41 4.4 24.7 1.0
C1' M:DA41 4.4 24.0 1.0
NE1 W:TRP64 4.4 26.4 1.0
C5' M:DA41 4.5 24.9 1.0
C3' M:DA40 4.6 26.4 1.0
O3' M:DA40 4.6 26.7 1.0
C4' M:DA41 4.6 23.9 1.0
O W:SER75 4.7 23.9 1.0
CE2 W:TRP64 4.7 29.2 1.0
CG1 W:VAL71 4.7 28.8 1.0
C W:SER75 4.8 22.1 1.0
O W:HOH322 4.8 27.9 1.0
OP1 M:DA41 4.9 31.4 1.0
C1' M:DA40 5.0 26.5 1.0

Cadmium binding site 8 out of 24 in 8b4b

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Cadmium binding site 8 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd104

b:48.9
occ:0.45
 O6 M:DG48 2.4 50.9 1.0
CD Y:CD203 2.7 96.8 0.3
C6 M:DG48 3.3 48.9 1.0
OE1 Y:GLN78 3.6 52.0 1.0
N7 M:DG48 4.0 47.2 1.0
C5 M:DG48 4.0 44.2 1.0
N4 L:DC-48 4.1 52.6 1.0
O4 M:DT47 4.2 41.4 1.0
CD Y:GLN78 4.3 53.9 1.0
N1 M:DG48 4.4 49.1 1.0
C4 M:DT47 4.5 37.0 1.0
CG Y:GLN78 4.6 50.5 1.0
C5 M:DT47 4.9 34.0 1.0
O M:HOH202 4.9 40.7 1.0
N3 M:DT47 5.0 34.9 1.0

Cadmium binding site 9 out of 24 in 8b4b

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Cadmium binding site 9 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Cd201

b:73.7
occ:0.43
 OD1 W:ASN57 2.6 43.0 1.0
O W:HOH312 2.8 57.9 1.0
OD1 W:ASP61 3.0 42.7 1.0
OD2 W:ASP61 3.1 38.9 1.0
CG W:ASP61 3.4 42.2 1.0
CG W:ASN57 3.4 42.5 1.0
ND2 W:ASN57 3.6 42.1 1.0
CD W:ARG65 4.5 47.6 1.0
O W:ASN57 4.5 28.0 1.0
CB W:ASN57 4.8 35.1 1.0
CB W:ASP61 4.9 33.6 1.0

Cadmium binding site 10 out of 24 in 8b4b

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Cadmium binding site 10 out of 24 in the Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Toxr Bacterial Transcriptional Regulator Bound to 19 Bp Ompu Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Cd202

b:38.8
occ:1.00
 OE2 W:GLU12 2.5 31.2 1.0
OE2 W:GLU112 2.5 31.9 1.0
OE1 W:GLU12 2.6 44.7 1.0
O W:HOH370 2.6 40.5 1.0
OE1 W:GLU112 2.8 37.9 1.0
CD W:GLU12 2.9 39.5 1.0
CD W:GLU112 2.9 34.0 1.0
CG W:GLU12 4.3 36.3 1.0
O W:HOH310 4.4 34.2 1.0
NE W:ARG110 4.4 31.5 1.0
CG W:GLU112 4.4 30.9 1.0
O W:HOH321 4.5 31.7 1.0
NH2 W:ARG110 4.6 30.3 1.0
CG2 W:ILE9 4.8 35.0 1.0
O W:HOH364 5.0 51.4 1.0

Reference:

A.Canals, S.Pieretti, M.Muriel-Masanes, N.El Yaman, S.C.Plecha, J.J.Thomson, M.Fabrega-Ferrer, R.Perez-Luque, E.S.Krukonis, M.Coll. Toxr Activates the Vibrio Cholerae Virulence Genes By Tethering Dna to the Membrane Through Versatile Binding to Multiple Sites. Proc.Natl.Acad.Sci.Usa V. 120 78120 2023.
ISSN: ESSN 1091-6490
PubMed: 37428913
DOI: 10.1073/PNAS.2304378120
Page generated: Fri Jul 19 20:20:25 2024

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