Cadmium in PDB 6xfj: Crystal Structure of the Type III Secretion Pilotin Invh

Protein crystallography data

The structure of Crystal Structure of the Type III Secretion Pilotin Invh, PDB code: 6xfj was solved by D.D.Majewski, M.Okon, F.Heinkel, C.S.Robb, M.Vuckovic, L.P.Mcintosh, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.36 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 25.503, 53.183, 56.851, 107.69, 97.20, 95.95
R / Rfree (%) 13.2 / 16.8

Other elements in 6xfj:

The structure of Crystal Structure of the Type III Secretion Pilotin Invh also contains other interesting chemical elements:

Chlorine (Cl) 18 atoms
Sodium (Na) 1 atom

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of the Type III Secretion Pilotin Invh (pdb code 6xfj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 19 binding sites of Cadmium where determined in the Crystal Structure of the Type III Secretion Pilotin Invh, PDB code: 6xfj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 19 in 6xfj

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Cadmium binding site 1 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:10.5
occ:1.00
 SG A:CYS85 2.5 9.9 1.0
CL A:CL206 2.5 11.9 1.0
CL A:CL205 2.5 10.5 1.0
SG B:CYS85 2.5 12.0 1.0
CB B:CYS85 3.3 11.3 1.0
CB A:CYS85 3.4 9.0 1.0
O A:HOH306 3.6 44.8 1.0
CD A:CD202 3.8 12.1 1.0
CL A:CL207 3.8 12.9 1.0
CD B:CD201 4.0 9.9 0.9
O A:HOH365 4.1 13.5 1.0
CL B:CL207 4.2 23.8 0.8
CA A:CYS85 4.2 10.2 1.0
O A:HOH312 4.4 38.2 1.0
NZ A:LYS92 4.6 35.2 1.0
CB A:THR91 4.7 10.3 1.0
O B:HOH372 4.7 19.7 1.0
CA B:CYS85 4.7 9.5 1.0
O A:HOH305 4.8 26.6 1.0
OG1 A:THR91 4.9 10.2 1.0
C A:CYS85 4.9 10.0 1.0
O A:CYS85 4.9 12.8 1.0
CG2 A:THR91 5.0 11.2 1.0

Cadmium binding site 2 out of 19 in 6xfj

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Cadmium binding site 2 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:12.1
occ:0.98
 CL B:CL207 2.2 23.8 0.8
O A:HOH322 2.4 17.5 1.0
SG A:CYS85 2.5 9.9 1.0
CL A:CL207 2.7 12.9 1.0
CB A:CYS85 3.4 9.0 1.0
O A:HOH306 3.8 44.8 1.0
CD A:CD201 3.8 10.5 1.0
CD B:CD201 4.2 9.9 0.9
SG B:CYS85 4.3 12.0 1.0
CL B:CL205 4.6 15.0 0.9
OE2 A:GLU86 4.6 13.3 0.5
O B:HOH336 4.7 21.3 1.0
CG A:GLU86 4.7 14.7 0.5
CA A:CYS85 4.8 10.2 1.0
O A:HOH314 4.9 35.5 1.0

Cadmium binding site 3 out of 19 in 6xfj

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Cadmium binding site 3 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:13.1
occ:0.20
 CD A:CD203 0.0 13.1 0.2
CD A:CD203 0.6 36.0 0.7
OE2 A:GLU142 2.2 18.1 1.0
OE1 A:GLN145 2.3 23.1 1.0
OE1 A:GLU142 2.4 19.8 1.0
CD A:GLU142 2.6 17.2 1.0
CL A:CL209 2.7 23.0 1.0
CL A:CL208 2.8 22.3 1.0
CD A:GLN145 3.3 19.6 1.0
NE2 A:GLN145 3.7 23.1 1.0
CG A:GLU142 4.2 16.7 1.0
O A:HOH313 4.3 21.3 1.0
NE2 A:HIS141 4.3 13.6 1.0
CD2 A:HIS141 4.5 11.0 1.0
CG A:GLN145 4.7 18.7 1.0
O A:HOH335 4.7 23.9 1.0
CB A:GLN145 4.8 18.1 1.0
CA A:GLU142 4.9 12.2 1.0
CB A:GLU142 5.0 13.4 1.0
O A:HOH410 5.0 42.5 1.0

Cadmium binding site 4 out of 19 in 6xfj

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Cadmium binding site 4 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:36.0
occ:0.67
 CD A:CD203 0.0 36.0 0.7
CD A:CD203 0.6 13.1 0.2
OE2 A:GLU142 2.3 18.1 1.0
CL A:CL209 2.3 23.0 1.0
CL A:CL208 2.4 22.3 1.0
OE1 A:GLN145 2.8 23.1 1.0
OE1 A:GLU142 2.9 19.8 1.0
CD A:GLU142 2.9 17.2 1.0
CD A:GLN145 3.7 19.6 1.0
NE2 A:GLN145 3.9 23.1 1.0
NE2 A:HIS141 4.3 13.6 1.0
CG A:GLU142 4.4 16.7 1.0
O A:HOH335 4.5 23.9 1.0
CD2 A:HIS141 4.6 11.0 1.0
O A:HOH331 4.7 21.5 1.0
O A:HOH410 4.7 42.5 1.0
O A:HOH313 4.9 21.3 1.0

Cadmium binding site 5 out of 19 in 6xfj

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Cadmium binding site 5 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:20.2
occ:0.48
 CD A:CD204 0.0 20.2 0.5
OE1 A:GLU93 2.1 23.6 0.7
O A:HOH375 2.3 26.7 1.0
CD A:CD204 2.3 29.0 0.3
O A:TYR88 2.3 12.1 1.0
OE2 A:GLU93 2.4 18.9 0.7
OE1 A:GLU93 2.5 20.4 0.3
CD A:GLU93 2.5 17.9 0.7
C A:TYR88 3.4 11.4 1.0
CD A:GLU93 3.4 17.0 0.3
OE1 A:GLN90 3.7 21.3 1.0
O A:HOH357 3.7 38.2 1.0
OE2 A:GLU93 3.8 16.9 0.3
CA A:TYR88 4.0 10.9 1.0
O B:HOH322 4.0 24.0 1.0
CG A:GLU93 4.0 15.7 0.7
O B:HOH397 4.2 43.5 1.0
CB A:TYR88 4.4 10.5 1.0
N A:LYS89 4.5 10.9 1.0
CG A:GLU93 4.6 15.0 0.3
CB A:LYS89 4.7 13.2 1.0
C A:LYS89 4.8 10.5 1.0
CD2 A:TYR88 4.8 10.9 1.0
O A:LYS89 4.8 11.0 1.0
CA A:LYS89 4.9 10.9 1.0
CD A:GLN90 4.9 17.0 1.0
CB A:GLU93 4.9 14.4 0.3
CB A:GLU93 5.0 14.2 0.7

Cadmium binding site 6 out of 19 in 6xfj

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Cadmium binding site 6 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:29.0
occ:0.29
 CD A:CD204 0.0 29.0 0.3
CD A:CD204 2.3 20.2 0.5
OE1 A:GLN90 2.4 21.3 1.0
OE2 A:GLU93 2.4 18.9 0.7
OE2 A:GLU93 2.5 16.9 0.3
O B:HOH322 2.5 24.0 1.0
OE1 A:GLU93 2.8 20.4 0.3
CD A:GLU93 3.0 17.0 0.3
CD A:GLU93 3.5 17.9 0.7
CD A:GLN90 3.5 17.0 1.0
O A:TYR88 3.6 12.1 1.0
OE1 A:GLU93 3.8 23.6 0.7
O A:HOH375 3.9 26.7 1.0
NE2 A:GLN90 4.0 15.5 1.0
O B:LEU123 4.2 12.2 1.0
O B:HOH397 4.2 43.5 1.0
O B:HOH329 4.3 18.6 1.0
CG A:GLU93 4.5 15.0 0.3
CD2 A:TYR88 4.5 10.9 1.0
O A:HOH304 4.5 26.7 1.0
CB A:TYR88 4.6 10.5 1.0
C A:TYR88 4.6 11.4 1.0
CG A:GLN90 4.7 16.6 1.0
CG A:GLU93 4.8 15.7 0.7
CA A:TYR88 4.9 10.9 1.0
CB A:GLU93 5.0 14.4 0.3

Cadmium binding site 7 out of 19 in 6xfj

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Cadmium binding site 7 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:9.9
occ:0.87
 CL B:CL206 2.4 12.8 1.0
CL B:CL205 2.5 15.0 0.9
SG B:CYS85 2.5 12.0 1.0
O B:CYS85 2.5 12.1 1.0
CL A:CL207 2.6 12.9 1.0
CL B:CL207 3.4 23.8 0.8
C B:CYS85 3.4 10.1 1.0
CB B:CYS85 3.5 11.3 1.0
CA B:CYS85 3.7 9.5 1.0
CD A:CD201 4.0 10.5 1.0
CD A:CD202 4.2 12.1 1.0
N B:GLU86 4.5 10.4 1.0
CE B:LYS92 4.5 18.4 1.0
CD B:LYS92 4.5 15.9 1.0
CG B:LYS92 4.7 14.1 1.0
NZ B:LYS92 4.8 21.7 1.0
CL A:CL206 4.8 11.9 1.0
CA B:LYS89 4.8 10.8 1.0
CA B:GLU86 4.9 11.1 1.0
CG B:LYS89 4.9 16.4 1.0

Cadmium binding site 8 out of 19 in 6xfj

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Cadmium binding site 8 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:14.2
occ:0.84
 O B:HOH311 2.1 23.3 1.0
O B:HOH349 2.2 16.9 1.0
OE1 B:GLU93 2.3 19.7 1.0
O A:HOH324 2.3 14.5 1.0
OE1 B:GLN90 2.3 12.8 1.0
O B:HOH367 2.6 17.6 1.0
OE2 B:GLU93 2.9 36.4 1.0
CD B:GLU93 2.9 26.6 1.0
CD B:GLN90 3.3 11.1 1.0
NE2 B:GLN90 3.6 14.1 1.0
O B:HOH377 3.9 32.0 1.0
O B:HOH335 4.1 29.3 1.0
O B:TYR88 4.2 11.5 1.0
CG B:GLU93 4.4 18.1 1.0
O A:LEU123 4.5 11.6 1.0
O A:HOH328 4.5 17.7 1.0
O A:HOH351 4.5 31.1 1.0
O A:HOH341 4.5 16.9 1.0
CD2 B:TYR88 4.6 10.0 1.0
CG B:GLN90 4.7 10.3 1.0
CB B:TYR88 4.9 11.1 1.0
O A:HOH391 5.0 32.9 1.0
CB B:GLU93 5.0 14.6 1.0

Cadmium binding site 9 out of 19 in 6xfj

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Cadmium binding site 9 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:16.5
occ:0.81
 OE2 B:GLU113 2.3 20.6 1.0
OE2 B:GLU110 2.3 28.1 1.0
OE1 B:GLU113 2.4 20.0 1.0
O B:HOH360 2.4 33.2 1.0
CL B:CL208 2.5 43.7 1.0
CD B:GLU113 2.6 16.4 1.0
CD B:GLU110 3.4 29.1 1.0
OE1 B:GLU110 3.8 33.8 1.0
CG B:GLU113 4.2 15.6 1.0
O B:HOH301 4.4 15.5 1.0
O B:HOH373 4.5 42.8 1.0
CG B:GLU110 4.7 26.9 1.0

Cadmium binding site 10 out of 19 in 6xfj

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Cadmium binding site 10 out of 19 in the Crystal Structure of the Type III Secretion Pilotin Invh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of the Type III Secretion Pilotin Invh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:40.7
occ:0.58
 O B:HOH378 2.4 35.3 1.0
O B:HOH398 2.5 37.1 1.0
O B:HOH366 2.7 25.4 1.0
CB B:PRO126 4.1 20.9 1.0
NZ B:LYS129 4.5 42.0 1.0
CG B:PRO126 4.8 23.2 1.0

Reference:

D.D.Majewski, M.Okon, F.Heinkel, C.S.Robb, M.Vuckovic, L.P.Mcintosh, N.C.J.Strynadka. Characterization of the Pilotin-Secretin Complex From the Salmonella Enterica Type III Secretion System Using Hybrid Structural Methods. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32877645
DOI: 10.1016/J.STR.2020.08.006
Page generated: Sat Dec 12 08:29:27 2020

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