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Cadmium in PDB 5fly: The Fhud Protein From S.Pseudintermedius

Protein crystallography data

The structure of The Fhud Protein From S.Pseudintermedius, PDB code: 5fly was solved by E.Malito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.582, 53.822, 120.248, 90.00, 99.17, 90.00
R / Rfree (%) 18.4 / 21.7

Other elements in 5fly:

The structure of The Fhud Protein From S.Pseudintermedius also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Fhud Protein From S.Pseudintermedius (pdb code 5fly). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the The Fhud Protein From S.Pseudintermedius, PDB code: 5fly:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 5fly

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Cadmium binding site 1 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1282

b:9.8
occ:0.57
 OE1 A:GLU210 2.3 19.0 1.0
O A:HOH2422 2.3 24.9 1.0
OE2 A:GLU210 2.3 14.9 1.0
CL A:CL1291 2.6 20.9 1.0
CD A:GLU210 2.6 16.0 1.0
CL A:CL1290 2.9 41.0 1.0
HH A:TYR214 3.5 24.7 1.0
HZ1 A:LYS213 3.6 24.0 1.0
HZ2 A:LYS213 4.0 24.0 1.0
HG2 A:PRO207 4.0 13.4 1.0
CG A:GLU210 4.2 12.3 1.0
OH A:TYR214 4.2 20.6 1.0
NZ A:LYS213 4.2 20.0 1.0
HD2 A:PRO207 4.4 12.4 1.0
HE2 A:LYS213 4.5 25.4 1.0
HG3 A:GLU210 4.6 14.8 1.0
HG2 A:GLU210 4.6 14.8 1.0
HB3 A:GLU210 4.6 12.2 1.0
CG A:PRO207 4.9 11.2 1.0
HZ3 A:LYS213 4.9 24.0 1.0
CB A:GLU210 4.9 10.2 1.0
CE A:LYS213 5.0 21.2 1.0
HE2 A:TYR214 5.0 22.0 1.0
CD A:PRO207 5.0 10.3 1.0
HB2 A:GLU210 5.0 12.2 1.0

Cadmium binding site 2 out of 9 in 5fly

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Cadmium binding site 2 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1283

b:10.0
occ:0.51
 OE2 A:GLU4 2.3 36.6 1.0
OD2 B:ASP136 2.3 16.9 1.0
O A:HOH2006 2.3 27.4 1.0
OD1 B:ASP136 2.3 16.9 1.0
CG A:GLU4 2.3 34.9 1.0
CL A:CL1289 2.6 29.3 0.9
CG B:ASP136 2.6 16.0 1.0
CD A:GLU4 2.7 36.6 1.0
CL A:CL1294 2.7 31.3 1.0
HE3 A:LYS23 3.5 35.6 1.0
HZ2 A:LYS23 3.7 38.9 1.0
CB A:GLU4 3.8 17.1 1.0
H A:GLU4 3.8 22.1 1.0
OE1 A:GLU4 3.9 39.6 1.0
HE2 A:LYS23 4.0 35.6 1.0
O A:HOH2005 4.0 32.7 1.0
CE A:LYS23 4.1 29.7 1.0
CB B:ASP136 4.1 13.4 1.0
NZ A:LYS23 4.3 32.4 1.0
HB3 B:ASP136 4.5 16.1 1.0
HB2 B:ASP136 4.6 16.1 1.0
O B:HOH2189 4.6 26.4 1.0
N A:GLU4 4.6 18.4 1.0
O B:LYS132 4.6 17.9 1.0
HZ3 A:LYS23 4.7 38.9 1.0
HB3 B:LYS132 4.7 23.4 1.0
O A:HOH2004 4.7 16.4 1.0
HA B:ASP136 4.8 13.3 1.0
CA A:GLU4 4.8 18.3 1.0
CA B:ASP136 5.0 11.1 1.0

Cadmium binding site 3 out of 9 in 5fly

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Cadmium binding site 3 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1284

b:15.4
occ:0.31
 O A:HOH2195 2.3 31.3 1.0
O A:HOH2196 2.3 28.3 1.0
OD1 A:ASP95 2.3 31.9 1.0
OD2 A:ASP95 2.3 36.4 1.0
CG A:ASP95 2.6 32.1 1.0
HZ1 A:LYS99 3.6 33.3 1.0
HZ2 A:LYS99 3.6 33.3 1.0
O A:HOH2085 3.7 18.5 1.0
NZ A:LYS99 4.0 27.8 1.0
HE2 A:LYS99 4.0 32.3 1.0
CB A:ASP95 4.2 24.3 1.0
O A:HOH2086 4.3 27.2 1.0
O A:HOH2197 4.4 24.7 1.0
HA A:ASP95 4.5 24.4 1.0
O A:ASP95 4.5 19.5 1.0
CE A:LYS99 4.6 26.9 1.0
HB3 A:ASP95 4.6 29.1 1.0
HZ1 A:LYS98 4.6 39.6 1.0
HB2 A:ASP95 4.6 29.1 1.0
HZ3 A:LYS99 4.8 33.3 1.0
CA A:ASP95 4.8 20.3 1.0
HG3 A:LYS99 4.8 29.7 1.0
C A:ASP95 5.0 19.5 1.0

Cadmium binding site 4 out of 9 in 5fly

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Cadmium binding site 4 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1285

b:10.7
occ:1.00
 OE2 A:GLU209 2.3 11.9 1.0
OE1 A:GLU209 2.3 10.6 1.0
CL A:CL1287 2.5 16.0 1.0
CL A:CL1288 2.6 12.6 1.0
CD A:GLU209 2.7 11.5 1.0
HG2 A:LYS208 3.3 12.1 1.0
HE2 A:LYS208 3.4 17.6 1.0
H A:LYS208 4.1 12.1 1.0
CG A:LYS208 4.2 10.1 1.0
CG A:GLU209 4.2 12.3 1.0
H A:GLU209 4.2 11.6 1.0
HB3 A:PRO207 4.2 12.6 1.0
CE A:LYS208 4.2 14.7 1.0
HE3 A:LYS208 4.3 17.6 1.0
HG3 A:LYS208 4.4 12.1 1.0
HG2 A:GLU209 4.5 14.7 1.0
HG3 A:GLU209 4.6 14.7 1.0
CD A:LYS208 4.7 11.8 1.0
N A:LYS208 4.7 10.1 1.0
HB2 A:GLU209 4.8 14.8 1.0
HD3 A:LYS208 4.9 14.2 1.0
N A:GLU209 5.0 9.6 1.0

Cadmium binding site 5 out of 9 in 5fly

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Cadmium binding site 5 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1286

b:16.8
occ:0.44
 O A:HOH2045 2.3 41.0 1.0
OD1 A:ASP20 2.3 22.1 1.0
OD2 A:ASP20 2.3 26.4 1.0
CG A:ASP20 2.7 23.6 1.0
CL A:CL1293 2.8 49.0 1.0
CL A:CL1292 2.8 23.4 1.0
HB3 A:ALA7 4.0 19.1 1.0
O A:HOH2010 4.1 20.6 1.0
CB A:ASP20 4.2 15.4 1.0
HB3 A:ASP20 4.6 18.5 1.0
HB2 A:ASP20 4.6 18.5 1.0
HA A:ASP20 4.8 16.8 1.0
CB A:ALA7 5.0 15.9 1.0

Cadmium binding site 6 out of 9 in 5fly

Go back to Cadmium Binding Sites List in 5fly
Cadmium binding site 6 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1282

b:29.2
occ:0.60
 OD2 B:ASP20 2.3 27.7 1.0
OD1 B:ASP20 2.3 21.4 1.0
CL B:CL1289 2.6 28.7 1.0
CG B:ASP20 2.6 22.2 1.0
CL B:CL1288 2.9 39.9 1.0
CB B:ASP20 4.2 17.0 1.0
O B:HOH2004 4.2 23.4 1.0
HB3 B:ALA7 4.5 24.3 1.0
HB3 B:ASP20 4.5 20.4 1.0
HB2 B:ASP20 4.6 20.4 1.0
HA B:ASP20 4.9 19.2 1.0
H B:ASP20 5.0 19.9 1.0

Cadmium binding site 7 out of 9 in 5fly

Go back to Cadmium Binding Sites List in 5fly
Cadmium binding site 7 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1283

b:11.4
occ:1.00
 OE2 B:GLU209 2.3 13.7 1.0
OE1 B:GLU209 2.3 12.6 1.0
CL B:CL1286 2.5 19.1 1.0
CD B:GLU209 2.7 13.9 1.0
HG2 B:LYS208 3.3 14.2 1.0
HE2 B:LYS208 3.5 19.3 1.0
H B:LYS208 4.1 14.1 1.0
HB3 B:PRO207 4.2 14.2 1.0
CG B:GLU209 4.2 14.5 1.0
CG B:LYS208 4.2 11.8 1.0
H B:GLU209 4.3 13.5 1.0
CE B:LYS208 4.4 16.1 1.0
HG2 B:GLU209 4.5 17.4 1.0
O B:HOH2275 4.6 17.3 1.0
HD3 B:LYS208 4.6 16.2 1.0
HG3 B:LYS208 4.6 14.2 1.0
HG3 B:GLU209 4.6 17.4 1.0
CD B:LYS208 4.7 13.5 1.0
HE3 B:LYS208 4.7 19.3 1.0
N B:LYS208 4.8 11.7 1.0
HB2 B:GLU209 4.8 15.7 1.0
CB B:PRO207 5.0 11.8 1.0
N B:GLU209 5.0 11.2 1.0

Cadmium binding site 8 out of 9 in 5fly

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Cadmium binding site 8 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1284

b:14.9
occ:0.53
 OE1 B:GLU210 2.3 22.4 1.0
O B:HOH2332 2.3 23.0 1.0
OE2 B:GLU210 2.3 18.5 1.0
CD B:GLU210 2.6 19.4 1.0
CL B:CL1291 2.6 28.0 1.0
CL B:CL1290 3.0 42.8 1.0
HZ1 B:LYS213 3.3 38.4 1.0
HH B:TYR214 3.6 26.8 1.0
HZ2 B:LYS213 3.7 38.4 1.0
NZ B:LYS213 3.9 32.0 1.0
HG2 B:PRO207 4.0 13.2 1.0
CG B:GLU210 4.1 15.7 1.0
OH B:TYR214 4.2 22.4 1.0
HD2 B:PRO207 4.4 12.2 1.0
HE2 B:LYS213 4.4 34.4 1.0
O B:HOH2239 4.5 24.7 1.0
HG3 B:GLU210 4.5 18.9 1.0
HZ3 B:LYS213 4.6 38.4 1.0
HG2 B:GLU210 4.6 18.9 1.0
HB3 B:GLU210 4.6 14.8 1.0
CE B:LYS213 4.8 28.7 1.0
CB B:GLU210 4.9 12.3 1.0
CG B:PRO207 4.9 11.0 1.0
HB2 B:GLU210 5.0 14.8 1.0

Cadmium binding site 9 out of 9 in 5fly

Go back to Cadmium Binding Sites List in 5fly
Cadmium binding site 9 out of 9 in the The Fhud Protein From S.Pseudintermedius


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of The Fhud Protein From S.Pseudintermedius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1285

b:12.8
occ:0.41
 OD1 B:ASP226 2.3 33.1 1.0
OD2 B:ASP226 2.3 32.0 1.0
O B:HOH2291 2.3 27.6 1.0
CG B:ASP226 2.6 30.3 1.0
CL B:CL1293 2.7 47.3 1.0
CL B:CL1292 2.8 27.6 1.0
HB2 B:ALA224 3.6 14.0 1.0
O B:HOH2289 4.1 26.4 1.0
HB1 B:ALA224 4.1 14.0 1.0
CB B:ASP226 4.2 24.0 1.0
CB B:ALA224 4.2 11.6 1.0
HB3 B:ALA224 4.3 14.0 1.0
O B:HOH2286 4.3 24.4 1.0
O B:HOH2290 4.5 9.4 1.0
O B:HOH2288 4.5 27.1 1.0
HB3 B:ASP226 4.6 28.8 1.0
HB2 B:ASP226 4.6 28.8 1.0
H B:ASP226 4.6 21.2 1.0
O B:HOH2032 4.7 32.1 1.0
C B:ASP226 4.9 20.0 1.0
HB3 B:ALA227 4.9 20.4 1.0
CA B:ASP226 5.0 19.3 1.0

Reference:

F.Abate, R.Cozzi, M.Maritan, P.Lo Surdo, D.Maione, E.Malito, M.J.Bottomley. Crystal Structure of Fhud at 1.6 Angstrom Resolution: A Ferrichrome-Binding Protein From the Animal and Human Pathogen Staphylococcus Pseudintermedius Acta Crystallogr.,Sect.F V. 72 214 2016.
ISSN: ESSN 1744-3091
PubMed: 26919525
DOI: 10.1107/S2053230X16002272
Page generated: Sat Dec 12 08:26:40 2020

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