Atomistry » Cadmium » PDB 5an6-5gu0 » 5fly
Atomistry »
  Cadmium »
    PDB 5an6-5gu0 »
      5fly »

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

Go back to Cadmium Binding Sites List in 5fly
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

Go back to Cadmium Binding Sites List in 5fly
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

Go back to Cadmium Binding Sites List in 5fly
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

Go back to Cadmium Binding Sites List in 5fly
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

Go back to Cadmium Binding Sites List in 5fly
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

Go back to Cadmium Binding Sites List in 5fly
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: Fri Jul 19 18:24:08 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy