Zinc in PDB 4fil: Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B

The structure of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B, PDB code: 4fil was solved by L.K.Briere, D.E.Heinrichs, B.H.Shilton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.343, 78.996, 116.811, 90.00, 109.87, 90.00
R / Rfree (%)	19.8 / 22.9

The structure of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 56;

Binding sites:

The binding sites of Zinc atom in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B (pdb code 4fil). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 56 binding sites of Zinc where determined in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B, PDB code: 4fil:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:57.6 occ:1.00 OD2 A:ASP195 2.2 29.8 1.0 O A:HOH505 2.6 26.3 1.0 CG A:ASP195 3.0 34.7 1.0 CB A:ASP195 3.3 25.6 1.0 O A:HOH517 3.7 21.1 1.0 CG A:GLN206 4.1 25.1 1.0 NZ A:LYS134 4.1 35.4 1.0 OD1 A:ASP195 4.2 41.5 1.0 CB A:TYR205 4.5 28.9 1.0 O A:TYR205 4.6 34.7 1.0 C A:TYR205 4.8 22.9 1.0 CE A:MET212 4.8 30.9 1.0 CA A:ASP195 4.8 18.6 1.0 CD A:GLN206 4.9 22.8 1.0

Zinc binding site 2 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:46.8 occ:1.00 OD1 A:ASP113 2.0 34.4 1.0 O A:HOH531 2.4 17.0 1.0 CG A:ASP113 3.1 45.2 1.0 OD2 A:ASP93 3.2 79.2 1.0 CB A:ASP113 3.7 28.9 1.0 CG1 A:VAL53 3.7 29.9 1.0 CD2 A:TYR110 3.8 30.6 1.0 CG A:ASP93 4.0 72.9 1.0 OD2 A:ASP113 4.0 45.4 1.0 OD1 A:ASP93 4.1 76.5 1.0 N A:TYR110 4.1 34.6 1.0 O A:VAL53 4.3 33.2 1.0 CB A:TYR110 4.4 22.7 1.0 CB A:VAL53 4.5 28.3 1.0 CB A:VAL109 4.5 38.0 1.0 C A:VAL53 4.5 26.5 1.0 CG A:TYR110 4.5 24.0 1.0 CA A:ASP113 4.6 33.3 1.0 CE2 A:TYR110 4.6 24.0 1.0 O A:HOH533 4.6 27.3 1.0 CG1 A:VAL109 4.7 34.2 1.0 N A:ALA54 4.7 32.7 1.0 CA A:VAL109 4.7 33.3 1.0 CA A:ALA54 4.8 21.4 1.0 CA A:TYR110 4.9 28.9 1.0 O A:HOH530 4.9 31.9 1.0 C A:VAL109 4.9 32.2 1.0 CB A:ALA54 5.0 21.7 1.0

Zinc binding site 3 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:48.7 occ:1.00 OD2 A:ASP129 2.0 35.9 1.0 CG A:ASP129 3.0 44.6 1.0 OD1 A:ASP129 3.4 43.3 1.0 NZ B:LYS114 4.0 39.5 1.0 CB A:ASN131 4.2 31.8 1.0 CB A:ASP129 4.4 31.1 1.0 CE A:LYS132 4.6 40.7 1.0 CD B:LYS114 4.6 63.0 1.0 ND2 A:ASN131 4.7 41.3 1.0 CE B:LYS114 4.9 46.1 1.0

Zinc binding site 4 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:63.3 occ:1.00 OE1 A:GLU149 2.4 59.4 1.0 CD A:GLU149 3.5 62.3 1.0 CB A:GLU149 3.5 56.6 1.0 CG A:GLU149 4.1 56.6 1.0 CA A:GLY147 4.4 30.6 1.0 OE2 A:GLU149 4.6 74.7 1.0 O A:GLY147 4.6 50.5 1.0 N A:GLU149 4.6 47.0 1.0 C A:GLY147 4.6 49.9 1.0 CA A:LYS144 4.6 25.9 1.0 CA A:GLU149 4.7 39.2 1.0 O A:GLY143 4.7 40.3 1.0 CG A:LYS144 4.8 27.9 1.0

Zinc binding site 5 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:47.4 occ:1.00 OE2 A:GLU185 2.2 32.6 1.0 OE1 A:GLU185 2.7 46.5 1.0 CD A:GLU185 2.8 33.1 1.0 NZ B:LYS188 3.2 78.5 1.0 CE B:LYS188 4.0 69.5 1.0 CD A:LYS248 4.3 44.6 1.0 CG A:GLU185 4.3 25.1 1.0 N A:LYS188 4.3 37.8 1.0 N A:ASP187 4.3 38.8 1.0 O A:GLU185 4.6 35.0 1.0 CE A:LYS248 4.6 31.4 1.0 NZ A:LYS248 4.6 26.1 1.0 CA A:PHE186 4.6 31.9 1.0 C A:PHE186 4.9 35.9 1.0 C A:GLU185 4.9 33.1 1.0 CG A:LYS248 4.9 62.2 1.0 CA A:LYS188 5.0 36.9 1.0 N A:PHE186 5.0 35.5 1.0 CG A:LYS188 5.0 50.8 1.0

Zinc binding site 6 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:47.0 occ:1.00 OE2 A:GLU267 2.1 46.1 1.0 OE1 A:GLU267 2.4 51.0 1.0 NZ A:LYS263 2.5 54.3 1.0 CD A:GLU267 2.6 35.9 1.0 CE A:LYS263 2.8 60.3 1.0 CG A:GLU267 4.1 30.7 1.0 NE2 A:HIS269 4.1 27.0 1.0 CD A:LYS263 4.1 45.0 1.0 CD2 A:HIS269 4.3 23.6 1.0 CB A:GLU267 4.7 32.1 1.0 OD1 A:ASP239 4.8 43.5 1.0 CG A:LYS263 4.9 49.5 1.0

Zinc binding site 7 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:42.8 occ:1.00 OD2 A:ASP187 2.3 64.9 1.0 OE2 B:GLU185 2.4 38.2 1.0 OE1 B:GLU185 2.8 47.5 1.0 CG A:ASP187 2.8 60.2 1.0 OD1 A:ASP187 2.8 51.2 1.0 CD B:GLU185 2.9 30.4 1.0 O B:HOH612 3.4 32.1 1.0 CB A:ASP187 4.1 55.9 1.0 N B:ASP187 4.2 37.2 1.0 CG B:GLU185 4.4 24.0 1.0 N B:LYS188 4.4 38.5 1.0 O B:GLU185 4.4 37.8 1.0 CA B:PHE186 4.4 35.6 1.0 CD B:LYS248 4.5 52.3 1.0 NZ B:LYS248 4.5 25.7 1.0 CE B:LYS248 4.6 35.5 1.0 O A:ASP187 4.6 46.0 1.0 C B:PHE186 4.7 41.2 1.0 C B:GLU185 4.8 39.5 1.0 N B:PHE186 4.9 38.5 1.0 CA A:ASP187 4.9 45.7 1.0 CA B:ASP187 5.0 42.7 1.0

Zinc binding site 8 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:56.8 occ:1.00 ND1 A:HIS133 2.1 30.6 1.0 O A:HOH532 2.1 17.3 1.0 CE1 A:HIS133 2.4 43.7 1.0 O A:HOH600 2.5 28.8 1.0 CG A:HIS133 3.4 30.8 1.0 CG1 A:VAL128 3.6 34.2 1.0 NE2 A:HIS133 3.7 39.8 1.0 O A:ASP129 3.7 46.2 1.0 CB A:LYS132 4.2 30.0 1.0 CD2 A:HIS133 4.2 25.9 1.0 CE A:MET141 4.3 36.1 1.0 CB A:HIS133 4.3 32.0 1.0 CG A:MET141 4.5 32.5 1.0 CG A:LYS132 4.5 28.1 1.0 O A:HOH552 4.5 34.9 1.0 N A:HIS133 4.6 23.1 1.0 N A:ASP129 4.6 32.1 1.0 C A:ASP129 4.7 35.0 1.0 CB A:VAL128 4.8 29.7 1.0 C A:LYS132 5.0 27.7 1.0

Zinc binding site 9 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:55.7 occ:1.00 OE2 C:GLU169 2.1 54.1 1.0 OE2 A:GLU169 2.4 52.8 1.0 CD C:GLU169 2.7 45.6 1.0 OE1 C:GLU169 2.7 48.8 1.0 C2 A:EDO419 2.9 73.7 1.0 OE1 A:GLU169 2.9 40.2 1.0 CD A:GLU169 3.0 39.6 1.0 O A:HOH544 3.7 24.8 1.0 O2 A:EDO419 3.7 60.2 1.0 NZ A:LYS294 3.8 39.1 1.0 CG C:GLU169 4.1 49.4 1.0 CD1 C:ILE298 4.1 27.4 1.0 C1 A:EDO419 4.1 51.5 1.0 O C:HOH571 4.5 37.2 1.0 CG A:GLU169 4.5 39.2 1.0 CE C:LYS294 4.7 30.9 1.0 NZ C:LYS294 4.9 43.0 1.0 CE A:LYS294 4.9 33.6 1.0

Zinc binding site 10 out of 56 in the Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of FHUD2 From Staphylococcus Aureus with Bound Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn411 b:64.3 occ:1.00 OD2 A:ASP95 2.2 49.7 1.0 O A:HOH591 2.2 45.1 1.0 CG A:ASP95 3.1 43.3 1.0 OD1 A:ASP95 3.3 44.1 1.0 N A:GLY92 3.5 43.6 1.0 CA A:GLY92 4.0 28.8 1.0 NZ A:LYS98 4.1 53.8 1.0 C A:ILE91 4.3 31.5 1.0 OE1 A:GLN73 4.4 43.2 1.0 CB A:ASP95 4.5 32.2 1.0 CE A:LYS98 4.6 60.2 1.0 CA A:ILE91 4.6 29.8 1.0 CD A:GLN73 4.7 39.0 1.0 C A:GLY92 4.8 34.6 1.0 NE2 A:GLN73 4.9 56.1 1.0 O A:LYS90 4.9 54.3 1.0 CD A:LYS98 4.9 35.1 1.0

K.J.Podkowa, L.A.Briere, D.E.Heinrichs, B.H.Shilton. Crystal and Solution Structure Analysis of FHUD2 From Staphylococcus Aureus in Multiple Unliganded Conformations and Bound to Ferrioxamine-B. Biochemistry V. 53 2017 2014.
ISSN: ISSN 0006-2960
PubMed: 24606332
DOI: 10.1021/BI401349D