Iron in PDB 3rur: Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2

The structure of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2, PDB code: 3rur was solved by C.F.M.Gaudin, J.C.Grigg, A.L.Arrieta, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.814, 79.378, 113.869, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.2

The structure of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Iron atom in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 (pdb code 3rur). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2, PDB code: 3rur:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:23.2 occ:1.00 FE A:HEM200 0.0 23.2 1.0 NA A:HEM200 2.0 23.6 1.0 NC A:HEM200 2.0 23.7 1.0 ND A:HEM200 2.0 20.4 1.0 NB A:HEM200 2.1 23.9 1.0 OH A:TYR440 2.4 29.5 1.0 SE A:MSE362 2.7 21.4 0.8 C1A A:HEM200 3.0 24.9 1.0 C1D A:HEM200 3.0 18.3 1.0 C4D A:HEM200 3.0 21.5 1.0 C4C A:HEM200 3.0 20.7 1.0 C4A A:HEM200 3.0 26.0 1.0 C1C A:HEM200 3.0 22.7 1.0 C4B A:HEM200 3.1 23.3 1.0 C1B A:HEM200 3.1 23.8 1.0 CZ A:TYR440 3.3 29.4 1.0 CHA A:HEM200 3.4 23.9 1.0 CHD A:HEM200 3.4 18.0 1.0 CHC A:HEM200 3.4 24.8 1.0 CHB A:HEM200 3.5 23.1 1.0 CG A:MSE362 3.6 19.5 0.2 CG A:MSE362 3.8 16.4 0.8 CE A:MSE362 3.8 17.0 0.8 CE2 A:TYR440 4.0 29.1 1.0 CE1 A:TYR440 4.1 31.0 1.0 OH A:TYR444 4.1 24.1 1.0 C3C A:HEM200 4.3 24.2 1.0 C3A A:HEM200 4.3 28.7 1.0 C2D A:HEM200 4.3 19.1 1.0 C2C A:HEM200 4.3 24.6 1.0 C2A A:HEM200 4.3 30.4 1.0 C3D A:HEM200 4.3 18.8 1.0 C2B A:HEM200 4.3 24.9 1.0 C3B A:HEM200 4.4 28.1 1.0 CE2 A:TYR444 4.4 20.2 1.0 CB A:MSE362 4.4 18.0 0.2 CB A:MSE362 4.5 16.8 0.8 CZ A:TYR444 4.6 21.0 1.0 CE A:MSE362 4.8 23.6 0.2

Iron binding site 2 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:20.6 occ:1.00 FE B:HEM200 0.0 20.6 1.0 NB B:HEM200 2.0 20.5 1.0 ND B:HEM200 2.0 20.3 1.0 NA B:HEM200 2.0 17.2 1.0 NC B:HEM200 2.0 19.8 1.0 OH B:TYR440 2.2 19.3 1.0 SE B:MSE362 2.7 19.2 0.2 C4A B:HEM200 3.0 15.7 1.0 C4C B:HEM200 3.0 21.6 1.0 C1B B:HEM200 3.0 18.3 1.0 C1A B:HEM200 3.1 17.7 1.0 C4B B:HEM200 3.1 21.4 1.0 CZ B:TYR440 3.1 19.6 1.0 C4D B:HEM200 3.1 18.2 1.0 C1C B:HEM200 3.1 23.4 1.0 C1D B:HEM200 3.1 20.7 1.0 CHB B:HEM200 3.4 18.0 1.0 CHD B:HEM200 3.4 19.9 1.0 CHC B:HEM200 3.4 22.0 1.0 CHA B:HEM200 3.4 16.2 1.0 CG B:MSE362 3.5 18.8 0.2 CG B:MSE362 3.5 21.1 0.8 CE2 B:TYR440 3.6 20.5 1.0 CE1 B:TYR440 3.9 20.8 1.0 OH B:TYR444 4.1 20.8 1.0 CE B:MSE362 4.1 25.6 0.8 C3A B:HEM200 4.2 16.9 1.0 C3C B:HEM200 4.2 23.3 1.0 C2A B:HEM200 4.3 16.3 1.0 C3B B:HEM200 4.3 21.2 1.0 C2C B:HEM200 4.3 24.6 1.0 C2B B:HEM200 4.3 20.0 1.0 C3D B:HEM200 4.3 19.8 1.0 C2D B:HEM200 4.3 21.2 1.0 CB B:MSE362 4.3 19.1 0.8 CE2 B:TYR444 4.4 18.7 1.0 CB B:MSE362 4.5 17.8 0.2 CZ B:TYR444 4.5 15.9 1.0 CE B:MSE362 4.6 21.3 0.2 SE B:MSE362 4.8 25.1 0.8 CD2 B:TYR440 4.8 22.7 1.0

Iron binding site 3 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:19.9 occ:1.00 FE C:HEM200 0.0 19.9 1.0 ND C:HEM200 2.0 19.2 1.0 NB C:HEM200 2.0 19.3 1.0 NC C:HEM200 2.0 21.4 1.0 NA C:HEM200 2.1 17.4 1.0 OH C:TYR440 2.3 19.6 1.0 SE C:MSE362 2.6 22.4 0.8 C1D C:HEM200 3.0 20.6 1.0 C4A C:HEM200 3.0 17.5 1.0 C4C C:HEM200 3.0 23.4 1.0 C1B C:HEM200 3.1 17.1 1.0 C4D C:HEM200 3.1 17.9 1.0 C4B C:HEM200 3.1 20.7 1.0 C1C C:HEM200 3.1 23.0 1.0 C1A C:HEM200 3.1 18.4 1.0 CZ C:TYR440 3.2 23.1 1.0 CHD C:HEM200 3.4 18.6 1.0 CHB C:HEM200 3.4 15.8 1.0 CHC C:HEM200 3.5 21.9 1.0 CG C:MSE362 3.5 18.4 0.2 CHA C:HEM200 3.5 18.3 1.0 CE C:MSE362 3.6 19.0 0.8 CG C:MSE362 3.7 17.8 0.8 CE2 C:TYR440 3.9 24.9 1.0 CE1 C:TYR440 4.0 23.3 1.0 OH C:TYR444 4.2 18.5 1.0 C3A C:HEM200 4.3 16.3 1.0 C3C C:HEM200 4.3 23.6 1.0 C2D C:HEM200 4.3 21.1 1.0 C3D C:HEM200 4.3 21.8 1.0 C2A C:HEM200 4.3 18.0 1.0 C3B C:HEM200 4.3 21.3 1.0 C2C C:HEM200 4.3 23.8 1.0 C2B C:HEM200 4.3 19.0 1.0 CE C:MSE362 4.3 20.2 0.2 CB C:MSE362 4.4 16.4 0.2 CB C:MSE362 4.4 16.1 0.8 CE2 C:TYR444 4.6 16.7 1.0 CZ C:TYR444 4.7 18.4 1.0 SE C:MSE362 4.7 21.9 0.2

Iron binding site 4 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:21.5 occ:1.00 FE D:HEM200 0.0 21.5 1.0 ND D:HEM200 2.0 20.2 1.0 NC D:HEM200 2.0 22.9 1.0 NB D:HEM200 2.1 22.8 1.0 NA D:HEM200 2.1 19.7 1.0 OH D:TYR440 2.2 22.4 1.0 SE D:MSE362 2.5 27.3 0.2 C4C D:HEM200 3.0 23.8 1.0 C4A D:HEM200 3.0 17.5 1.0 CZ D:TYR440 3.0 22.9 1.0 C1D D:HEM200 3.1 22.8 1.0 C4D D:HEM200 3.1 19.4 1.0 C1C D:HEM200 3.1 23.3 1.0 C1A D:HEM200 3.1 16.8 1.0 C1B D:HEM200 3.1 19.7 1.0 C4B D:HEM200 3.1 19.0 1.0 CHD D:HEM200 3.4 22.4 1.0 CHB D:HEM200 3.4 19.1 1.0 CG D:MSE362 3.5 20.0 0.2 CHA D:HEM200 3.5 19.4 1.0 CHC D:HEM200 3.5 22.1 1.0 CG D:MSE362 3.5 14.9 0.8 CE2 D:TYR440 3.7 25.9 1.0 CE1 D:TYR440 3.9 24.6 1.0 OH D:TYR444 4.1 22.4 1.0 CE D:MSE362 4.1 23.5 0.2 CE D:MSE362 4.2 20.5 0.8 C3A D:HEM200 4.3 16.9 1.0 C3C D:HEM200 4.3 24.7 1.0 C2C D:HEM200 4.3 24.0 1.0 C2A D:HEM200 4.3 15.5 1.0 C2D D:HEM200 4.3 21.8 1.0 C3B D:HEM200 4.3 21.8 1.0 C3D D:HEM200 4.3 21.6 1.0 CB D:MSE362 4.3 18.7 0.2 CB D:MSE362 4.3 17.8 0.8 CE2 D:TYR444 4.3 20.3 1.0 C2B D:HEM200 4.3 19.9 1.0 CZ D:TYR444 4.5 19.1 1.0 SE D:MSE362 4.8 22.3 0.8 CD2 D:TYR440 4.9 28.5 1.0 CG2 D:VAL433 4.9 24.7 1.0

C.F.Gaudin, J.C.Grigg, A.L.Arrieta, M.E.Murphy. Unique Heme-Iron Coordination By the Hemoglobin Receptor Isdb of Staphylococcus Aureus. Biochemistry V. 50 5443 2011.
ISSN: ISSN 0006-2960
PubMed: 21574663
DOI: 10.1021/BI200369P