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Iron in PDB 3rtl: Staphylococcus Aureus Heme-Bound Isdb-N2

Protein crystallography data

The structure of Staphylococcus Aureus Heme-Bound Isdb-N2, PDB code: 3rtl 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) 67.42 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.527, 82.608, 116.888, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.7

Other elements in 3rtl:

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

Magnesium (Mg) 5 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Staphylococcus Aureus Heme-Bound Isdb-N2 (pdb code 3rtl). 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 Isdb-N2, PDB code: 3rtl:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3rtl

Go back to Iron Binding Sites List in 3rtl
Iron binding site 1 out of 4 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:14.2
occ:1.00
FE A:HEM200 0.0 14.2 1.0
ND A:HEM200 2.0 15.0 0.5
NC A:HEM200 2.0 12.6 0.5
NA A:HEM200 2.0 11.3 0.5
NB A:HEM200 2.0 13.9 0.5
ND A:HEM200 2.1 11.8 0.5
NA A:HEM200 2.1 13.2 0.5
NC A:HEM200 2.1 13.9 0.5
NB A:HEM200 2.1 12.2 0.5
OH A:TYR440 2.2 15.3 1.0
SD A:MET362 2.5 12.8 0.8
C1D A:HEM200 3.0 15.8 0.5
C4D A:HEM200 3.0 15.1 0.5
C4A A:HEM200 3.0 10.7 0.5
C1C A:HEM200 3.0 12.6 0.5
C4C A:HEM200 3.0 11.9 0.5
C4B A:HEM200 3.0 13.5 0.5
C1A A:HEM200 3.0 11.7 0.5
C1B A:HEM200 3.1 14.1 0.5
C1D A:HEM200 3.1 11.7 0.5
C4C A:HEM200 3.1 15.3 0.5
C1A A:HEM200 3.1 13.0 0.5
C4D A:HEM200 3.1 12.2 0.5
C4A A:HEM200 3.1 13.0 0.5
C1B A:HEM200 3.1 12.1 0.5
C1C A:HEM200 3.1 14.0 0.5
C4B A:HEM200 3.2 13.0 0.5
CZ A:TYR440 3.2 16.6 1.0
CHC A:HEM200 3.4 13.9 0.5
CHA A:HEM200 3.4 12.9 0.5
CHD A:HEM200 3.4 15.2 0.5
CHD A:HEM200 3.4 10.9 0.5
CHB A:HEM200 3.5 10.7 0.5
CHA A:HEM200 3.5 12.3 0.5
CHB A:HEM200 3.5 12.3 0.5
CE A:MET362 3.5 13.3 0.8
CHC A:HEM200 3.5 14.2 0.5
CG A:MET362 3.6 12.3 0.8
CG A:MET362 3.7 13.8 0.2
CE2 A:TYR440 3.9 17.6 1.0
CE1 A:TYR440 4.0 16.5 1.0
OH A:TYR444 4.1 15.1 1.0
C2D A:HEM200 4.2 16.8 0.5
C3A A:HEM200 4.2 10.8 0.5
C3D A:HEM200 4.2 17.1 0.5
C2C A:HEM200 4.2 12.5 0.5
C3C A:HEM200 4.2 11.4 0.5
C2A A:HEM200 4.2 11.1 0.5
C3B A:HEM200 4.3 14.8 0.5
C2B A:HEM200 4.3 14.0 0.5
CB A:MET362 4.3 11.6 0.2
CB A:MET362 4.3 10.8 0.8
C3C A:HEM200 4.3 15.8 0.5
C2D A:HEM200 4.3 12.7 0.5
C2A A:HEM200 4.3 14.1 0.5
C3A A:HEM200 4.3 12.2 0.5
C3D A:HEM200 4.3 12.8 0.5
C2B A:HEM200 4.4 12.3 0.5
C2C A:HEM200 4.4 15.0 0.5
C3B A:HEM200 4.4 13.2 0.5
CE2 A:TYR444 4.5 13.5 1.0
CZ A:TYR444 4.6 13.8 1.0
SD A:MET362 4.9 18.2 0.2

Iron binding site 2 out of 4 in 3rtl

Go back to Iron Binding Sites List in 3rtl
Iron binding site 2 out of 4 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:12.4
occ:1.00
FE B:HEM200 0.0 12.4 1.0
NC B:HEM200 2.0 15.8 0.5
NA B:HEM200 2.0 11.9 0.5
ND B:HEM200 2.1 13.0 0.5
NC B:HEM200 2.1 9.5 0.5
NB B:HEM200 2.1 17.6 0.5
NA B:HEM200 2.1 9.2 0.5
ND B:HEM200 2.1 9.4 0.5
OH B:TYR440 2.1 12.3 1.0
NB B:HEM200 2.1 6.6 0.5
SD B:MET362 2.6 19.7 0.3
C4C B:HEM200 2.9 15.1 0.5
C1C B:HEM200 3.0 16.3 0.5
CZ B:TYR440 3.0 12.7 1.0
C4D B:HEM200 3.0 12.0 0.5
C1B B:HEM200 3.1 16.2 0.5
C1A B:HEM200 3.1 9.7 0.5
C4A B:HEM200 3.1 9.3 0.5
C4A B:HEM200 3.1 11.4 0.5
C1D B:HEM200 3.1 10.9 0.5
C4C B:HEM200 3.1 10.3 0.5
C1D B:HEM200 3.1 11.8 0.5
C1C B:HEM200 3.1 7.9 0.5
C1A B:HEM200 3.1 9.2 0.5
C4B B:HEM200 3.1 17.4 0.5
C4D B:HEM200 3.1 8.9 0.5
C4B B:HEM200 3.1 6.8 0.5
C1B B:HEM200 3.2 6.9 0.5
CHD B:HEM200 3.4 13.9 0.5
CHA B:HEM200 3.4 12.1 0.5
CHB B:HEM200 3.4 14.0 0.5
CHC B:HEM200 3.5 17.8 0.5
CHD B:HEM200 3.5 11.0 0.5
CHC B:HEM200 3.5 7.0 0.5
CHB B:HEM200 3.5 8.3 0.5
CG B:MET362 3.5 14.4 0.3
CHA B:HEM200 3.5 7.1 0.5
CG B:MET362 3.5 10.4 0.7
CE2 B:TYR440 3.7 15.5 1.0
CE1 B:TYR440 3.9 14.1 1.0
OH B:TYR444 4.0 13.4 1.0
C3C B:HEM200 4.2 15.8 0.5
C2C B:HEM200 4.2 16.2 0.5
CE2 B:TYR444 4.3 11.6 1.0
C3D B:HEM200 4.3 12.5 0.5
C3A B:HEM200 4.3 11.6 0.5
C2A B:HEM200 4.3 9.0 0.5
C3A B:HEM200 4.3 9.0 0.5
C2A B:HEM200 4.3 11.0 0.5
C2B B:HEM200 4.3 16.5 0.5
C3C B:HEM200 4.3 11.1 0.5
CE B:MET362 4.3 19.0 0.3
C2D B:HEM200 4.3 10.9 0.5
CE B:MET362 4.3 15.0 0.7
C3B B:HEM200 4.3 18.0 0.5
C2C B:HEM200 4.3 10.0 0.5
C2D B:HEM200 4.3 12.3 0.5
C3B B:HEM200 4.4 8.9 0.5
C3D B:HEM200 4.4 12.2 0.5
CB B:MET362 4.4 9.5 0.7
C2B B:HEM200 4.4 8.3 0.5
CB B:MET362 4.4 11.4 0.3
CZ B:TYR444 4.4 10.3 1.0
SD B:MET362 4.8 11.6 0.7
CG2 B:VAL433 4.9 18.7 1.0
CD2 B:TYR440 4.9 16.0 1.0

Iron binding site 3 out of 4 in 3rtl

Go back to Iron Binding Sites List in 3rtl
Iron binding site 3 out of 4 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:14.3
occ:1.00
FE C:HEM200 0.0 14.3 1.0
NA C:HEM200 2.0 18.5 0.5
NB C:HEM200 2.0 19.0 0.5
NA C:HEM200 2.0 11.2 0.5
ND C:HEM200 2.0 10.0 0.5
NC C:HEM200 2.1 14.7 0.5
NC C:HEM200 2.1 11.9 0.5
ND C:HEM200 2.1 12.3 0.5
NB C:HEM200 2.1 12.7 0.5
OH C:TYR440 2.2 14.7 1.0
SD C:MET362 2.6 18.0 0.3
CZ C:TYR440 3.0 15.1 1.0
C1B C:HEM200 3.1 19.3 0.5
C4A C:HEM200 3.1 19.0 0.5
C4B C:HEM200 3.1 18.6 0.5
C1D C:HEM200 3.1 9.0 0.5
C1A C:HEM200 3.1 10.7 0.5
C4D C:HEM200 3.1 9.6 0.5
C1A C:HEM200 3.1 17.8 0.5
C4C C:HEM200 3.1 14.1 0.5
C1C C:HEM200 3.1 12.8 0.5
C1C C:HEM200 3.1 16.2 0.5
C4A C:HEM200 3.1 10.3 0.5
C1D C:HEM200 3.1 13.5 0.5
C4C C:HEM200 3.1 11.0 0.5
C4B C:HEM200 3.1 12.7 0.5
C4D C:HEM200 3.1 14.3 0.5
C1B C:HEM200 3.2 11.2 0.5
CHB C:HEM200 3.4 20.5 0.5
CHC C:HEM200 3.4 18.8 0.5
CHA C:HEM200 3.4 10.3 0.5
CHC C:HEM200 3.4 13.7 0.5
CHD C:HEM200 3.4 10.0 0.5
CHD C:HEM200 3.5 13.0 0.5
CHA C:HEM200 3.5 15.2 0.5
CG C:MET362 3.5 12.5 0.7
CHB C:HEM200 3.5 10.8 0.5
CE C:MET362 3.5 15.7 0.3
CE2 C:TYR440 3.7 16.4 1.0
CG C:MET362 3.7 14.0 0.3
CE1 C:TYR440 3.9 17.1 1.0
OH C:TYR444 4.0 15.5 1.0
C2B C:HEM200 4.3 18.2 0.5
C3B C:HEM200 4.3 18.6 0.5
C3A C:HEM200 4.3 19.5 0.5
C2D C:HEM200 4.3 9.7 0.5
CE C:MET362 4.3 15.7 0.7
C2A C:HEM200 4.3 19.9 0.5
C2C C:HEM200 4.3 16.2 0.5
C3C C:HEM200 4.3 15.0 0.5
C2A C:HEM200 4.3 9.5 0.5
C3A C:HEM200 4.3 9.2 0.5
C3D C:HEM200 4.3 10.7 0.5
C2C C:HEM200 4.3 13.0 0.5
C3C C:HEM200 4.3 13.7 0.5
C2D C:HEM200 4.3 14.1 0.5
CB C:MET362 4.3 12.5 0.7
C3B C:HEM200 4.3 12.5 0.5
C3D C:HEM200 4.3 14.6 0.5
CE2 C:TYR444 4.3 11.9 1.0
C2B C:HEM200 4.4 11.4 0.5
CB C:MET362 4.4 12.5 0.3
CZ C:TYR444 4.5 12.1 1.0
SD C:MET362 4.8 13.7 0.7
CG2 C:VAL433 4.8 17.9 0.5
CD2 C:TYR440 4.9 18.1 1.0

Iron binding site 4 out of 4 in 3rtl

Go back to Iron Binding Sites List in 3rtl
Iron binding site 4 out of 4 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:17.6
occ:1.00
FE D:HEM200 0.0 17.6 1.0
NA D:HEM200 2.0 14.1 0.5
NC D:HEM200 2.0 16.6 0.5
NB D:HEM200 2.0 18.5 0.5
ND D:HEM200 2.1 18.1 0.5
NA D:HEM200 2.1 18.0 0.5
NB D:HEM200 2.1 15.0 0.5
NC D:HEM200 2.1 17.6 0.5
ND D:HEM200 2.1 16.7 0.5
OH D:TYR440 2.3 21.2 1.0
SD D:MET362 2.5 14.3 0.7
C4C D:HEM200 3.0 16.2 0.5
C1A D:HEM200 3.0 14.3 0.5
C4A D:HEM200 3.0 13.1 0.5
C1C D:HEM200 3.0 16.7 0.5
C4B D:HEM200 3.1 19.1 0.5
C4D D:HEM200 3.1 17.9 0.5
C1D D:HEM200 3.1 19.6 0.5
C1B D:HEM200 3.1 19.9 0.5
C4A D:HEM200 3.1 19.1 0.5
C1D D:HEM200 3.1 16.4 0.5
C4C D:HEM200 3.1 19.4 0.5
C1C D:HEM200 3.1 18.0 0.5
C4B D:HEM200 3.1 15.2 0.5
C1B D:HEM200 3.1 14.3 0.5
C1A D:HEM200 3.1 18.0 0.5
C4D D:HEM200 3.2 17.0 0.5
CZ D:TYR440 3.3 23.2 1.0
CHD D:HEM200 3.4 15.6 0.5
CHA D:HEM200 3.4 15.4 0.5
CHC D:HEM200 3.4 18.7 0.5
CHB D:HEM200 3.4 20.1 0.5
CHD D:HEM200 3.4 19.0 0.5
CHB D:HEM200 3.4 12.6 0.5
CHC D:HEM200 3.5 17.7 0.5
CHA D:HEM200 3.5 17.0 0.5
CE D:MET362 3.5 13.6 0.7
CG D:MET362 3.6 13.3 0.7
CG D:MET362 3.7 16.6 0.3
CE2 D:TYR440 4.0 23.9 1.0
CE1 D:TYR440 4.1 23.6 1.0
OH D:TYR444 4.1 18.1 1.0
C2A D:HEM200 4.2 12.6 0.5
C3A D:HEM200 4.2 12.0 0.5
C3C D:HEM200 4.2 16.4 0.5
C2C D:HEM200 4.2 17.5 0.5
C3B D:HEM200 4.3 20.9 0.5
C2B D:HEM200 4.3 21.1 0.5
C3D D:HEM200 4.3 20.1 0.5
C2D D:HEM200 4.3 20.6 0.5
C3A D:HEM200 4.3 19.6 0.5
C3C D:HEM200 4.3 19.9 0.5
CB D:MET362 4.3 12.2 0.7
C2C D:HEM200 4.3 19.4 0.5
C2A D:HEM200 4.3 19.5 0.5
C3B D:HEM200 4.3 15.7 0.5
C2B D:HEM200 4.3 14.6 0.5
CB D:MET362 4.3 13.6 0.3
C2D D:HEM200 4.3 16.1 0.5
C3D D:HEM200 4.4 17.0 0.5
CE D:MET362 4.4 22.4 0.3
CE2 D:TYR444 4.5 15.4 1.0
CZ D:TYR444 4.6 14.8 1.0

Reference:

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
Page generated: Sun Aug 4 19:45:40 2024

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