Atomistry » Iron » PDB 3rmz-3s66 » 3rtl
Atomistry »
  Iron »
    PDB 3rmz-3s66 »
      3rtl »

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: Tue Aug 5 06:37:19 2025

Last articles

Na in 4C6S
Na in 4C75
Na in 4C6W
Na in 4C3Y
Na in 4C3X
Na in 4C3V
Na in 4C44
Na in 4C3W
Na in 4C2U
Na in 4C10
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy