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: Sun Aug 4 19:45:40 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