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:
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
|