Iron in PDB 2itf: Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound
Protein crystallography data
The structure of Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound, PDB code: 2itf
was solved by
J.C.Grigg,
C.L.Vermeiren,
D.E.Heinrichs,
M.E.Murphy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.089,
58.533,
95.584,
90.00,
93.28,
90.00
|
R / Rfree (%)
|
17.1 /
21.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound
(pdb code 2itf). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound, PDB code: 2itf:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2itf
Go back to
Iron Binding Sites List in 2itf
Iron binding site 1 out
of 4 in the Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:13.8
occ:1.00
|
FE
|
A:HEM200
|
0.0
|
13.8
|
1.0
|
NC
|
A:HEM200
|
2.0
|
11.5
|
0.5
|
ND
|
A:HEM200
|
2.1
|
12.6
|
0.5
|
NC
|
A:HEM200
|
2.1
|
11.5
|
0.5
|
NA
|
A:HEM200
|
2.1
|
12.8
|
0.5
|
NA
|
A:HEM200
|
2.1
|
12.3
|
0.5
|
OH
|
A:TYR166
|
2.1
|
13.5
|
1.0
|
ND
|
A:HEM200
|
2.1
|
12.4
|
0.5
|
NB
|
A:HEM200
|
2.1
|
12.0
|
0.5
|
NB
|
A:HEM200
|
2.2
|
10.0
|
0.5
|
C4C
|
A:HEM200
|
3.0
|
11.2
|
0.5
|
C1D
|
A:HEM200
|
3.0
|
11.1
|
0.5
|
C1C
|
A:HEM200
|
3.0
|
11.3
|
0.5
|
C1C
|
A:HEM200
|
3.0
|
11.6
|
0.5
|
C4C
|
A:HEM200
|
3.1
|
12.6
|
0.5
|
C1A
|
A:HEM200
|
3.1
|
12.5
|
0.5
|
C4D
|
A:HEM200
|
3.1
|
11.9
|
0.5
|
C1A
|
A:HEM200
|
3.1
|
11.9
|
0.5
|
C4D
|
A:HEM200
|
3.1
|
12.4
|
0.5
|
C4B
|
A:HEM200
|
3.1
|
11.4
|
0.5
|
C1D
|
A:HEM200
|
3.1
|
13.0
|
0.5
|
C4A
|
A:HEM200
|
3.1
|
11.0
|
0.5
|
C4A
|
A:HEM200
|
3.1
|
12.7
|
0.5
|
C4B
|
A:HEM200
|
3.2
|
11.1
|
0.5
|
CZ
|
A:TYR166
|
3.2
|
13.3
|
1.0
|
C1B
|
A:HEM200
|
3.2
|
11.8
|
0.5
|
C1B
|
A:HEM200
|
3.2
|
10.7
|
0.5
|
CHD
|
A:HEM200
|
3.4
|
11.1
|
0.5
|
CHA
|
A:HEM200
|
3.4
|
11.3
|
0.5
|
CHC
|
A:HEM200
|
3.4
|
11.5
|
0.5
|
CHC
|
A:HEM200
|
3.4
|
11.6
|
0.5
|
CHA
|
A:HEM200
|
3.5
|
11.2
|
0.5
|
CHD
|
A:HEM200
|
3.5
|
12.4
|
0.5
|
CHB
|
A:HEM200
|
3.5
|
11.9
|
0.5
|
CHB
|
A:HEM200
|
3.6
|
11.2
|
0.5
|
CE1
|
A:TYR166
|
3.6
|
12.3
|
1.0
|
OH
|
A:TYR170
|
3.9
|
13.5
|
1.0
|
CB
|
A:HIS83
|
4.0
|
12.0
|
1.0
|
CG
|
A:HIS83
|
4.1
|
12.5
|
1.0
|
C3C
|
A:HEM200
|
4.2
|
10.5
|
0.5
|
C2C
|
A:HEM200
|
4.2
|
11.8
|
0.5
|
C2C
|
A:HEM200
|
4.2
|
11.3
|
0.5
|
C3C
|
A:HEM200
|
4.2
|
12.8
|
0.5
|
CE2
|
A:TYR166
|
4.3
|
11.9
|
1.0
|
C2D
|
A:HEM200
|
4.3
|
11.2
|
0.5
|
C2A
|
A:HEM200
|
4.3
|
12.3
|
0.5
|
C3D
|
A:HEM200
|
4.3
|
12.0
|
0.5
|
C2A
|
A:HEM200
|
4.3
|
12.3
|
0.5
|
C3A
|
A:HEM200
|
4.3
|
11.4
|
0.5
|
C3D
|
A:HEM200
|
4.3
|
12.8
|
0.5
|
C3A
|
A:HEM200
|
4.3
|
11.1
|
0.5
|
C2D
|
A:HEM200
|
4.4
|
11.5
|
0.5
|
C3B
|
A:HEM200
|
4.4
|
10.2
|
0.5
|
CE2
|
A:TYR170
|
4.4
|
12.9
|
1.0
|
C2B
|
A:HEM200
|
4.4
|
11.4
|
0.5
|
C3B
|
A:HEM200
|
4.4
|
11.7
|
0.5
|
C2B
|
A:HEM200
|
4.4
|
10.0
|
0.5
|
CZ
|
A:TYR170
|
4.4
|
11.5
|
1.0
|
CD2
|
A:HIS83
|
4.4
|
13.3
|
1.0
|
ND1
|
A:HIS83
|
4.4
|
14.0
|
1.0
|
CD1
|
A:TYR166
|
4.9
|
12.3
|
1.0
|
CE1
|
A:HIS83
|
5.0
|
13.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 2itf
Go back to
Iron Binding Sites List in 2itf
Iron binding site 2 out
of 4 in the Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe200
b:14.8
occ:1.00
|
FE
|
B:HEM200
|
0.0
|
14.8
|
1.0
|
OH
|
B:TYR166
|
2.0
|
13.5
|
1.0
|
NC
|
B:HEM200
|
2.1
|
8.6
|
0.5
|
ND
|
B:HEM200
|
2.1
|
14.5
|
0.5
|
NC
|
B:HEM200
|
2.1
|
13.6
|
0.5
|
NA
|
B:HEM200
|
2.1
|
14.2
|
0.5
|
ND
|
B:HEM200
|
2.1
|
9.3
|
0.5
|
NB
|
B:HEM200
|
2.1
|
13.9
|
0.5
|
NA
|
B:HEM200
|
2.2
|
12.0
|
0.5
|
NB
|
B:HEM200
|
2.2
|
11.0
|
0.5
|
C4C
|
B:HEM200
|
3.0
|
12.1
|
0.5
|
CZ
|
B:TYR166
|
3.0
|
13.2
|
1.0
|
C1C
|
B:HEM200
|
3.0
|
11.5
|
0.5
|
C1D
|
B:HEM200
|
3.0
|
14.3
|
0.5
|
C4D
|
B:HEM200
|
3.1
|
14.2
|
0.5
|
C4C
|
B:HEM200
|
3.1
|
14.6
|
0.5
|
C1D
|
B:HEM200
|
3.1
|
11.2
|
0.5
|
C1A
|
B:HEM200
|
3.1
|
14.4
|
0.5
|
C1C
|
B:HEM200
|
3.1
|
13.9
|
0.5
|
C4D
|
B:HEM200
|
3.1
|
10.4
|
0.5
|
C4B
|
B:HEM200
|
3.1
|
11.3
|
0.5
|
C4A
|
B:HEM200
|
3.1
|
15.0
|
0.5
|
C4B
|
B:HEM200
|
3.1
|
15.2
|
0.5
|
C1A
|
B:HEM200
|
3.1
|
11.3
|
0.5
|
C1B
|
B:HEM200
|
3.2
|
15.3
|
0.5
|
C4A
|
B:HEM200
|
3.2
|
11.8
|
0.5
|
C1B
|
B:HEM200
|
3.2
|
12.4
|
0.5
|
CHD
|
B:HEM200
|
3.4
|
11.6
|
0.5
|
CHD
|
B:HEM200
|
3.4
|
14.4
|
0.5
|
CHA
|
B:HEM200
|
3.4
|
14.7
|
0.5
|
CHC
|
B:HEM200
|
3.4
|
11.5
|
0.5
|
CHA
|
B:HEM200
|
3.5
|
11.7
|
0.5
|
CHC
|
B:HEM200
|
3.5
|
14.7
|
0.5
|
CHB
|
B:HEM200
|
3.5
|
15.1
|
0.5
|
CE1
|
B:TYR166
|
3.5
|
14.8
|
1.0
|
CHB
|
B:HEM200
|
3.6
|
11.9
|
0.5
|
OH
|
B:TYR170
|
3.8
|
13.4
|
1.0
|
CE2
|
B:TYR166
|
4.1
|
11.0
|
1.0
|
CB
|
B:HIS83
|
4.2
|
17.1
|
1.0
|
C3C
|
B:HEM200
|
4.2
|
11.4
|
0.5
|
C2C
|
B:HEM200
|
4.2
|
12.4
|
0.5
|
CE2
|
B:TYR170
|
4.2
|
13.2
|
1.0
|
C2D
|
B:HEM200
|
4.3
|
13.9
|
0.5
|
C3D
|
B:HEM200
|
4.3
|
14.8
|
0.5
|
C3C
|
B:HEM200
|
4.3
|
14.0
|
0.5
|
C2C
|
B:HEM200
|
4.3
|
13.2
|
0.5
|
CZ
|
B:TYR170
|
4.3
|
14.4
|
1.0
|
C2D
|
B:HEM200
|
4.3
|
9.6
|
0.5
|
CG
|
B:HIS83
|
4.3
|
20.1
|
1.0
|
C3D
|
B:HEM200
|
4.3
|
10.9
|
0.5
|
C2A
|
B:HEM200
|
4.3
|
15.1
|
0.5
|
C3A
|
B:HEM200
|
4.4
|
13.9
|
0.5
|
C3B
|
B:HEM200
|
4.4
|
11.7
|
0.5
|
C3B
|
B:HEM200
|
4.4
|
15.8
|
0.5
|
C2A
|
B:HEM200
|
4.4
|
12.4
|
0.5
|
C2B
|
B:HEM200
|
4.4
|
14.4
|
0.5
|
C2B
|
B:HEM200
|
4.4
|
12.2
|
0.5
|
C3A
|
B:HEM200
|
4.4
|
11.2
|
0.5
|
O
|
B:HOH248
|
4.5
|
36.0
|
1.0
|
ND1
|
B:HIS83
|
4.6
|
22.6
|
1.0
|
CD1
|
B:TYR166
|
4.9
|
11.9
|
1.0
|
CD2
|
B:HIS83
|
4.9
|
22.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 2itf
Go back to
Iron Binding Sites List in 2itf
Iron binding site 3 out
of 4 in the Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe200
b:14.1
occ:1.00
|
FE
|
C:HEM200
|
0.0
|
14.1
|
1.0
|
ND
|
C:HEM200
|
2.0
|
13.5
|
0.5
|
NC
|
C:HEM200
|
2.0
|
13.2
|
0.5
|
NB
|
C:HEM200
|
2.0
|
8.3
|
0.5
|
NA
|
C:HEM200
|
2.1
|
14.5
|
0.5
|
NC
|
C:HEM200
|
2.1
|
13.6
|
0.5
|
NB
|
C:HEM200
|
2.1
|
14.2
|
0.5
|
NA
|
C:HEM200
|
2.2
|
10.6
|
0.5
|
ND
|
C:HEM200
|
2.2
|
12.8
|
0.5
|
OH
|
C:TYR166
|
2.2
|
17.7
|
1.0
|
C4D
|
C:HEM200
|
3.0
|
14.1
|
0.5
|
C1C
|
C:HEM200
|
3.0
|
12.0
|
0.5
|
C1D
|
C:HEM200
|
3.0
|
14.2
|
0.5
|
C4B
|
C:HEM200
|
3.0
|
10.6
|
0.5
|
C4C
|
C:HEM200
|
3.0
|
13.5
|
0.5
|
C1A
|
C:HEM200
|
3.0
|
15.2
|
0.5
|
C1B
|
C:HEM200
|
3.1
|
10.4
|
0.5
|
C4A
|
C:HEM200
|
3.1
|
15.3
|
0.5
|
C4A
|
C:HEM200
|
3.1
|
11.2
|
0.5
|
C4C
|
C:HEM200
|
3.1
|
14.1
|
0.5
|
C1B
|
C:HEM200
|
3.2
|
14.6
|
0.5
|
C1C
|
C:HEM200
|
3.2
|
14.0
|
0.5
|
C1D
|
C:HEM200
|
3.2
|
13.6
|
0.5
|
C4B
|
C:HEM200
|
3.2
|
14.2
|
0.5
|
C1A
|
C:HEM200
|
3.2
|
11.1
|
0.5
|
CZ
|
C:TYR166
|
3.3
|
16.1
|
1.0
|
C4D
|
C:HEM200
|
3.3
|
13.8
|
0.5
|
CD2
|
C:HIS83
|
3.3
|
13.1
|
1.0
|
CHA
|
C:HEM200
|
3.3
|
14.2
|
0.5
|
CHC
|
C:HEM200
|
3.4
|
11.3
|
0.5
|
CHD
|
C:HEM200
|
3.4
|
13.8
|
0.5
|
CHB
|
C:HEM200
|
3.4
|
9.8
|
0.5
|
CHD
|
C:HEM200
|
3.4
|
13.3
|
0.5
|
CHB
|
C:HEM200
|
3.5
|
15.3
|
0.5
|
CHC
|
C:HEM200
|
3.5
|
14.8
|
0.5
|
NE2
|
C:HIS83
|
3.6
|
15.6
|
1.0
|
CHA
|
C:HEM200
|
3.6
|
11.6
|
0.5
|
CG
|
C:HIS83
|
3.8
|
13.8
|
1.0
|
CE1
|
C:TYR166
|
3.9
|
14.3
|
1.0
|
OH
|
C:TYR170
|
4.0
|
15.9
|
1.0
|
C2C
|
C:HEM200
|
4.2
|
12.5
|
0.5
|
CE2
|
C:TYR166
|
4.2
|
15.2
|
1.0
|
CE1
|
C:HIS83
|
4.2
|
14.2
|
1.0
|
C3C
|
C:HEM200
|
4.2
|
13.5
|
0.5
|
C3D
|
C:HEM200
|
4.2
|
13.9
|
0.5
|
C2D
|
C:HEM200
|
4.2
|
13.5
|
0.5
|
CE2
|
C:TYR170
|
4.2
|
17.1
|
1.0
|
C3B
|
C:HEM200
|
4.3
|
9.1
|
0.5
|
C2A
|
C:HEM200
|
4.3
|
15.6
|
0.5
|
C2B
|
C:HEM200
|
4.3
|
9.3
|
0.5
|
C3A
|
C:HEM200
|
4.3
|
15.3
|
0.5
|
ND1
|
C:HIS83
|
4.3
|
15.2
|
1.0
|
C3A
|
C:HEM200
|
4.3
|
9.9
|
0.5
|
C3C
|
C:HEM200
|
4.4
|
13.5
|
0.5
|
C2C
|
C:HEM200
|
4.4
|
13.4
|
0.5
|
C2B
|
C:HEM200
|
4.4
|
15.2
|
0.5
|
C3B
|
C:HEM200
|
4.4
|
14.5
|
0.5
|
C2A
|
C:HEM200
|
4.4
|
10.4
|
0.5
|
CZ
|
C:TYR170
|
4.4
|
14.3
|
1.0
|
C2D
|
C:HEM200
|
4.4
|
13.3
|
0.5
|
C3D
|
C:HEM200
|
4.5
|
14.5
|
0.5
|
CB
|
C:HIS83
|
4.5
|
12.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 2itf
Go back to
Iron Binding Sites List in 2itf
Iron binding site 4 out
of 4 in the Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure Isda Neat Domain From Staphylococcus Aureus with Heme Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:15.2
occ:1.00
|
FE
|
D:HEM200
|
0.0
|
15.2
|
1.0
|
NA
|
D:HEM200
|
2.0
|
14.8
|
0.5
|
NB
|
D:HEM200
|
2.0
|
8.7
|
0.5
|
NA
|
D:HEM200
|
2.1
|
7.8
|
0.5
|
NC
|
D:HEM200
|
2.1
|
14.6
|
0.5
|
ND
|
D:HEM200
|
2.1
|
14.2
|
0.5
|
NC
|
D:HEM200
|
2.1
|
13.3
|
0.5
|
NB
|
D:HEM200
|
2.1
|
15.3
|
0.5
|
ND
|
D:HEM200
|
2.1
|
11.9
|
0.5
|
OH
|
D:TYR166
|
2.1
|
14.0
|
1.0
|
C1A
|
D:HEM200
|
3.0
|
14.5
|
0.5
|
C4A
|
D:HEM200
|
3.1
|
16.7
|
0.5
|
C4B
|
D:HEM200
|
3.1
|
10.4
|
0.5
|
C4B
|
D:HEM200
|
3.1
|
15.5
|
0.5
|
C1B
|
D:HEM200
|
3.1
|
9.1
|
0.5
|
C1C
|
D:HEM200
|
3.1
|
12.6
|
0.5
|
C4A
|
D:HEM200
|
3.1
|
9.5
|
0.5
|
C1B
|
D:HEM200
|
3.1
|
15.9
|
0.5
|
C4D
|
D:HEM200
|
3.1
|
14.1
|
0.5
|
C1D
|
D:HEM200
|
3.1
|
14.4
|
0.5
|
C1C
|
D:HEM200
|
3.1
|
15.3
|
0.5
|
C4C
|
D:HEM200
|
3.1
|
14.1
|
0.5
|
C1D
|
D:HEM200
|
3.1
|
14.2
|
0.5
|
C4C
|
D:HEM200
|
3.1
|
14.7
|
0.5
|
C1A
|
D:HEM200
|
3.1
|
9.0
|
0.5
|
C4D
|
D:HEM200
|
3.1
|
11.7
|
0.5
|
CZ
|
D:TYR166
|
3.2
|
13.4
|
1.0
|
CD2
|
D:HIS83
|
3.3
|
14.2
|
1.0
|
CHA
|
D:HEM200
|
3.4
|
14.2
|
0.5
|
CHC
|
D:HEM200
|
3.4
|
11.0
|
0.5
|
CHB
|
D:HEM200
|
3.4
|
9.2
|
0.5
|
CHC
|
D:HEM200
|
3.4
|
15.1
|
0.5
|
CHB
|
D:HEM200
|
3.4
|
15.3
|
0.5
|
CHD
|
D:HEM200
|
3.5
|
14.6
|
0.5
|
CHD
|
D:HEM200
|
3.5
|
12.5
|
0.5
|
CHA
|
D:HEM200
|
3.5
|
10.1
|
0.5
|
NE2
|
D:HIS83
|
3.5
|
15.1
|
1.0
|
CG
|
D:HIS83
|
3.7
|
12.5
|
1.0
|
CE1
|
D:TYR166
|
3.8
|
14.2
|
1.0
|
CE2
|
D:TYR166
|
4.0
|
13.7
|
1.0
|
OH
|
D:TYR170
|
4.1
|
13.1
|
1.0
|
CE1
|
D:HIS83
|
4.1
|
13.3
|
1.0
|
ND1
|
D:HIS83
|
4.2
|
15.5
|
1.0
|
C3B
|
D:HEM200
|
4.3
|
16.4
|
0.5
|
C2A
|
D:HEM200
|
4.3
|
15.4
|
0.5
|
CE2
|
D:TYR170
|
4.3
|
13.8
|
1.0
|
C3A
|
D:HEM200
|
4.3
|
16.0
|
0.5
|
C2B
|
D:HEM200
|
4.3
|
15.6
|
0.5
|
C2B
|
D:HEM200
|
4.3
|
8.0
|
0.5
|
C3B
|
D:HEM200
|
4.3
|
10.2
|
0.5
|
C2C
|
D:HEM200
|
4.3
|
13.6
|
0.5
|
C3A
|
D:HEM200
|
4.3
|
8.5
|
0.5
|
C3C
|
D:HEM200
|
4.3
|
13.5
|
0.5
|
C2D
|
D:HEM200
|
4.3
|
13.6
|
0.5
|
C3D
|
D:HEM200
|
4.3
|
13.9
|
0.5
|
C2C
|
D:HEM200
|
4.3
|
15.6
|
0.5
|
C3C
|
D:HEM200
|
4.3
|
15.1
|
0.5
|
C2A
|
D:HEM200
|
4.4
|
9.3
|
0.5
|
CB
|
D:HIS83
|
4.4
|
11.8
|
1.0
|
C2D
|
D:HEM200
|
4.4
|
13.2
|
0.5
|
C3D
|
D:HEM200
|
4.4
|
12.7
|
0.5
|
CZ
|
D:TYR170
|
4.5
|
13.2
|
1.0
|
|
Reference:
J.C.Grigg,
C.L.Vermeiren,
D.E.Heinrichs,
M.E.Murphy.
Haem Recognition By A Staphylococcus Aureus Neat Domain. Mol.Microbiol. V. 63 139 2007.
ISSN: ISSN 0950-382X
PubMed: 17229211
DOI: 10.1111/J.1365-2958.2006.05502.X
Page generated: Sat Aug 3 23:24:30 2024
|