Iron in PDB 6hk2: Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo)
Protein crystallography data
The structure of Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo), PDB code: 6hk2
was solved by
G.Cerutti,
C.Savino,
L.C.Montemiglio,
A.Boffi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.69 /
1.55
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.807,
62.863,
153.594,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.7 /
21.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo)
(pdb code 6hk2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo), PDB code: 6hk2:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 6hk2
Go back to
Iron Binding Sites List in 6hk2
Iron binding site 1 out
of 5 in the Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:23.9
occ:0.50
|
FE
|
A:HEM201
|
0.0
|
23.9
|
0.5
|
|
FE
|
A:HEM201
|
0.2
|
29.4
|
0.5
|
|
O2
|
A:OXY202
|
1.8
|
30.2
|
0.5
|
|
ND
|
A:HEM201
|
1.9
|
25.5
|
0.5
|
|
ND
|
A:HEM201
|
2.0
|
30.2
|
0.5
|
|
NA
|
A:HEM201
|
2.0
|
24.9
|
0.5
|
|
NB
|
A:HEM201
|
2.0
|
27.5
|
0.5
|
|
NA
|
A:HEM201
|
2.0
|
29.4
|
0.5
|
|
O
|
A:HOH301
|
2.0
|
8.6
|
0.5
|
|
NC
|
A:HEM201
|
2.0
|
28.0
|
0.5
|
|
NC
|
A:HEM201
|
2.1
|
23.4
|
0.5
|
|
NB
|
A:HEM201
|
2.1
|
22.7
|
0.5
|
|
NE2
|
A:HIS87
|
2.1
|
28.7
|
1.0
|
|
C1D
|
A:HEM201
|
3.0
|
30.6
|
0.5
|
|
C4B
|
A:HEM201
|
3.0
|
26.5
|
0.5
|
|
C4D
|
A:HEM201
|
3.0
|
26.6
|
0.5
|
|
C1D
|
A:HEM201
|
3.0
|
25.8
|
0.5
|
|
C1B
|
A:HEM201
|
3.0
|
27.5
|
0.5
|
|
C1A
|
A:HEM201
|
3.0
|
26.2
|
0.5
|
|
C4C
|
A:HEM201
|
3.0
|
28.7
|
0.5
|
|
C4B
|
A:HEM201
|
3.0
|
21.8
|
0.5
|
|
C4D
|
A:HEM201
|
3.0
|
31.3
|
0.5
|
|
C4A
|
A:HEM201
|
3.0
|
24.7
|
0.5
|
|
C4A
|
A:HEM201
|
3.0
|
29.2
|
0.5
|
|
C1A
|
A:HEM201
|
3.1
|
30.4
|
0.5
|
|
C1C
|
A:HEM201
|
3.1
|
27.4
|
0.5
|
|
C1C
|
A:HEM201
|
3.1
|
22.8
|
0.5
|
|
C4C
|
A:HEM201
|
3.1
|
24.2
|
0.5
|
|
C1B
|
A:HEM201
|
3.1
|
22.6
|
0.5
|
|
CE1
|
A:HIS87
|
3.1
|
29.0
|
1.0
|
|
CD2
|
A:HIS87
|
3.1
|
29.1
|
1.0
|
|
O1
|
A:OXY202
|
3.2
|
26.9
|
0.5
|
|
CHD
|
A:HEM201
|
3.4
|
29.9
|
0.5
|
|
CHA
|
A:HEM201
|
3.4
|
26.9
|
0.5
|
|
CHB
|
A:HEM201
|
3.4
|
27.8
|
0.5
|
|
CHC
|
A:HEM201
|
3.4
|
26.7
|
0.5
|
|
CHC
|
A:HEM201
|
3.4
|
22.1
|
0.5
|
|
CHA
|
A:HEM201
|
3.5
|
31.4
|
0.5
|
|
CHB
|
A:HEM201
|
3.5
|
23.2
|
0.5
|
|
CHD
|
A:HEM201
|
3.5
|
25.2
|
0.5
|
|
C3A
|
A:HEM201
|
4.2
|
26.0
|
0.5
|
|
C2A
|
A:HEM201
|
4.2
|
27.3
|
0.5
|
|
C2B
|
A:HEM201
|
4.2
|
26.6
|
0.5
|
|
ND1
|
A:HIS87
|
4.2
|
31.0
|
1.0
|
|
C3C
|
A:HEM201
|
4.2
|
28.1
|
0.5
|
|
C2C
|
A:HEM201
|
4.2
|
27.4
|
0.5
|
|
C3A
|
A:HEM201
|
4.2
|
30.0
|
0.5
|
|
C3B
|
A:HEM201
|
4.2
|
26.1
|
0.5
|
|
C2C
|
A:HEM201
|
4.3
|
23.1
|
0.5
|
|
C2D
|
A:HEM201
|
4.3
|
31.6
|
0.5
|
|
C2A
|
A:HEM201
|
4.3
|
31.1
|
0.5
|
|
CG
|
A:HIS87
|
4.3
|
31.2
|
1.0
|
|
C2D
|
A:HEM201
|
4.3
|
27.0
|
0.5
|
|
NE2
|
A:HIS58
|
4.3
|
27.1
|
1.0
|
|
C3B
|
A:HEM201
|
4.3
|
21.3
|
0.5
|
|
C2B
|
A:HEM201
|
4.3
|
21.7
|
0.5
|
|
C3D
|
A:HEM201
|
4.3
|
27.8
|
0.5
|
|
C3C
|
A:HEM201
|
4.3
|
23.8
|
0.5
|
|
C3D
|
A:HEM201
|
4.3
|
32.5
|
0.5
|
|
CE1
|
A:HIS58
|
4.8
|
29.2
|
1.0
|
|
CG2
|
A:VAL62
|
4.8
|
23.6
|
1.0
|
|
Iron binding site 2 out
of 5 in 6hk2
Go back to
Iron Binding Sites List in 6hk2
Iron binding site 2 out
of 5 in the Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:29.4
occ:0.50
|
FE
|
A:HEM201
|
0.0
|
29.4
|
0.5
|
|
FE
|
A:HEM201
|
0.2
|
23.9
|
0.5
|
|
NE2
|
A:HIS87
|
1.9
|
28.7
|
1.0
|
|
ND
|
A:HEM201
|
1.9
|
30.2
|
0.5
|
|
ND
|
A:HEM201
|
1.9
|
25.5
|
0.5
|
|
NA
|
A:HEM201
|
2.0
|
29.4
|
0.5
|
|
NA
|
A:HEM201
|
2.0
|
24.9
|
0.5
|
|
O2
|
A:OXY202
|
2.0
|
30.2
|
0.5
|
|
NC
|
A:HEM201
|
2.1
|
28.0
|
0.5
|
|
NB
|
A:HEM201
|
2.1
|
27.5
|
0.5
|
|
NC
|
A:HEM201
|
2.1
|
23.4
|
0.5
|
|
NB
|
A:HEM201
|
2.2
|
22.7
|
0.5
|
|
O
|
A:HOH301
|
2.3
|
8.6
|
0.5
|
|
CE1
|
A:HIS87
|
2.9
|
29.0
|
1.0
|
|
CD2
|
A:HIS87
|
2.9
|
29.1
|
1.0
|
|
C1D
|
A:HEM201
|
2.9
|
30.6
|
0.5
|
|
C4D
|
A:HEM201
|
3.0
|
31.3
|
0.5
|
|
C4D
|
A:HEM201
|
3.0
|
26.6
|
0.5
|
|
C1A
|
A:HEM201
|
3.0
|
26.2
|
0.5
|
|
C1D
|
A:HEM201
|
3.0
|
25.8
|
0.5
|
|
C4C
|
A:HEM201
|
3.0
|
28.7
|
0.5
|
|
C1A
|
A:HEM201
|
3.0
|
30.4
|
0.5
|
|
C4B
|
A:HEM201
|
3.0
|
26.5
|
0.5
|
|
C1B
|
A:HEM201
|
3.1
|
27.5
|
0.5
|
|
C4A
|
A:HEM201
|
3.1
|
29.2
|
0.5
|
|
C4A
|
A:HEM201
|
3.1
|
24.7
|
0.5
|
|
C4B
|
A:HEM201
|
3.1
|
21.8
|
0.5
|
|
C1C
|
A:HEM201
|
3.1
|
27.4
|
0.5
|
|
C4C
|
A:HEM201
|
3.1
|
24.2
|
0.5
|
|
C1C
|
A:HEM201
|
3.1
|
22.8
|
0.5
|
|
C1B
|
A:HEM201
|
3.2
|
22.6
|
0.5
|
|
CHA
|
A:HEM201
|
3.4
|
26.9
|
0.5
|
|
CHD
|
A:HEM201
|
3.4
|
29.9
|
0.5
|
|
CHA
|
A:HEM201
|
3.4
|
31.4
|
0.5
|
|
O1
|
A:OXY202
|
3.4
|
26.9
|
0.5
|
|
CHB
|
A:HEM201
|
3.5
|
27.8
|
0.5
|
|
CHD
|
A:HEM201
|
3.5
|
25.2
|
0.5
|
|
CHC
|
A:HEM201
|
3.5
|
26.7
|
0.5
|
|
CHC
|
A:HEM201
|
3.5
|
22.1
|
0.5
|
|
CHB
|
A:HEM201
|
3.5
|
23.2
|
0.5
|
|
ND1
|
A:HIS87
|
4.0
|
31.0
|
1.0
|
|
CG
|
A:HIS87
|
4.0
|
31.2
|
1.0
|
|
C2A
|
A:HEM201
|
4.2
|
27.3
|
0.5
|
|
C2D
|
A:HEM201
|
4.2
|
31.6
|
0.5
|
|
C3A
|
A:HEM201
|
4.2
|
26.0
|
0.5
|
|
C2A
|
A:HEM201
|
4.2
|
31.1
|
0.5
|
|
C3A
|
A:HEM201
|
4.2
|
30.0
|
0.5
|
|
C3C
|
A:HEM201
|
4.2
|
28.1
|
0.5
|
|
C3D
|
A:HEM201
|
4.2
|
32.5
|
0.5
|
|
C2D
|
A:HEM201
|
4.3
|
27.0
|
0.5
|
|
C3D
|
A:HEM201
|
4.3
|
27.8
|
0.5
|
|
C2B
|
A:HEM201
|
4.3
|
26.6
|
0.5
|
|
C2C
|
A:HEM201
|
4.3
|
27.4
|
0.5
|
|
C3B
|
A:HEM201
|
4.3
|
26.1
|
0.5
|
|
C2C
|
A:HEM201
|
4.3
|
23.1
|
0.5
|
|
C3C
|
A:HEM201
|
4.3
|
23.8
|
0.5
|
|
C3B
|
A:HEM201
|
4.4
|
21.3
|
0.5
|
|
C2B
|
A:HEM201
|
4.4
|
21.7
|
0.5
|
|
NE2
|
A:HIS58
|
4.5
|
27.1
|
1.0
|
|
CD1
|
A:LEU91
|
4.9
|
36.0
|
1.0
|
|
CE1
|
A:HIS58
|
5.0
|
29.2
|
1.0
|
|
Iron binding site 3 out
of 5 in 6hk2
Go back to
Iron Binding Sites List in 6hk2
Iron binding site 3 out
of 5 in the Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:18.5
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
18.5
|
1.0
|
|
NA
|
B:HEM201
|
2.0
|
19.6
|
1.0
|
|
ND
|
B:HEM201
|
2.0
|
18.6
|
1.0
|
|
NC
|
B:HEM201
|
2.0
|
18.1
|
1.0
|
|
NB
|
B:HEM201
|
2.1
|
18.3
|
1.0
|
|
NE2
|
B:HIS92
|
2.1
|
19.1
|
1.0
|
|
O
|
B:HOH343
|
2.1
|
17.2
|
1.0
|
|
C1D
|
B:HEM201
|
3.0
|
19.3
|
1.0
|
|
C4D
|
B:HEM201
|
3.0
|
19.6
|
1.0
|
|
C1A
|
B:HEM201
|
3.0
|
20.1
|
1.0
|
|
C4C
|
B:HEM201
|
3.0
|
17.9
|
1.0
|
|
C1B
|
B:HEM201
|
3.0
|
19.7
|
1.0
|
|
C4B
|
B:HEM201
|
3.0
|
18.1
|
1.0
|
|
C4A
|
B:HEM201
|
3.0
|
19.7
|
1.0
|
|
C1C
|
B:HEM201
|
3.1
|
18.3
|
1.0
|
|
CE1
|
B:HIS92
|
3.1
|
19.9
|
1.0
|
|
CD2
|
B:HIS92
|
3.1
|
19.3
|
1.0
|
|
CHD
|
B:HEM201
|
3.3
|
19.3
|
1.0
|
|
CHA
|
B:HEM201
|
3.4
|
20.2
|
1.0
|
|
CHC
|
B:HEM201
|
3.4
|
18.3
|
1.0
|
|
CHB
|
B:HEM201
|
3.4
|
19.7
|
1.0
|
|
NE2
|
B:HIS63
|
4.2
|
20.4
|
1.0
|
|
C2D
|
B:HEM201
|
4.2
|
20.3
|
1.0
|
|
C3A
|
B:HEM201
|
4.2
|
20.7
|
1.0
|
|
C2A
|
B:HEM201
|
4.2
|
21.2
|
1.0
|
|
ND1
|
B:HIS92
|
4.2
|
20.4
|
1.0
|
|
C3D
|
B:HEM201
|
4.3
|
20.8
|
1.0
|
|
C2B
|
B:HEM201
|
4.3
|
20.0
|
1.0
|
|
C2C
|
B:HEM201
|
4.3
|
17.4
|
1.0
|
|
CG
|
B:HIS92
|
4.3
|
20.1
|
1.0
|
|
C3C
|
B:HEM201
|
4.3
|
17.8
|
1.0
|
|
C3B
|
B:HEM201
|
4.3
|
19.9
|
1.0
|
|
CE1
|
B:HIS63
|
4.7
|
20.4
|
1.0
|
|
CD1
|
B:LEU96
|
4.9
|
22.3
|
1.0
|
|
CG2
|
B:VAL67
|
5.0
|
18.5
|
1.0
|
|
Iron binding site 4 out
of 5 in 6hk2
Go back to
Iron Binding Sites List in 6hk2
Iron binding site 4 out
of 5 in the Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:22.2
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
22.2
|
1.0
|
|
ND
|
C:HEM201
|
1.9
|
23.2
|
1.0
|
|
NA
|
C:HEM201
|
2.0
|
23.6
|
1.0
|
|
NC
|
C:HEM201
|
2.0
|
21.2
|
1.0
|
|
NB
|
C:HEM201
|
2.1
|
22.3
|
1.0
|
|
NE2
|
C:HIS87
|
2.1
|
21.4
|
1.0
|
|
O
|
C:HOH328
|
2.2
|
23.1
|
1.0
|
|
C4D
|
C:HEM201
|
2.9
|
23.9
|
1.0
|
|
C1D
|
C:HEM201
|
3.0
|
22.2
|
1.0
|
|
C4B
|
C:HEM201
|
3.0
|
21.8
|
1.0
|
|
C1A
|
C:HEM201
|
3.0
|
25.1
|
1.0
|
|
C4C
|
C:HEM201
|
3.0
|
20.4
|
1.0
|
|
C1B
|
C:HEM201
|
3.0
|
23.2
|
1.0
|
|
CE1
|
C:HIS87
|
3.1
|
22.2
|
1.0
|
|
C1C
|
C:HEM201
|
3.1
|
20.6
|
1.0
|
|
C4A
|
C:HEM201
|
3.1
|
24.3
|
1.0
|
|
CD2
|
C:HIS87
|
3.1
|
21.4
|
1.0
|
|
CHA
|
C:HEM201
|
3.3
|
25.5
|
1.0
|
|
CHD
|
C:HEM201
|
3.4
|
21.5
|
1.0
|
|
CHB
|
C:HEM201
|
3.5
|
23.3
|
1.0
|
|
CHC
|
C:HEM201
|
3.5
|
21.2
|
1.0
|
|
ND1
|
C:HIS87
|
4.2
|
22.3
|
1.0
|
|
C3D
|
C:HEM201
|
4.2
|
25.0
|
1.0
|
|
C2D
|
C:HEM201
|
4.2
|
24.1
|
1.0
|
|
NE2
|
C:HIS58
|
4.2
|
26.0
|
1.0
|
|
CG
|
C:HIS87
|
4.2
|
21.8
|
1.0
|
|
C2B
|
C:HEM201
|
4.2
|
23.2
|
1.0
|
|
C2A
|
C:HEM201
|
4.3
|
26.8
|
1.0
|
|
C2C
|
C:HEM201
|
4.3
|
19.9
|
1.0
|
|
C3B
|
C:HEM201
|
4.3
|
23.0
|
1.0
|
|
C3A
|
C:HEM201
|
4.3
|
25.9
|
1.0
|
|
C3C
|
C:HEM201
|
4.3
|
20.1
|
1.0
|
|
CE1
|
C:HIS58
|
4.8
|
26.2
|
1.0
|
|
CG2
|
C:VAL62
|
4.9
|
26.2
|
1.0
|
|
Iron binding site 5 out
of 5 in 6hk2
Go back to
Iron Binding Sites List in 6hk2
Iron binding site 5 out
of 5 in the Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Ferric R-State Human Methemoglobin Bound to Maleimide-Deferoxamine Bifunctional Chelator (Dfo) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:24.2
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
24.2
|
1.0
|
|
ND
|
D:HEM201
|
1.9
|
26.0
|
1.0
|
|
NA
|
D:HEM201
|
2.0
|
25.0
|
1.0
|
|
O
|
D:HOH334
|
2.0
|
24.6
|
1.0
|
|
NE2
|
D:HIS92
|
2.0
|
23.8
|
1.0
|
|
NC
|
D:HEM201
|
2.0
|
23.0
|
1.0
|
|
NB
|
D:HEM201
|
2.1
|
23.4
|
1.0
|
|
CE1
|
D:HIS92
|
2.9
|
24.5
|
1.0
|
|
C1D
|
D:HEM201
|
3.0
|
26.3
|
1.0
|
|
C4D
|
D:HEM201
|
3.0
|
27.5
|
1.0
|
|
C4A
|
D:HEM201
|
3.0
|
25.7
|
1.0
|
|
C1A
|
D:HEM201
|
3.0
|
26.9
|
1.0
|
|
C4B
|
D:HEM201
|
3.0
|
22.6
|
1.0
|
|
C4C
|
D:HEM201
|
3.0
|
25.0
|
1.0
|
|
C1B
|
D:HEM201
|
3.0
|
24.0
|
1.0
|
|
C1C
|
D:HEM201
|
3.1
|
23.1
|
1.0
|
|
CD2
|
D:HIS92
|
3.1
|
24.6
|
1.0
|
|
CHB
|
D:HEM201
|
3.4
|
24.4
|
1.0
|
|
CHC
|
D:HEM201
|
3.4
|
22.6
|
1.0
|
|
CHD
|
D:HEM201
|
3.4
|
25.8
|
1.0
|
|
CHA
|
D:HEM201
|
3.4
|
27.9
|
1.0
|
|
ND1
|
D:HIS92
|
4.1
|
25.2
|
1.0
|
|
C3A
|
D:HEM201
|
4.2
|
27.1
|
1.0
|
|
C2D
|
D:HEM201
|
4.2
|
28.1
|
1.0
|
|
CG
|
D:HIS92
|
4.2
|
25.9
|
1.0
|
|
C3D
|
D:HEM201
|
4.2
|
29.9
|
1.0
|
|
C2C
|
D:HEM201
|
4.2
|
23.3
|
1.0
|
|
C3C
|
D:HEM201
|
4.2
|
24.3
|
1.0
|
|
C2A
|
D:HEM201
|
4.2
|
28.6
|
1.0
|
|
C2B
|
D:HEM201
|
4.2
|
23.9
|
1.0
|
|
NE2
|
D:HIS63
|
4.3
|
27.4
|
1.0
|
|
C3B
|
D:HEM201
|
4.3
|
23.4
|
1.0
|
|
CE1
|
D:HIS63
|
4.8
|
29.7
|
1.0
|
|
CG2
|
D:VAL67
|
4.8
|
27.6
|
1.0
|
|
CD1
|
D:LEU96
|
4.9
|
33.2
|
1.0
|
|
Reference:
G.Cerutti,
L.Kiraga,
A.Boffi,
C.Savino,
L.C.Montemiglio,
T.Rygiel,
A.Bonamore,
S.J.Paisey,
A.M.Dabkowski,
M.Krol.
Human Hemoglobin-Dfo 89ZR Complex, A New Tool For CD163 Imaging To Be Published.
Page generated: Sun Dec 13 16:28:35 2020
|
