Iron in PDB 2d5z: Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules
Protein crystallography data
The structure of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules, PDB code: 2d5z
was solved by
T.Yokoyama,
S.Neya,
A.Tsuneshige,
T.Yonetani,
S.Y.Park,
J.R.Tame,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.65 /
1.45
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.028,
82.697,
110.343,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.6 /
21.5
|
Other elements in 2d5z:
The structure of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules
(pdb code 2d5z). 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 of T-State Human Hemoglobin Complexed with Three L35 Molecules, PDB code: 2d5z:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2d5z
Go back to
Iron Binding Sites List in 2d5z
Iron binding site 1 out
of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules
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 T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe142
b:13.9
occ:1.00
|
FE
|
A:HEM142
|
0.0
|
13.9
|
1.0
|
NA
|
A:HEM142
|
2.1
|
12.4
|
1.0
|
NC
|
A:HEM142
|
2.1
|
12.5
|
1.0
|
NB
|
A:HEM142
|
2.1
|
14.1
|
1.0
|
ND
|
A:HEM142
|
2.1
|
15.1
|
1.0
|
NE2
|
A:HIS87
|
2.2
|
14.0
|
1.0
|
CE1
|
A:HIS87
|
3.0
|
14.6
|
1.0
|
C4A
|
A:HEM142
|
3.1
|
13.8
|
1.0
|
C4C
|
A:HEM142
|
3.1
|
13.2
|
1.0
|
C1A
|
A:HEM142
|
3.1
|
13.6
|
1.0
|
C1D
|
A:HEM142
|
3.1
|
13.7
|
1.0
|
C1B
|
A:HEM142
|
3.1
|
14.0
|
1.0
|
C1C
|
A:HEM142
|
3.1
|
12.7
|
1.0
|
C4D
|
A:HEM142
|
3.1
|
14.3
|
1.0
|
C4B
|
A:HEM142
|
3.1
|
15.1
|
1.0
|
O
|
A:HOH1238
|
3.1
|
22.4
|
1.0
|
CD2
|
A:HIS87
|
3.3
|
13.4
|
1.0
|
CHB
|
A:HEM142
|
3.4
|
13.9
|
1.0
|
CHD
|
A:HEM142
|
3.5
|
13.3
|
1.0
|
CHA
|
A:HEM142
|
3.5
|
13.4
|
1.0
|
CHC
|
A:HEM142
|
3.5
|
13.4
|
1.0
|
ND1
|
A:HIS87
|
4.2
|
13.3
|
1.0
|
C3A
|
A:HEM142
|
4.3
|
14.1
|
1.0
|
C2A
|
A:HEM142
|
4.3
|
15.1
|
1.0
|
C3C
|
A:HEM142
|
4.3
|
13.0
|
1.0
|
C2C
|
A:HEM142
|
4.3
|
11.0
|
1.0
|
C2B
|
A:HEM142
|
4.3
|
13.9
|
1.0
|
C2D
|
A:HEM142
|
4.3
|
15.0
|
1.0
|
C3B
|
A:HEM142
|
4.3
|
13.7
|
1.0
|
C3D
|
A:HEM142
|
4.3
|
14.7
|
1.0
|
CG
|
A:HIS87
|
4.4
|
13.4
|
1.0
|
CE1
|
A:HIS58
|
4.5
|
20.5
|
1.0
|
NE2
|
A:HIS58
|
4.5
|
20.5
|
1.0
|
CD1
|
A:LEU91
|
4.6
|
13.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 2d5z
Go back to
Iron Binding Sites List in 2d5z
Iron binding site 2 out
of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules
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 T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe147
b:18.0
occ:1.00
|
FE
|
B:HEM147
|
0.0
|
18.0
|
1.0
|
NC
|
B:HEM147
|
2.0
|
18.0
|
1.0
|
NB
|
B:HEM147
|
2.1
|
14.8
|
1.0
|
ND
|
B:HEM147
|
2.1
|
17.4
|
1.0
|
NA
|
B:HEM147
|
2.1
|
19.9
|
1.0
|
NE2
|
B:HIS92
|
2.1
|
17.2
|
1.0
|
O
|
B:HOH196
|
2.6
|
29.2
|
1.0
|
CE1
|
B:HIS92
|
3.0
|
17.2
|
1.0
|
C1B
|
B:HEM147
|
3.1
|
17.6
|
1.0
|
C1D
|
B:HEM147
|
3.1
|
18.1
|
1.0
|
C4D
|
B:HEM147
|
3.1
|
19.0
|
1.0
|
C4C
|
B:HEM147
|
3.1
|
16.8
|
1.0
|
C1A
|
B:HEM147
|
3.1
|
20.2
|
1.0
|
C4A
|
B:HEM147
|
3.1
|
19.1
|
1.0
|
C1C
|
B:HEM147
|
3.1
|
16.7
|
1.0
|
C4B
|
B:HEM147
|
3.1
|
17.6
|
1.0
|
CD2
|
B:HIS92
|
3.2
|
16.4
|
1.0
|
CHB
|
B:HEM147
|
3.4
|
18.8
|
1.0
|
CHA
|
B:HEM147
|
3.4
|
19.7
|
1.0
|
CHD
|
B:HEM147
|
3.4
|
17.9
|
1.0
|
CHC
|
B:HEM147
|
3.5
|
17.5
|
1.0
|
ND1
|
B:HIS92
|
4.1
|
16.9
|
1.0
|
NE2
|
B:HIS63
|
4.2
|
19.4
|
1.0
|
C2B
|
B:HEM147
|
4.3
|
17.4
|
1.0
|
CG
|
B:HIS92
|
4.3
|
17.4
|
1.0
|
C3D
|
B:HEM147
|
4.3
|
18.8
|
1.0
|
C2C
|
B:HEM147
|
4.3
|
16.7
|
1.0
|
C2D
|
B:HEM147
|
4.3
|
18.6
|
1.0
|
C3C
|
B:HEM147
|
4.3
|
16.8
|
1.0
|
C2A
|
B:HEM147
|
4.3
|
21.2
|
1.0
|
C3B
|
B:HEM147
|
4.3
|
17.9
|
1.0
|
C3A
|
B:HEM147
|
4.3
|
20.6
|
1.0
|
CG2
|
B:VAL67
|
4.5
|
18.6
|
1.0
|
CE1
|
B:HIS63
|
4.9
|
20.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 2d5z
Go back to
Iron Binding Sites List in 2d5z
Iron binding site 3 out
of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules
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 T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe142
b:16.4
occ:1.00
|
FE
|
C:HEM142
|
0.0
|
16.4
|
1.0
|
NA
|
C:HEM142
|
2.1
|
14.2
|
1.0
|
NB
|
C:HEM142
|
2.1
|
16.8
|
1.0
|
NC
|
C:HEM142
|
2.1
|
14.6
|
1.0
|
ND
|
C:HEM142
|
2.1
|
16.8
|
1.0
|
NE2
|
C:HIS87
|
2.2
|
17.8
|
1.0
|
CE1
|
C:HIS87
|
3.0
|
17.1
|
1.0
|
C4A
|
C:HEM142
|
3.1
|
16.3
|
1.0
|
C1B
|
C:HEM142
|
3.1
|
15.8
|
1.0
|
C1C
|
C:HEM142
|
3.1
|
14.9
|
1.0
|
C4B
|
C:HEM142
|
3.1
|
14.1
|
1.0
|
C1A
|
C:HEM142
|
3.1
|
17.8
|
1.0
|
C4D
|
C:HEM142
|
3.1
|
16.8
|
1.0
|
C4C
|
C:HEM142
|
3.1
|
14.1
|
1.0
|
C1D
|
C:HEM142
|
3.1
|
15.8
|
1.0
|
O
|
C:HOH1258
|
3.3
|
27.3
|
1.0
|
CD2
|
C:HIS87
|
3.3
|
18.1
|
1.0
|
CHB
|
C:HEM142
|
3.4
|
16.4
|
1.0
|
CHA
|
C:HEM142
|
3.5
|
16.5
|
1.0
|
CHC
|
C:HEM142
|
3.5
|
15.3
|
1.0
|
CHD
|
C:HEM142
|
3.5
|
15.7
|
1.0
|
ND1
|
C:HIS87
|
4.2
|
17.9
|
1.0
|
C2C
|
C:HEM142
|
4.3
|
13.7
|
1.0
|
C2B
|
C:HEM142
|
4.3
|
14.8
|
1.0
|
C3A
|
C:HEM142
|
4.3
|
18.4
|
1.0
|
C2A
|
C:HEM142
|
4.3
|
18.5
|
1.0
|
C3B
|
C:HEM142
|
4.3
|
15.1
|
1.0
|
C3C
|
C:HEM142
|
4.3
|
14.3
|
1.0
|
C3D
|
C:HEM142
|
4.4
|
16.6
|
1.0
|
CG
|
C:HIS87
|
4.4
|
17.5
|
1.0
|
C2D
|
C:HEM142
|
4.4
|
15.6
|
1.0
|
CE1
|
C:HIS58
|
4.4
|
22.8
|
1.0
|
CD1
|
C:LEU91
|
4.4
|
18.1
|
1.0
|
NE2
|
C:HIS58
|
4.4
|
22.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 2d5z
Go back to
Iron Binding Sites List in 2d5z
Iron binding site 4 out
of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules
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 T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe147
b:13.2
occ:1.00
|
FE
|
D:HEM147
|
0.0
|
13.2
|
1.0
|
NA
|
D:HEM147
|
2.1
|
12.8
|
1.0
|
ND
|
D:HEM147
|
2.1
|
12.7
|
1.0
|
NC
|
D:HEM147
|
2.1
|
12.2
|
1.0
|
NB
|
D:HEM147
|
2.1
|
12.9
|
1.0
|
NE2
|
D:HIS92
|
2.2
|
11.1
|
1.0
|
CE1
|
D:HIS92
|
3.0
|
11.1
|
1.0
|
C4A
|
D:HEM147
|
3.1
|
13.4
|
1.0
|
C4D
|
D:HEM147
|
3.1
|
13.0
|
1.0
|
C1A
|
D:HEM147
|
3.1
|
13.8
|
1.0
|
C1B
|
D:HEM147
|
3.1
|
12.6
|
1.0
|
C1D
|
D:HEM147
|
3.1
|
12.6
|
1.0
|
C4B
|
D:HEM147
|
3.1
|
12.8
|
1.0
|
C1C
|
D:HEM147
|
3.1
|
12.5
|
1.0
|
C4C
|
D:HEM147
|
3.1
|
12.1
|
1.0
|
CD2
|
D:HIS92
|
3.2
|
11.1
|
1.0
|
CHB
|
D:HEM147
|
3.4
|
13.9
|
1.0
|
CHA
|
D:HEM147
|
3.4
|
13.8
|
1.0
|
CHC
|
D:HEM147
|
3.5
|
12.2
|
1.0
|
CHD
|
D:HEM147
|
3.5
|
12.2
|
1.0
|
CG2
|
D:VAL67
|
3.9
|
14.9
|
1.0
|
NE2
|
D:HIS63
|
4.2
|
18.1
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
11.6
|
1.0
|
C3A
|
D:HEM147
|
4.3
|
14.9
|
1.0
|
C2A
|
D:HEM147
|
4.3
|
14.5
|
1.0
|
C2B
|
D:HEM147
|
4.3
|
12.2
|
1.0
|
C3B
|
D:HEM147
|
4.3
|
12.3
|
1.0
|
C3D
|
D:HEM147
|
4.3
|
14.6
|
1.0
|
CG
|
D:HIS92
|
4.3
|
12.4
|
1.0
|
C2D
|
D:HEM147
|
4.3
|
14.0
|
1.0
|
C2C
|
D:HEM147
|
4.3
|
9.8
|
1.0
|
C3C
|
D:HEM147
|
4.4
|
12.9
|
1.0
|
CE1
|
D:HIS63
|
4.5
|
19.3
|
1.0
|
CD1
|
D:LEU96
|
4.8
|
15.6
|
1.0
|
|
Reference:
T.Yokoyama,
S.Neya,
A.Tsuneshige,
T.Yonetani,
S.Y.Park,
J.R.Tame.
R-State Haemoglobin with Low Oxygen Affinity: Crystal Structures of Deoxy Human and Carbonmonoxy Horse Haemoglobin Bound to the Effector Molecule L35 J.Mol.Biol. V. 356 790 2006.
ISSN: ISSN 0022-2836
PubMed: 16403522
DOI: 10.1016/J.JMB.2005.12.018
Page generated: Sat Aug 3 20:43:20 2024
|