Iron in PDB 2h8d: Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4
Protein crystallography data
The structure of Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4, PDB code: 2h8d
was solved by
L.Mazzarella,
A.Vergara,
L.Vitagliano,
A.Merlino,
G.Bonomi,
S.Scala,
C.Verde,
G.Di Prisco,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.78
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.800,
94.630,
61.860,
90.00,
90.19,
90.00
|
R / Rfree (%)
|
18 /
22.4
|
Other elements in 2h8d:
The structure of Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4
(pdb code 2h8d). 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 Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4, PDB code: 2h8d:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2h8d
Go back to
Iron Binding Sites List in 2h8d
Iron binding site 1 out
of 4 in the Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4
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 Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:14.7
occ:1.00
|
FE
|
A:HEM200
|
0.0
|
14.7
|
1.0
|
NB
|
A:HEM200
|
2.0
|
13.7
|
1.0
|
ND
|
A:HEM200
|
2.0
|
17.2
|
1.0
|
NA
|
A:HEM200
|
2.0
|
16.9
|
1.0
|
NC
|
A:HEM200
|
2.1
|
13.6
|
1.0
|
NE2
|
A:HIS88
|
2.2
|
16.0
|
1.0
|
CE1
|
A:HIS88
|
3.0
|
16.0
|
1.0
|
C1B
|
A:HEM200
|
3.0
|
14.2
|
1.0
|
C4B
|
A:HEM200
|
3.1
|
13.2
|
1.0
|
C4D
|
A:HEM200
|
3.1
|
17.7
|
1.0
|
C1A
|
A:HEM200
|
3.1
|
17.4
|
1.0
|
C4A
|
A:HEM200
|
3.1
|
16.6
|
1.0
|
C1D
|
A:HEM200
|
3.1
|
17.0
|
1.0
|
C1C
|
A:HEM200
|
3.1
|
13.4
|
1.0
|
C4C
|
A:HEM200
|
3.1
|
14.4
|
1.0
|
CD2
|
A:HIS88
|
3.3
|
15.8
|
1.0
|
CHB
|
A:HEM200
|
3.4
|
15.3
|
1.0
|
CHA
|
A:HEM200
|
3.4
|
17.6
|
1.0
|
CHD
|
A:HEM200
|
3.5
|
15.6
|
1.0
|
CHC
|
A:HEM200
|
3.5
|
13.0
|
1.0
|
NE2
|
A:HIS59
|
4.2
|
18.4
|
1.0
|
ND1
|
A:HIS88
|
4.2
|
15.9
|
1.0
|
C2B
|
A:HEM200
|
4.3
|
13.7
|
1.0
|
C3B
|
A:HEM200
|
4.3
|
13.3
|
1.0
|
C2A
|
A:HEM200
|
4.3
|
18.2
|
1.0
|
C3D
|
A:HEM200
|
4.3
|
18.3
|
1.0
|
C3A
|
A:HEM200
|
4.3
|
17.5
|
1.0
|
C2D
|
A:HEM200
|
4.3
|
17.8
|
1.0
|
C2C
|
A:HEM200
|
4.3
|
13.6
|
1.0
|
CG
|
A:HIS88
|
4.4
|
15.8
|
1.0
|
C3C
|
A:HEM200
|
4.4
|
14.0
|
1.0
|
CE1
|
A:HIS59
|
4.5
|
18.3
|
1.0
|
CG2
|
A:VAL63
|
4.5
|
12.2
|
1.0
|
CD1
|
A:LEU92
|
4.8
|
17.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 2h8d
Go back to
Iron Binding Sites List in 2h8d
Iron binding site 2 out
of 4 in the Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4
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 Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe400
b:21.1
occ:1.00
|
FE
|
B:HEM400
|
0.0
|
21.1
|
1.0
|
NB
|
B:HEM400
|
1.9
|
22.2
|
1.0
|
NC
|
B:HEM400
|
2.0
|
21.4
|
1.0
|
ND
|
B:HEM400
|
2.0
|
23.9
|
1.0
|
NA
|
B:HEM400
|
2.1
|
23.6
|
1.0
|
NE2
|
B:HIS92
|
2.2
|
21.1
|
1.0
|
C4B
|
B:HEM400
|
3.0
|
22.0
|
1.0
|
C1C
|
B:HEM400
|
3.0
|
21.5
|
1.0
|
C1B
|
B:HEM400
|
3.0
|
22.3
|
1.0
|
C4C
|
B:HEM400
|
3.0
|
21.9
|
1.0
|
C1D
|
B:HEM400
|
3.1
|
23.7
|
1.0
|
C4A
|
B:HEM400
|
3.1
|
23.4
|
1.0
|
C4D
|
B:HEM400
|
3.1
|
24.1
|
1.0
|
C1A
|
B:HEM400
|
3.2
|
23.9
|
1.0
|
CE1
|
B:HIS92
|
3.2
|
21.0
|
1.0
|
CD2
|
B:HIS92
|
3.2
|
21.2
|
1.0
|
CHC
|
B:HEM400
|
3.4
|
21.7
|
1.0
|
CHB
|
B:HEM400
|
3.4
|
22.8
|
1.0
|
CHD
|
B:HEM400
|
3.4
|
22.9
|
1.0
|
CHA
|
B:HEM400
|
3.5
|
23.9
|
1.0
|
CG2
|
B:VAL67
|
4.1
|
22.0
|
1.0
|
NE2
|
B:HIS63
|
4.1
|
25.7
|
1.0
|
C3B
|
B:HEM400
|
4.2
|
22.0
|
1.0
|
C2B
|
B:HEM400
|
4.2
|
22.2
|
1.0
|
C2C
|
B:HEM400
|
4.3
|
21.2
|
1.0
|
C3C
|
B:HEM400
|
4.3
|
21.5
|
1.0
|
C2D
|
B:HEM400
|
4.3
|
24.4
|
1.0
|
C3D
|
B:HEM400
|
4.3
|
24.5
|
1.0
|
ND1
|
B:HIS92
|
4.3
|
21.1
|
1.0
|
C3A
|
B:HEM400
|
4.3
|
23.9
|
1.0
|
C2A
|
B:HEM400
|
4.4
|
24.4
|
1.0
|
CG
|
B:HIS92
|
4.4
|
21.4
|
1.0
|
CE1
|
B:HIS63
|
4.8
|
25.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 2h8d
Go back to
Iron Binding Sites List in 2h8d
Iron binding site 3 out
of 4 in the Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4
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 Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe600
b:15.7
occ:1.00
|
FE
|
C:HEM600
|
0.0
|
15.7
|
1.0
|
ND
|
C:HEM600
|
1.9
|
17.1
|
1.0
|
NC
|
C:HEM600
|
2.0
|
13.8
|
1.0
|
NA
|
C:HEM600
|
2.1
|
17.3
|
1.0
|
NB
|
C:HEM600
|
2.1
|
14.2
|
1.0
|
NE2
|
C:HIS88
|
2.2
|
12.5
|
1.0
|
C1D
|
C:HEM600
|
3.0
|
16.8
|
1.0
|
C4C
|
C:HEM600
|
3.0
|
14.5
|
1.0
|
C4D
|
C:HEM600
|
3.0
|
17.7
|
1.0
|
C1C
|
C:HEM600
|
3.0
|
13.6
|
1.0
|
C1A
|
C:HEM600
|
3.1
|
17.9
|
1.0
|
C4B
|
C:HEM600
|
3.1
|
13.8
|
1.0
|
CE1
|
C:HIS88
|
3.2
|
12.8
|
1.0
|
C4A
|
C:HEM600
|
3.2
|
17.1
|
1.0
|
C1B
|
C:HEM600
|
3.2
|
14.8
|
1.0
|
CD2
|
C:HIS88
|
3.3
|
12.7
|
1.0
|
CHD
|
C:HEM600
|
3.3
|
15.5
|
1.0
|
CHA
|
C:HEM600
|
3.4
|
17.8
|
1.0
|
CHC
|
C:HEM600
|
3.5
|
13.6
|
1.0
|
CHB
|
C:HEM600
|
3.5
|
15.9
|
1.0
|
NE2
|
C:HIS59
|
4.2
|
18.4
|
1.0
|
C2D
|
C:HEM600
|
4.2
|
17.8
|
1.0
|
C3D
|
C:HEM600
|
4.2
|
18.6
|
1.0
|
C3C
|
C:HEM600
|
4.2
|
14.4
|
1.0
|
C2C
|
C:HEM600
|
4.3
|
14.0
|
1.0
|
ND1
|
C:HIS88
|
4.3
|
12.3
|
1.0
|
CE1
|
C:HIS59
|
4.4
|
18.4
|
1.0
|
C2A
|
C:HEM600
|
4.4
|
18.8
|
1.0
|
C2B
|
C:HEM600
|
4.4
|
14.4
|
1.0
|
C3B
|
C:HEM600
|
4.4
|
13.9
|
1.0
|
C3A
|
C:HEM600
|
4.4
|
18.0
|
1.0
|
CG
|
C:HIS88
|
4.4
|
12.8
|
1.0
|
CD1
|
C:LEU92
|
4.7
|
17.1
|
1.0
|
CG2
|
C:VAL63
|
4.7
|
13.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 2h8d
Go back to
Iron Binding Sites List in 2h8d
Iron binding site 4 out
of 4 in the Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4
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 Deoxy Hemoglobin From Trematomus Bernacchii at pH 8.4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe800
b:20.0
occ:1.00
|
FE
|
D:HEM800
|
0.0
|
20.0
|
1.0
|
ND
|
D:HEM800
|
1.9
|
22.4
|
1.0
|
NC
|
D:HEM800
|
2.0
|
18.7
|
1.0
|
NB
|
D:HEM800
|
2.1
|
19.9
|
1.0
|
NA
|
D:HEM800
|
2.1
|
21.9
|
1.0
|
NE2
|
D:HIS92
|
2.3
|
16.7
|
1.0
|
C1D
|
D:HEM800
|
3.0
|
21.9
|
1.0
|
C4D
|
D:HEM800
|
3.0
|
22.9
|
1.0
|
C4C
|
D:HEM800
|
3.0
|
19.2
|
1.0
|
C1C
|
D:HEM800
|
3.1
|
18.8
|
1.0
|
C4B
|
D:HEM800
|
3.1
|
19.6
|
1.0
|
C1A
|
D:HEM800
|
3.1
|
22.4
|
1.0
|
C4A
|
D:HEM800
|
3.1
|
21.6
|
1.0
|
C1B
|
D:HEM800
|
3.2
|
20.4
|
1.0
|
CE1
|
D:HIS92
|
3.2
|
16.6
|
1.0
|
CD2
|
D:HIS92
|
3.3
|
16.9
|
1.0
|
CHD
|
D:HEM800
|
3.3
|
20.4
|
1.0
|
CHA
|
D:HEM800
|
3.4
|
22.7
|
1.0
|
CHC
|
D:HEM800
|
3.5
|
19.2
|
1.0
|
CHB
|
D:HEM800
|
3.5
|
20.9
|
1.0
|
NE2
|
D:HIS63
|
3.9
|
22.7
|
1.0
|
CG2
|
D:VAL67
|
4.0
|
24.0
|
1.0
|
C2D
|
D:HEM800
|
4.2
|
22.8
|
1.0
|
C3D
|
D:HEM800
|
4.2
|
23.4
|
1.0
|
C3C
|
D:HEM800
|
4.3
|
19.1
|
1.0
|
C2C
|
D:HEM800
|
4.3
|
18.6
|
1.0
|
ND1
|
D:HIS92
|
4.3
|
16.6
|
1.0
|
C2A
|
D:HEM800
|
4.3
|
22.9
|
1.0
|
C3A
|
D:HEM800
|
4.4
|
22.4
|
1.0
|
C3B
|
D:HEM800
|
4.4
|
19.8
|
1.0
|
C2B
|
D:HEM800
|
4.4
|
20.3
|
1.0
|
CG
|
D:HIS92
|
4.4
|
17.2
|
1.0
|
CE1
|
D:HIS63
|
4.5
|
22.4
|
1.0
|
|
Reference:
L.Mazzarella,
A.Vergara,
L.Vitagliano,
A.Merlino,
G.Bonomi,
S.Scala,
C.Verde,
G.Di Prisco.
High Resolution Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii at Different pH Values: the Role of Histidine Residues in Modulating the Strength of the Root Effect. Proteins V. 65 490 2006.
ISSN: ISSN 0887-3585
PubMed: 16909420
DOI: 10.1002/PROT.21114
Page generated: Sat Aug 3 22:50:42 2024
|