Iron in PDB 1s5y: The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide
Protein crystallography data
The structure of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide, PDB code: 1s5y
was solved by
L.Vitagliano,
G.Bonomi,
A.Riccio,
G.Di Prisco,
G.Smulevich,
L.Mazzarella,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.993,
62.980,
63.502,
77.06,
69.79,
84.17
|
R / Rfree (%)
|
19.9 /
24.7
|
Iron Binding Sites:
The binding sites of Iron atom in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide
(pdb code 1s5y). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide, PDB code: 1s5y:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1s5y
Go back to
Iron Binding Sites List in 1s5y
Iron binding site 1 out
of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:21.5
occ:1.00
|
FE
|
A:HEM200
|
0.0
|
21.5
|
1.0
|
NC
|
A:HEM200
|
2.0
|
20.3
|
1.0
|
NE2
|
A:HIS88
|
2.0
|
16.4
|
1.0
|
ND
|
A:HEM200
|
2.0
|
23.7
|
1.0
|
NA
|
A:HEM200
|
2.0
|
23.7
|
1.0
|
NB
|
A:HEM200
|
2.0
|
21.3
|
1.0
|
O
|
A:HOH850
|
2.1
|
17.8
|
1.0
|
CE1
|
A:HIS88
|
2.9
|
14.3
|
1.0
|
C4C
|
A:HEM200
|
3.0
|
20.2
|
1.0
|
C1C
|
A:HEM200
|
3.0
|
19.9
|
1.0
|
C1D
|
A:HEM200
|
3.1
|
22.9
|
1.0
|
C4A
|
A:HEM200
|
3.1
|
24.4
|
1.0
|
C4D
|
A:HEM200
|
3.1
|
24.5
|
1.0
|
C1A
|
A:HEM200
|
3.1
|
25.6
|
1.0
|
C4B
|
A:HEM200
|
3.1
|
20.4
|
1.0
|
C1B
|
A:HEM200
|
3.1
|
21.4
|
1.0
|
CD2
|
A:HIS88
|
3.1
|
14.2
|
1.0
|
CHD
|
A:HEM200
|
3.3
|
22.2
|
1.0
|
CHC
|
A:HEM200
|
3.4
|
19.5
|
1.0
|
CHA
|
A:HEM200
|
3.4
|
25.2
|
1.0
|
CHB
|
A:HEM200
|
3.4
|
22.8
|
1.0
|
NE2
|
A:HIS59
|
4.1
|
31.0
|
1.0
|
ND1
|
A:HIS88
|
4.1
|
13.9
|
1.0
|
CG
|
A:HIS88
|
4.2
|
15.4
|
1.0
|
C3C
|
A:HEM200
|
4.3
|
21.5
|
1.0
|
C2C
|
A:HEM200
|
4.3
|
21.4
|
1.0
|
C3A
|
A:HEM200
|
4.3
|
25.4
|
1.0
|
CE1
|
A:HIS59
|
4.4
|
29.8
|
1.0
|
C2A
|
A:HEM200
|
4.4
|
27.1
|
1.0
|
C3D
|
A:HEM200
|
4.4
|
25.4
|
1.0
|
C2D
|
A:HEM200
|
4.4
|
23.7
|
1.0
|
C3B
|
A:HEM200
|
4.4
|
20.4
|
1.0
|
C2B
|
A:HEM200
|
4.4
|
20.7
|
1.0
|
CG2
|
A:VAL63
|
4.9
|
25.0
|
1.0
|
CD1
|
A:LEU92
|
4.9
|
37.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 1s5y
Go back to
Iron Binding Sites List in 1s5y
Iron binding site 2 out
of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe400
b:31.0
occ:1.00
|
FE
|
B:HEM400
|
0.0
|
31.0
|
1.0
|
NE2
|
B:HIS92
|
2.0
|
35.0
|
1.0
|
ND
|
B:HEM400
|
2.0
|
33.8
|
1.0
|
NA
|
B:HEM400
|
2.0
|
35.4
|
1.0
|
NC
|
B:HEM400
|
2.0
|
32.8
|
1.0
|
NB
|
B:HEM400
|
2.0
|
31.1
|
1.0
|
NE2
|
B:HIS63
|
2.1
|
27.8
|
1.0
|
CE1
|
B:HIS63
|
2.9
|
26.4
|
1.0
|
C4D
|
B:HEM400
|
3.0
|
35.1
|
1.0
|
CE1
|
B:HIS92
|
3.0
|
37.8
|
1.0
|
CD2
|
B:HIS92
|
3.0
|
38.0
|
1.0
|
C1A
|
B:HEM400
|
3.0
|
36.2
|
1.0
|
C1D
|
B:HEM400
|
3.1
|
33.5
|
1.0
|
C4B
|
B:HEM400
|
3.1
|
29.4
|
1.0
|
C4A
|
B:HEM400
|
3.1
|
34.2
|
1.0
|
C1C
|
B:HEM400
|
3.1
|
30.8
|
1.0
|
C4C
|
B:HEM400
|
3.1
|
32.5
|
1.0
|
C1B
|
B:HEM400
|
3.1
|
30.5
|
1.0
|
CHA
|
B:HEM400
|
3.3
|
35.4
|
1.0
|
CD2
|
B:HIS63
|
3.4
|
25.6
|
1.0
|
CHC
|
B:HEM400
|
3.4
|
30.1
|
1.0
|
CHD
|
B:HEM400
|
3.4
|
33.6
|
1.0
|
CHB
|
B:HEM400
|
3.4
|
32.1
|
1.0
|
ND1
|
B:HIS63
|
4.1
|
25.4
|
1.0
|
ND1
|
B:HIS92
|
4.1
|
38.9
|
1.0
|
CG
|
B:HIS92
|
4.2
|
39.1
|
1.0
|
C3D
|
B:HEM400
|
4.3
|
35.8
|
1.0
|
C2A
|
B:HEM400
|
4.3
|
37.3
|
1.0
|
C3A
|
B:HEM400
|
4.3
|
35.9
|
1.0
|
C3C
|
B:HEM400
|
4.3
|
32.0
|
1.0
|
C2D
|
B:HEM400
|
4.3
|
35.1
|
1.0
|
C3B
|
B:HEM400
|
4.4
|
28.9
|
1.0
|
CG
|
B:HIS63
|
4.4
|
23.4
|
1.0
|
C2C
|
B:HEM400
|
4.4
|
31.1
|
1.0
|
C2B
|
B:HEM400
|
4.4
|
30.8
|
1.0
|
CG2
|
B:VAL67
|
4.9
|
17.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 1s5y
Go back to
Iron Binding Sites List in 1s5y
Iron binding site 3 out
of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe600
b:18.5
occ:1.00
|
FE
|
C:HEM600
|
0.0
|
18.5
|
1.0
|
ND
|
C:HEM600
|
2.0
|
18.4
|
1.0
|
NB
|
C:HEM600
|
2.0
|
14.6
|
1.0
|
NA
|
C:HEM600
|
2.0
|
19.2
|
1.0
|
NC
|
C:HEM600
|
2.0
|
16.6
|
1.0
|
NE2
|
C:HIS88
|
2.1
|
18.8
|
1.0
|
O
|
C:HOH900
|
2.1
|
21.1
|
1.0
|
CE1
|
C:HIS88
|
2.8
|
17.7
|
1.0
|
C4D
|
C:HEM600
|
3.0
|
20.6
|
1.0
|
C1D
|
C:HEM600
|
3.0
|
19.6
|
1.0
|
C4A
|
C:HEM600
|
3.0
|
18.4
|
1.0
|
C1A
|
C:HEM600
|
3.1
|
20.6
|
1.0
|
C1B
|
C:HEM600
|
3.1
|
14.8
|
1.0
|
C4C
|
C:HEM600
|
3.1
|
16.2
|
1.0
|
C4B
|
C:HEM600
|
3.1
|
16.0
|
1.0
|
C1C
|
C:HEM600
|
3.1
|
13.9
|
1.0
|
CD2
|
C:HIS88
|
3.3
|
18.9
|
1.0
|
CHD
|
C:HEM600
|
3.3
|
18.1
|
1.0
|
CHA
|
C:HEM600
|
3.4
|
18.5
|
1.0
|
CHB
|
C:HEM600
|
3.4
|
15.7
|
1.0
|
CHC
|
C:HEM600
|
3.4
|
13.6
|
1.0
|
ND1
|
C:HIS88
|
4.1
|
17.8
|
1.0
|
NE2
|
C:HIS59
|
4.1
|
23.5
|
1.0
|
C2D
|
C:HEM600
|
4.3
|
20.4
|
1.0
|
C3D
|
C:HEM600
|
4.3
|
22.8
|
1.0
|
C2A
|
C:HEM600
|
4.3
|
24.4
|
1.0
|
C3A
|
C:HEM600
|
4.3
|
22.0
|
1.0
|
CG
|
C:HIS88
|
4.3
|
19.1
|
1.0
|
C2B
|
C:HEM600
|
4.4
|
16.0
|
1.0
|
C3C
|
C:HEM600
|
4.4
|
13.9
|
1.0
|
C3B
|
C:HEM600
|
4.4
|
17.1
|
1.0
|
CE1
|
C:HIS59
|
4.4
|
24.9
|
1.0
|
C2C
|
C:HEM600
|
4.4
|
12.4
|
1.0
|
CG2
|
C:VAL63
|
4.8
|
21.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 1s5y
Go back to
Iron Binding Sites List in 1s5y
Iron binding site 4 out
of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe800
b:46.3
occ:1.00
|
FE
|
D:HEM800
|
0.0
|
46.3
|
1.0
|
ND
|
D:HEM800
|
2.0
|
48.8
|
1.0
|
NE2
|
D:HIS92
|
2.0
|
37.0
|
1.0
|
NC
|
D:HEM800
|
2.0
|
48.7
|
1.0
|
NA
|
D:HEM800
|
2.0
|
50.2
|
1.0
|
NB
|
D:HEM800
|
2.1
|
47.5
|
1.0
|
NE2
|
D:HIS63
|
2.1
|
35.0
|
1.0
|
CE1
|
D:HIS63
|
2.8
|
30.9
|
1.0
|
CE1
|
D:HIS92
|
2.9
|
36.7
|
1.0
|
C1D
|
D:HEM800
|
3.0
|
50.3
|
1.0
|
C4D
|
D:HEM800
|
3.0
|
49.8
|
1.0
|
C4C
|
D:HEM800
|
3.1
|
49.5
|
1.0
|
C1A
|
D:HEM800
|
3.1
|
51.8
|
1.0
|
CD2
|
D:HIS92
|
3.1
|
38.1
|
1.0
|
C1C
|
D:HEM800
|
3.1
|
48.0
|
1.0
|
C4A
|
D:HEM800
|
3.1
|
50.1
|
1.0
|
C4B
|
D:HEM800
|
3.1
|
47.2
|
1.0
|
C1B
|
D:HEM800
|
3.2
|
46.9
|
1.0
|
CHD
|
D:HEM800
|
3.3
|
50.7
|
1.0
|
CHA
|
D:HEM800
|
3.4
|
51.0
|
1.0
|
CD2
|
D:HIS63
|
3.4
|
30.7
|
1.0
|
CHC
|
D:HEM800
|
3.4
|
47.8
|
1.0
|
CHB
|
D:HEM800
|
3.5
|
48.4
|
1.0
|
ND1
|
D:HIS63
|
4.1
|
30.2
|
1.0
|
ND1
|
D:HIS92
|
4.1
|
36.3
|
1.0
|
CG
|
D:HIS92
|
4.2
|
38.5
|
1.0
|
C3D
|
D:HEM800
|
4.2
|
51.5
|
1.0
|
C2D
|
D:HEM800
|
4.3
|
51.1
|
1.0
|
C3C
|
D:HEM800
|
4.3
|
49.5
|
1.0
|
C2A
|
D:HEM800
|
4.3
|
54.1
|
1.0
|
C3A
|
D:HEM800
|
4.3
|
52.5
|
1.0
|
C2C
|
D:HEM800
|
4.4
|
49.5
|
1.0
|
CG
|
D:HIS63
|
4.4
|
28.3
|
1.0
|
C3B
|
D:HEM800
|
4.4
|
46.9
|
1.0
|
C2B
|
D:HEM800
|
4.4
|
47.2
|
1.0
|
CG2
|
D:VAL67
|
4.5
|
13.9
|
1.0
|
|
Reference:
L.Vitagliano,
G.Bonomi,
A.Riccio,
G.Di Prisco,
G.Smulevich,
L.Mazzarella.
The Oxidation Process of Antarctic Fish Hemoglobins Eur.J.Biochem. V. 271 1651 2004.
ISSN: ISSN 0014-2956
PubMed: 15096204
DOI: 10.1111/J.1432-1033.2004.04054.X
Page generated: Sat Aug 3 14:34:03 2024
|