Iron in PDB 6ls8: The Monomeric Structure of G80A/H81A/H82A Myoglobin
Protein crystallography data
The structure of The Monomeric Structure of G80A/H81A/H82A Myoglobin, PDB code: 6ls8
was solved by
S.Nagao,
A.Suda,
H.Kobayashi,
N.Shibata,
Y.Higuchi,
S.Hirota,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
43.41 /
2.30
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.147,
61.490,
70.323,
78.83,
81.14,
63.12
|
|
R / Rfree (%)
|
21.6 /
27.4
|
Iron Binding Sites:
The binding sites of Iron atom in the The Monomeric Structure of G80A/H81A/H82A Myoglobin
(pdb code 6ls8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
The Monomeric Structure of G80A/H81A/H82A Myoglobin, PDB code: 6ls8:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 6ls8
Go back to
Iron Binding Sites List in 6ls8
Iron binding site 1 out
of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:27.9
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
27.9
|
1.0
|
|
O
|
A:HOH307
|
1.8
|
22.3
|
1.0
|
|
ND
|
A:HEM201
|
2.0
|
24.4
|
1.0
|
|
NC
|
A:HEM201
|
2.0
|
26.1
|
1.0
|
|
NB
|
A:HEM201
|
2.0
|
21.6
|
1.0
|
|
NE2
|
A:HIS93
|
2.1
|
29.0
|
1.0
|
|
NA
|
A:HEM201
|
2.1
|
24.1
|
1.0
|
|
C1C
|
A:HEM201
|
3.0
|
21.8
|
1.0
|
|
C4B
|
A:HEM201
|
3.0
|
22.5
|
1.0
|
|
C4D
|
A:HEM201
|
3.0
|
25.2
|
1.0
|
|
CE1
|
A:HIS93
|
3.0
|
28.2
|
1.0
|
|
C1D
|
A:HEM201
|
3.1
|
28.8
|
1.0
|
|
C1A
|
A:HEM201
|
3.1
|
25.1
|
1.0
|
|
CD2
|
A:HIS93
|
3.1
|
29.3
|
1.0
|
|
C4C
|
A:HEM201
|
3.1
|
25.3
|
1.0
|
|
C1B
|
A:HEM201
|
3.1
|
23.7
|
1.0
|
|
C4A
|
A:HEM201
|
3.2
|
25.3
|
1.0
|
|
CHC
|
A:HEM201
|
3.3
|
22.0
|
1.0
|
|
CHA
|
A:HEM201
|
3.4
|
25.3
|
1.0
|
|
CHD
|
A:HEM201
|
3.5
|
27.6
|
1.0
|
|
CHB
|
A:HEM201
|
3.6
|
26.5
|
1.0
|
|
ND1
|
A:HIS93
|
4.2
|
30.8
|
1.0
|
|
C2C
|
A:HEM201
|
4.2
|
27.6
|
1.0
|
|
CG
|
A:HIS93
|
4.2
|
32.7
|
1.0
|
|
C3D
|
A:HEM201
|
4.2
|
32.3
|
1.0
|
|
C3B
|
A:HEM201
|
4.3
|
23.6
|
1.0
|
|
C2D
|
A:HEM201
|
4.3
|
28.2
|
1.0
|
|
C3C
|
A:HEM201
|
4.3
|
22.6
|
1.0
|
|
C2A
|
A:HEM201
|
4.3
|
25.4
|
1.0
|
|
C2B
|
A:HEM201
|
4.3
|
27.1
|
1.0
|
|
C3A
|
A:HEM201
|
4.3
|
22.3
|
1.0
|
|
NE2
|
A:HIS64
|
4.4
|
20.9
|
1.0
|
|
CG2
|
A:VAL68
|
4.7
|
19.2
|
1.0
|
|
CE1
|
A:HIS64
|
4.7
|
24.8
|
1.0
|
|
CD2
|
A:HIS97
|
5.0
|
30.5
|
1.0
|
|
Iron binding site 2 out
of 6 in 6ls8
Go back to
Iron Binding Sites List in 6ls8
Iron binding site 2 out
of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:21.6
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
21.6
|
1.0
|
|
ND
|
C:HEM201
|
2.0
|
26.2
|
1.0
|
|
O
|
C:HOH304
|
2.0
|
26.5
|
1.0
|
|
NA
|
C:HEM201
|
2.0
|
23.5
|
1.0
|
|
NE2
|
C:HIS93
|
2.0
|
28.2
|
1.0
|
|
NC
|
C:HEM201
|
2.1
|
23.3
|
1.0
|
|
NB
|
C:HEM201
|
2.1
|
25.4
|
1.0
|
|
CE1
|
C:HIS93
|
2.9
|
26.3
|
1.0
|
|
C4D
|
C:HEM201
|
3.0
|
28.1
|
1.0
|
|
C1A
|
C:HEM201
|
3.0
|
23.3
|
1.0
|
|
C1D
|
C:HEM201
|
3.0
|
23.3
|
1.0
|
|
C4C
|
C:HEM201
|
3.1
|
25.7
|
1.0
|
|
C4A
|
C:HEM201
|
3.1
|
24.7
|
1.0
|
|
C1C
|
C:HEM201
|
3.1
|
26.2
|
1.0
|
|
CD2
|
C:HIS93
|
3.1
|
24.8
|
1.0
|
|
C1B
|
C:HEM201
|
3.2
|
30.0
|
1.0
|
|
C4B
|
C:HEM201
|
3.2
|
27.7
|
1.0
|
|
CHA
|
C:HEM201
|
3.4
|
26.4
|
1.0
|
|
CHD
|
C:HEM201
|
3.4
|
21.7
|
1.0
|
|
CHB
|
C:HEM201
|
3.5
|
24.9
|
1.0
|
|
CHC
|
C:HEM201
|
3.5
|
26.7
|
1.0
|
|
ND1
|
C:HIS93
|
4.1
|
25.6
|
1.0
|
|
C2D
|
C:HEM201
|
4.2
|
25.1
|
1.0
|
|
CG
|
C:HIS93
|
4.2
|
26.2
|
1.0
|
|
C3D
|
C:HEM201
|
4.2
|
27.8
|
1.0
|
|
C2A
|
C:HEM201
|
4.2
|
27.1
|
1.0
|
|
C3A
|
C:HEM201
|
4.3
|
27.9
|
1.0
|
|
C3C
|
C:HEM201
|
4.3
|
23.8
|
1.0
|
|
C2C
|
C:HEM201
|
4.3
|
27.5
|
1.0
|
|
NE2
|
C:HIS64
|
4.4
|
25.5
|
1.0
|
|
C2B
|
C:HEM201
|
4.4
|
26.0
|
1.0
|
|
C3B
|
C:HEM201
|
4.4
|
24.0
|
1.0
|
|
CG2
|
C:VAL68
|
4.5
|
22.5
|
1.0
|
|
CE1
|
C:HIS64
|
4.7
|
24.0
|
1.0
|
|
CD2
|
C:HIS97
|
4.9
|
31.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 6ls8
Go back to
Iron Binding Sites List in 6ls8
Iron binding site 3 out
of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:32.0
occ:1.00
|
FE
|
E:HEM201
|
0.0
|
32.0
|
1.0
|
|
NE2
|
E:HIS93
|
2.0
|
38.1
|
1.0
|
|
ND
|
E:HEM201
|
2.0
|
29.8
|
1.0
|
|
NC
|
E:HEM201
|
2.0
|
29.9
|
1.0
|
|
NB
|
E:HEM201
|
2.1
|
24.4
|
1.0
|
|
NA
|
E:HEM201
|
2.1
|
31.7
|
1.0
|
|
O
|
E:HOH304
|
2.1
|
30.9
|
1.0
|
|
CE1
|
E:HIS93
|
2.9
|
32.4
|
1.0
|
|
C1D
|
E:HEM201
|
3.0
|
35.8
|
1.0
|
|
C4C
|
E:HEM201
|
3.0
|
33.0
|
1.0
|
|
C4D
|
E:HEM201
|
3.0
|
28.8
|
1.0
|
|
C1C
|
E:HEM201
|
3.1
|
27.5
|
1.0
|
|
CD2
|
E:HIS93
|
3.1
|
29.5
|
1.0
|
|
C4B
|
E:HEM201
|
3.1
|
25.2
|
1.0
|
|
C1A
|
E:HEM201
|
3.1
|
28.6
|
1.0
|
|
C1B
|
E:HEM201
|
3.1
|
26.8
|
1.0
|
|
C4A
|
E:HEM201
|
3.1
|
25.9
|
1.0
|
|
CHD
|
E:HEM201
|
3.3
|
29.5
|
1.0
|
|
CHA
|
E:HEM201
|
3.4
|
33.0
|
1.0
|
|
CHC
|
E:HEM201
|
3.5
|
24.1
|
1.0
|
|
CHB
|
E:HEM201
|
3.5
|
26.5
|
1.0
|
|
ND1
|
E:HIS93
|
4.0
|
30.6
|
1.0
|
|
CG
|
E:HIS93
|
4.2
|
33.2
|
1.0
|
|
C2D
|
E:HEM201
|
4.2
|
31.2
|
1.0
|
|
C3C
|
E:HEM201
|
4.2
|
29.0
|
1.0
|
|
C3D
|
E:HEM201
|
4.2
|
34.6
|
1.0
|
|
C2C
|
E:HEM201
|
4.3
|
29.4
|
1.0
|
|
C3B
|
E:HEM201
|
4.3
|
26.4
|
1.0
|
|
C2A
|
E:HEM201
|
4.3
|
28.0
|
1.0
|
|
C2B
|
E:HEM201
|
4.3
|
23.9
|
1.0
|
|
C3A
|
E:HEM201
|
4.3
|
22.3
|
1.0
|
|
NE2
|
E:HIS64
|
4.4
|
24.9
|
1.0
|
|
CE1
|
E:HIS64
|
4.6
|
31.9
|
1.0
|
|
CD2
|
E:HIS97
|
4.8
|
32.6
|
1.0
|
|
CG2
|
E:VAL68
|
4.8
|
24.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 6ls8
Go back to
Iron Binding Sites List in 6ls8
Iron binding site 4 out
of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:33.9
occ:1.00
|
FE
|
G:HEM201
|
0.0
|
33.9
|
1.0
|
|
O
|
G:HOH303
|
2.0
|
31.6
|
1.0
|
|
NC
|
G:HEM201
|
2.0
|
24.6
|
1.0
|
|
ND
|
G:HEM201
|
2.0
|
39.4
|
1.0
|
|
NA
|
G:HEM201
|
2.0
|
30.0
|
1.0
|
|
NE2
|
G:HIS93
|
2.1
|
37.8
|
1.0
|
|
NB
|
G:HEM201
|
2.1
|
26.6
|
1.0
|
|
CE1
|
G:HIS93
|
2.9
|
41.3
|
1.0
|
|
C4C
|
G:HEM201
|
3.0
|
29.4
|
1.0
|
|
C1D
|
G:HEM201
|
3.0
|
28.0
|
1.0
|
|
C4A
|
G:HEM201
|
3.0
|
30.4
|
1.0
|
|
C1B
|
G:HEM201
|
3.1
|
29.8
|
1.0
|
|
C1C
|
G:HEM201
|
3.1
|
28.8
|
1.0
|
|
C4D
|
G:HEM201
|
3.1
|
36.1
|
1.0
|
|
C4B
|
G:HEM201
|
3.1
|
25.3
|
1.0
|
|
C1A
|
G:HEM201
|
3.1
|
34.1
|
1.0
|
|
CD2
|
G:HIS93
|
3.2
|
36.7
|
1.0
|
|
CHD
|
G:HEM201
|
3.4
|
32.7
|
1.0
|
|
CHB
|
G:HEM201
|
3.4
|
33.2
|
1.0
|
|
CHC
|
G:HEM201
|
3.5
|
20.6
|
1.0
|
|
CHA
|
G:HEM201
|
3.5
|
29.5
|
1.0
|
|
ND1
|
G:HIS93
|
4.1
|
43.6
|
1.0
|
|
C2D
|
G:HEM201
|
4.2
|
31.1
|
1.0
|
|
CG
|
G:HIS93
|
4.2
|
41.0
|
1.0
|
|
C3C
|
G:HEM201
|
4.2
|
29.9
|
1.0
|
|
C3D
|
G:HEM201
|
4.3
|
37.1
|
1.0
|
|
C3A
|
G:HEM201
|
4.3
|
26.9
|
1.0
|
|
C2C
|
G:HEM201
|
4.3
|
24.5
|
1.0
|
|
C2B
|
G:HEM201
|
4.3
|
29.4
|
1.0
|
|
C2A
|
G:HEM201
|
4.3
|
34.1
|
1.0
|
|
C3B
|
G:HEM201
|
4.3
|
30.4
|
1.0
|
|
NE2
|
G:HIS64
|
4.4
|
27.4
|
1.0
|
|
CG2
|
G:VAL68
|
4.5
|
27.4
|
1.0
|
|
CE1
|
G:HIS64
|
4.5
|
27.4
|
1.0
|
|
CD2
|
G:HIS97
|
4.9
|
38.9
|
1.0
|
|
CZ
|
G:PHE43
|
5.0
|
28.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 6ls8
Go back to
Iron Binding Sites List in 6ls8
Iron binding site 5 out
of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe201
b:25.5
occ:1.00
|
FE
|
I:HEM201
|
0.0
|
25.5
|
1.0
|
|
ND
|
I:HEM201
|
2.0
|
27.5
|
1.0
|
|
NC
|
I:HEM201
|
2.0
|
26.4
|
1.0
|
|
NE2
|
I:HIS93
|
2.1
|
34.0
|
1.0
|
|
NB
|
I:HEM201
|
2.1
|
22.8
|
1.0
|
|
NA
|
I:HEM201
|
2.1
|
29.7
|
1.0
|
|
O
|
I:HOH301
|
2.3
|
35.7
|
1.0
|
|
CE1
|
I:HIS93
|
2.9
|
33.0
|
1.0
|
|
C1D
|
I:HEM201
|
3.0
|
35.9
|
1.0
|
|
C4D
|
I:HEM201
|
3.0
|
32.6
|
1.0
|
|
C4C
|
I:HEM201
|
3.0
|
29.7
|
1.0
|
|
C1C
|
I:HEM201
|
3.1
|
26.6
|
1.0
|
|
C4B
|
I:HEM201
|
3.1
|
26.1
|
1.0
|
|
C1A
|
I:HEM201
|
3.1
|
28.4
|
1.0
|
|
CD2
|
I:HIS93
|
3.1
|
30.8
|
1.0
|
|
C1B
|
I:HEM201
|
3.2
|
28.8
|
1.0
|
|
C4A
|
I:HEM201
|
3.2
|
30.8
|
1.0
|
|
CHD
|
I:HEM201
|
3.4
|
34.2
|
1.0
|
|
CHA
|
I:HEM201
|
3.4
|
31.8
|
1.0
|
|
CHC
|
I:HEM201
|
3.4
|
18.7
|
1.0
|
|
CHB
|
I:HEM201
|
3.6
|
29.6
|
1.0
|
|
ND1
|
I:HIS93
|
4.1
|
32.9
|
1.0
|
|
C3D
|
I:HEM201
|
4.2
|
36.9
|
1.0
|
|
C2D
|
I:HEM201
|
4.2
|
31.3
|
1.0
|
|
CG
|
I:HIS93
|
4.2
|
35.7
|
1.0
|
|
C3C
|
I:HEM201
|
4.2
|
27.4
|
1.0
|
|
C2C
|
I:HEM201
|
4.3
|
28.9
|
1.0
|
|
NE2
|
I:HIS64
|
4.3
|
42.4
|
1.0
|
|
C3B
|
I:HEM201
|
4.3
|
27.4
|
1.0
|
|
C2B
|
I:HEM201
|
4.4
|
29.5
|
1.0
|
|
C2A
|
I:HEM201
|
4.4
|
31.0
|
1.0
|
|
C3A
|
I:HEM201
|
4.4
|
28.6
|
1.0
|
|
CE1
|
I:HIS64
|
4.5
|
37.7
|
1.0
|
|
CG2
|
I:VAL68
|
4.7
|
29.7
|
1.0
|
|
CZ
|
I:PHE43
|
4.8
|
28.7
|
1.0
|
|
CD2
|
I:HIS97
|
4.9
|
33.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 6ls8
Go back to
Iron Binding Sites List in 6ls8
Iron binding site 6 out
of 6 in the The Monomeric Structure of G80A/H81A/H82A Myoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The Monomeric Structure of G80A/H81A/H82A Myoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe201
b:27.9
occ:1.00
|
FE
|
K:HEM201
|
0.0
|
27.9
|
1.0
|
|
NE2
|
K:HIS93
|
2.0
|
36.8
|
1.0
|
|
NB
|
K:HEM201
|
2.0
|
30.9
|
1.0
|
|
O
|
K:HOH301
|
2.0
|
32.4
|
1.0
|
|
NC
|
K:HEM201
|
2.0
|
41.1
|
1.0
|
|
ND
|
K:HEM201
|
2.1
|
35.8
|
1.0
|
|
NA
|
K:HEM201
|
2.1
|
36.3
|
1.0
|
|
CE1
|
K:HIS93
|
2.8
|
32.3
|
1.0
|
|
C4B
|
K:HEM201
|
3.0
|
34.9
|
1.0
|
|
C1B
|
K:HEM201
|
3.0
|
33.3
|
1.0
|
|
C1C
|
K:HEM201
|
3.0
|
34.4
|
1.0
|
|
C1D
|
K:HEM201
|
3.0
|
40.2
|
1.0
|
|
CD2
|
K:HIS93
|
3.0
|
35.8
|
1.0
|
|
C4C
|
K:HEM201
|
3.0
|
36.5
|
1.0
|
|
C4A
|
K:HEM201
|
3.0
|
37.2
|
1.0
|
|
C4D
|
K:HEM201
|
3.1
|
38.1
|
1.0
|
|
C1A
|
K:HEM201
|
3.1
|
31.3
|
1.0
|
|
CHB
|
K:HEM201
|
3.4
|
36.8
|
1.0
|
|
CHC
|
K:HEM201
|
3.4
|
33.9
|
1.0
|
|
CHD
|
K:HEM201
|
3.4
|
35.6
|
1.0
|
|
CHA
|
K:HEM201
|
3.5
|
34.6
|
1.0
|
|
ND1
|
K:HIS93
|
4.0
|
34.0
|
1.0
|
|
CG
|
K:HIS93
|
4.1
|
35.5
|
1.0
|
|
NE2
|
K:HIS64
|
4.2
|
44.5
|
1.0
|
|
C3B
|
K:HEM201
|
4.2
|
34.8
|
1.0
|
|
C2B
|
K:HEM201
|
4.2
|
28.6
|
1.0
|
|
C2C
|
K:HEM201
|
4.3
|
38.6
|
1.0
|
|
C3C
|
K:HEM201
|
4.3
|
42.9
|
1.0
|
|
C2D
|
K:HEM201
|
4.3
|
38.3
|
1.0
|
|
C3A
|
K:HEM201
|
4.3
|
34.7
|
1.0
|
|
C3D
|
K:HEM201
|
4.3
|
41.2
|
1.0
|
|
C2A
|
K:HEM201
|
4.3
|
31.6
|
1.0
|
|
CE1
|
K:HIS64
|
4.5
|
46.9
|
1.0
|
|
CG2
|
K:VAL68
|
4.6
|
33.6
|
1.0
|
|
CD2
|
K:HIS97
|
4.9
|
31.6
|
1.0
|
|
Reference:
S.Nagao,
A.Suda,
H.Kobayashi,
N.Shibata,
Y.Higuchi,
S.Hirota.
Thermodynamic Control of Domain Swapping By Modulating Helical Propensity in the Hinge Region of Myoglobin. Chem Asian J 2020.
ISSN: ESSN 1861-471X
PubMed: 32329228
DOI: 10.1002/ASIA.202000307
Page generated: Wed Aug 7 01:35:06 2024
|
