Iron in PDB 1bcf: The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
Protein crystallography data
The structure of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site, PDB code: 1bcf
was solved by
F.Frolow,
A.J.Kalb(Gilboa),
J.Yariv,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.90
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
211.100,
211.100,
145.200,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
n/a
|
Other elements in 1bcf:
The structure of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
(pdb code 1bcf). 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 Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site, PDB code: 1bcf:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1bcf
Go back to
Iron Binding Sites List in 1bcf
Iron binding site 1 out
of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:16.1
occ:1.00
|
FE
|
A:HEM200
|
0.0
|
16.1
|
1.0
|
NC
|
A:HEM200
|
2.0
|
8.8
|
1.0
|
NA
|
A:HEM200
|
2.0
|
7.6
|
1.0
|
NB
|
A:HEM200
|
2.0
|
8.4
|
1.0
|
ND
|
A:HEM200
|
2.0
|
7.8
|
1.0
|
SD
|
B:MET52
|
2.6
|
4.5
|
1.0
|
SD
|
A:MET52
|
2.7
|
7.0
|
1.0
|
C4C
|
A:HEM200
|
3.0
|
10.1
|
1.0
|
C4A
|
A:HEM200
|
3.1
|
7.2
|
1.0
|
C1A
|
A:HEM200
|
3.1
|
6.2
|
1.0
|
C1B
|
A:HEM200
|
3.1
|
8.5
|
1.0
|
C1D
|
A:HEM200
|
3.1
|
7.7
|
1.0
|
C4B
|
A:HEM200
|
3.1
|
7.3
|
1.0
|
C4D
|
A:HEM200
|
3.1
|
8.2
|
1.0
|
C1C
|
A:HEM200
|
3.1
|
7.2
|
1.0
|
CG
|
B:MET52
|
3.5
|
5.8
|
1.0
|
CHD
|
A:HEM200
|
3.5
|
9.0
|
1.0
|
CHB
|
A:HEM200
|
3.5
|
9.0
|
1.0
|
CG
|
A:MET52
|
3.5
|
7.4
|
1.0
|
CHA
|
A:HEM200
|
3.5
|
5.0
|
1.0
|
CHC
|
A:HEM200
|
3.5
|
6.3
|
1.0
|
CE
|
B:MET52
|
3.5
|
7.7
|
1.0
|
CE
|
A:MET52
|
3.6
|
8.7
|
1.0
|
C2A
|
A:HEM200
|
4.2
|
6.7
|
1.0
|
C3C
|
A:HEM200
|
4.3
|
9.6
|
1.0
|
C3A
|
A:HEM200
|
4.3
|
7.1
|
1.0
|
C3D
|
A:HEM200
|
4.3
|
8.3
|
1.0
|
C2D
|
A:HEM200
|
4.3
|
7.9
|
1.0
|
C3B
|
A:HEM200
|
4.3
|
8.1
|
1.0
|
C2B
|
A:HEM200
|
4.3
|
7.0
|
1.0
|
C2C
|
A:HEM200
|
4.4
|
7.3
|
1.0
|
CB
|
B:MET52
|
4.4
|
2.6
|
1.0
|
CB
|
A:MET52
|
4.4
|
3.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 1bcf
Go back to
Iron Binding Sites List in 1bcf
Iron binding site 2 out
of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:16.1
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
16.1
|
1.0
|
NC
|
C:HEM201
|
2.0
|
8.8
|
1.0
|
NA
|
C:HEM201
|
2.0
|
7.6
|
1.0
|
NB
|
C:HEM201
|
2.0
|
8.4
|
1.0
|
ND
|
C:HEM201
|
2.0
|
7.8
|
1.0
|
SD
|
D:MET52
|
2.6
|
4.5
|
1.0
|
SD
|
C:MET52
|
2.7
|
7.0
|
1.0
|
C4C
|
C:HEM201
|
3.0
|
10.1
|
1.0
|
C4A
|
C:HEM201
|
3.1
|
7.2
|
1.0
|
C1A
|
C:HEM201
|
3.1
|
6.2
|
1.0
|
C1B
|
C:HEM201
|
3.1
|
8.5
|
1.0
|
C1D
|
C:HEM201
|
3.1
|
7.7
|
1.0
|
C4B
|
C:HEM201
|
3.1
|
7.3
|
1.0
|
C4D
|
C:HEM201
|
3.1
|
8.2
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
7.2
|
1.0
|
CG
|
D:MET52
|
3.5
|
5.8
|
1.0
|
CHD
|
C:HEM201
|
3.5
|
9.0
|
1.0
|
CHB
|
C:HEM201
|
3.5
|
9.0
|
1.0
|
CG
|
C:MET52
|
3.5
|
7.4
|
1.0
|
CHA
|
C:HEM201
|
3.5
|
5.0
|
1.0
|
CHC
|
C:HEM201
|
3.5
|
6.3
|
1.0
|
CE
|
D:MET52
|
3.5
|
7.7
|
1.0
|
CE
|
C:MET52
|
3.6
|
8.7
|
1.0
|
C2A
|
C:HEM201
|
4.2
|
6.7
|
1.0
|
C3C
|
C:HEM201
|
4.3
|
9.6
|
1.0
|
C3A
|
C:HEM201
|
4.3
|
7.1
|
1.0
|
C3D
|
C:HEM201
|
4.3
|
8.3
|
1.0
|
C2D
|
C:HEM201
|
4.3
|
7.9
|
1.0
|
C3B
|
C:HEM201
|
4.3
|
8.1
|
1.0
|
C2B
|
C:HEM201
|
4.3
|
7.0
|
1.0
|
C2C
|
C:HEM201
|
4.4
|
7.3
|
1.0
|
CB
|
D:MET52
|
4.4
|
2.6
|
1.0
|
CB
|
C:MET52
|
4.4
|
3.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 1bcf
Go back to
Iron Binding Sites List in 1bcf
Iron binding site 3 out
of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe202
b:16.1
occ:1.00
|
FE
|
E:HEM202
|
0.0
|
16.1
|
1.0
|
NC
|
E:HEM202
|
2.0
|
8.8
|
1.0
|
NA
|
E:HEM202
|
2.0
|
7.6
|
1.0
|
NB
|
E:HEM202
|
2.0
|
8.4
|
1.0
|
ND
|
E:HEM202
|
2.0
|
7.8
|
1.0
|
SD
|
F:MET52
|
2.6
|
4.5
|
1.0
|
SD
|
E:MET52
|
2.7
|
7.0
|
1.0
|
C4C
|
E:HEM202
|
3.0
|
10.1
|
1.0
|
C4A
|
E:HEM202
|
3.1
|
7.2
|
1.0
|
C1A
|
E:HEM202
|
3.1
|
6.2
|
1.0
|
C1B
|
E:HEM202
|
3.1
|
8.5
|
1.0
|
C1D
|
E:HEM202
|
3.1
|
7.7
|
1.0
|
C4B
|
E:HEM202
|
3.1
|
7.3
|
1.0
|
C4D
|
E:HEM202
|
3.1
|
8.2
|
1.0
|
C1C
|
E:HEM202
|
3.1
|
7.2
|
1.0
|
CG
|
F:MET52
|
3.5
|
5.8
|
1.0
|
CHD
|
E:HEM202
|
3.5
|
9.0
|
1.0
|
CHB
|
E:HEM202
|
3.5
|
9.0
|
1.0
|
CG
|
E:MET52
|
3.5
|
7.4
|
1.0
|
CHA
|
E:HEM202
|
3.5
|
5.0
|
1.0
|
CHC
|
E:HEM202
|
3.5
|
6.3
|
1.0
|
CE
|
F:MET52
|
3.5
|
7.7
|
1.0
|
CE
|
E:MET52
|
3.6
|
8.7
|
1.0
|
C2A
|
E:HEM202
|
4.2
|
6.7
|
1.0
|
C3C
|
E:HEM202
|
4.3
|
9.6
|
1.0
|
C3A
|
E:HEM202
|
4.3
|
7.1
|
1.0
|
C3D
|
E:HEM202
|
4.3
|
8.3
|
1.0
|
C2D
|
E:HEM202
|
4.3
|
7.9
|
1.0
|
C3B
|
E:HEM202
|
4.3
|
8.1
|
1.0
|
C2B
|
E:HEM202
|
4.3
|
7.0
|
1.0
|
C2C
|
E:HEM202
|
4.4
|
7.3
|
1.0
|
CB
|
F:MET52
|
4.4
|
2.6
|
1.0
|
CB
|
E:MET52
|
4.4
|
3.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 1bcf
Go back to
Iron Binding Sites List in 1bcf
Iron binding site 4 out
of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe203
b:16.1
occ:1.00
|
FE
|
G:HEM203
|
0.0
|
16.1
|
1.0
|
NC
|
G:HEM203
|
2.0
|
8.8
|
1.0
|
NB
|
G:HEM203
|
2.0
|
8.4
|
1.0
|
NA
|
G:HEM203
|
2.0
|
7.6
|
1.0
|
ND
|
G:HEM203
|
2.0
|
7.8
|
1.0
|
SD
|
H:MET52
|
2.6
|
4.5
|
1.0
|
SD
|
G:MET52
|
2.7
|
7.0
|
1.0
|
C4C
|
G:HEM203
|
3.0
|
10.1
|
1.0
|
C4A
|
G:HEM203
|
3.1
|
7.2
|
1.0
|
C1A
|
G:HEM203
|
3.1
|
6.2
|
1.0
|
C1B
|
G:HEM203
|
3.1
|
8.5
|
1.0
|
C1D
|
G:HEM203
|
3.1
|
7.7
|
1.0
|
C4B
|
G:HEM203
|
3.1
|
7.3
|
1.0
|
C4D
|
G:HEM203
|
3.1
|
8.2
|
1.0
|
C1C
|
G:HEM203
|
3.1
|
7.2
|
1.0
|
CG
|
H:MET52
|
3.5
|
5.8
|
1.0
|
CHD
|
G:HEM203
|
3.5
|
9.0
|
1.0
|
CHB
|
G:HEM203
|
3.5
|
9.0
|
1.0
|
CG
|
G:MET52
|
3.5
|
7.4
|
1.0
|
CHA
|
G:HEM203
|
3.5
|
5.0
|
1.0
|
CHC
|
G:HEM203
|
3.5
|
6.3
|
1.0
|
CE
|
H:MET52
|
3.5
|
7.7
|
1.0
|
CE
|
G:MET52
|
3.6
|
8.7
|
1.0
|
C2A
|
G:HEM203
|
4.2
|
6.7
|
1.0
|
C3C
|
G:HEM203
|
4.3
|
9.6
|
1.0
|
C3A
|
G:HEM203
|
4.3
|
7.1
|
1.0
|
C3D
|
G:HEM203
|
4.3
|
8.3
|
1.0
|
C2D
|
G:HEM203
|
4.3
|
7.9
|
1.0
|
C3B
|
G:HEM203
|
4.3
|
8.1
|
1.0
|
C2B
|
G:HEM203
|
4.3
|
7.0
|
1.0
|
C2C
|
G:HEM203
|
4.4
|
7.3
|
1.0
|
CB
|
H:MET52
|
4.4
|
2.6
|
1.0
|
CB
|
G:MET52
|
4.4
|
3.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 1bcf
Go back to
Iron Binding Sites List in 1bcf
Iron binding site 5 out
of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe204
b:16.1
occ:1.00
|
FE
|
I:HEM204
|
0.0
|
16.1
|
1.0
|
NC
|
I:HEM204
|
2.0
|
8.8
|
1.0
|
NA
|
I:HEM204
|
2.0
|
7.6
|
1.0
|
NB
|
I:HEM204
|
2.0
|
8.4
|
1.0
|
ND
|
I:HEM204
|
2.0
|
7.8
|
1.0
|
SD
|
J:MET52
|
2.6
|
4.5
|
1.0
|
SD
|
I:MET52
|
2.7
|
7.0
|
1.0
|
C4C
|
I:HEM204
|
3.0
|
10.1
|
1.0
|
C4A
|
I:HEM204
|
3.1
|
7.2
|
1.0
|
C1A
|
I:HEM204
|
3.1
|
6.2
|
1.0
|
C1B
|
I:HEM204
|
3.1
|
8.5
|
1.0
|
C1D
|
I:HEM204
|
3.1
|
7.7
|
1.0
|
C4B
|
I:HEM204
|
3.1
|
7.3
|
1.0
|
C4D
|
I:HEM204
|
3.1
|
8.2
|
1.0
|
C1C
|
I:HEM204
|
3.1
|
7.2
|
1.0
|
CG
|
J:MET52
|
3.5
|
5.8
|
1.0
|
CHD
|
I:HEM204
|
3.5
|
9.0
|
1.0
|
CHB
|
I:HEM204
|
3.5
|
9.0
|
1.0
|
CG
|
I:MET52
|
3.5
|
7.4
|
1.0
|
CHA
|
I:HEM204
|
3.5
|
5.0
|
1.0
|
CHC
|
I:HEM204
|
3.5
|
6.3
|
1.0
|
CE
|
J:MET52
|
3.5
|
7.7
|
1.0
|
CE
|
I:MET52
|
3.6
|
8.7
|
1.0
|
C2A
|
I:HEM204
|
4.2
|
6.7
|
1.0
|
C3C
|
I:HEM204
|
4.3
|
9.6
|
1.0
|
C3A
|
I:HEM204
|
4.3
|
7.1
|
1.0
|
C3D
|
I:HEM204
|
4.3
|
8.3
|
1.0
|
C2D
|
I:HEM204
|
4.3
|
7.9
|
1.0
|
C3B
|
I:HEM204
|
4.3
|
8.1
|
1.0
|
C2B
|
I:HEM204
|
4.3
|
7.0
|
1.0
|
C2C
|
I:HEM204
|
4.4
|
7.3
|
1.0
|
CB
|
J:MET52
|
4.4
|
2.6
|
1.0
|
CB
|
I:MET52
|
4.4
|
3.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 1bcf
Go back to
Iron Binding Sites List in 1bcf
Iron binding site 6 out
of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe205
b:16.1
occ:1.00
|
FE
|
K:HEM205
|
0.0
|
16.1
|
1.0
|
NC
|
K:HEM205
|
2.0
|
8.8
|
1.0
|
NA
|
K:HEM205
|
2.0
|
7.6
|
1.0
|
NB
|
K:HEM205
|
2.0
|
8.4
|
1.0
|
ND
|
K:HEM205
|
2.0
|
7.8
|
1.0
|
SD
|
L:MET52
|
2.6
|
4.5
|
1.0
|
SD
|
K:MET52
|
2.7
|
7.0
|
1.0
|
C4C
|
K:HEM205
|
3.0
|
10.1
|
1.0
|
C4A
|
K:HEM205
|
3.1
|
7.2
|
1.0
|
C1A
|
K:HEM205
|
3.1
|
6.2
|
1.0
|
C1B
|
K:HEM205
|
3.1
|
8.5
|
1.0
|
C1D
|
K:HEM205
|
3.1
|
7.7
|
1.0
|
C4B
|
K:HEM205
|
3.1
|
7.3
|
1.0
|
C4D
|
K:HEM205
|
3.1
|
8.2
|
1.0
|
C1C
|
K:HEM205
|
3.1
|
7.2
|
1.0
|
CG
|
L:MET52
|
3.5
|
5.8
|
1.0
|
CHD
|
K:HEM205
|
3.5
|
9.0
|
1.0
|
CHB
|
K:HEM205
|
3.5
|
9.0
|
1.0
|
CG
|
K:MET52
|
3.5
|
7.4
|
1.0
|
CHA
|
K:HEM205
|
3.5
|
5.0
|
1.0
|
CHC
|
K:HEM205
|
3.5
|
6.3
|
1.0
|
CE
|
L:MET52
|
3.5
|
7.7
|
1.0
|
CE
|
K:MET52
|
3.6
|
8.7
|
1.0
|
C2A
|
K:HEM205
|
4.2
|
6.7
|
1.0
|
C3C
|
K:HEM205
|
4.3
|
9.6
|
1.0
|
C3A
|
K:HEM205
|
4.3
|
7.1
|
1.0
|
C3D
|
K:HEM205
|
4.3
|
8.3
|
1.0
|
C2D
|
K:HEM205
|
4.3
|
7.9
|
1.0
|
C3B
|
K:HEM205
|
4.3
|
8.1
|
1.0
|
C2B
|
K:HEM205
|
4.3
|
7.0
|
1.0
|
C2C
|
K:HEM205
|
4.4
|
7.3
|
1.0
|
CB
|
L:MET52
|
4.4
|
2.6
|
1.0
|
CB
|
K:MET52
|
4.4
|
3.3
|
1.0
|
|
Reference:
F.Frolow,
A.J.Kalb,
J.Yariv.
Structure of A Unique Twofold Symmetric Haem-Binding Site. Nat.Struct.Biol. V. 1 453 1994.
ISSN: ISSN 1072-8368
PubMed: 7664064
DOI: 10.1038/NSB0794-453
Page generated: Sat Aug 3 02:42:36 2024
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