Iron in PDB 4ynr: Doss Gafa Domain Reduced Co Bound Crystal Structure
Enzymatic activity of Doss Gafa Domain Reduced Co Bound Crystal Structure
All present enzymatic activity of Doss Gafa Domain Reduced Co Bound Crystal Structure:
2.7.13.3;
Protein crystallography data
The structure of Doss Gafa Domain Reduced Co Bound Crystal Structure, PDB code: 4ynr
was solved by
Y.Madrona,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.01 /
1.92
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
33.505,
79.247,
109.451,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.9 /
23.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Doss Gafa Domain Reduced Co Bound Crystal Structure
(pdb code 4ynr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Doss Gafa Domain Reduced Co Bound Crystal Structure, PDB code: 4ynr:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 4ynr
Go back to
Iron Binding Sites List in 4ynr
Iron binding site 1 out
of 2 in the Doss Gafa Domain Reduced Co Bound Crystal Structure
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Doss Gafa Domain Reduced Co Bound Crystal Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:24.0
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
24.0
|
1.0
|
C
|
A:CMO302
|
1.9
|
17.3
|
1.0
|
NB
|
A:HEM301
|
2.1
|
22.8
|
1.0
|
NE2
|
A:HIS149
|
2.2
|
22.3
|
1.0
|
NA
|
A:HEM301
|
2.2
|
21.3
|
1.0
|
NC
|
A:HEM301
|
2.2
|
23.3
|
1.0
|
ND
|
A:HEM301
|
2.2
|
29.1
|
1.0
|
CD2
|
A:HIS149
|
3.0
|
19.8
|
1.0
|
C4A
|
A:HEM301
|
3.1
|
26.9
|
1.0
|
O
|
A:CMO302
|
3.1
|
27.4
|
1.0
|
C4C
|
A:HEM301
|
3.1
|
24.3
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
25.5
|
1.0
|
C1D
|
A:HEM301
|
3.1
|
26.4
|
1.0
|
C4B
|
A:HEM301
|
3.1
|
25.5
|
1.0
|
C1C
|
A:HEM301
|
3.1
|
25.1
|
1.0
|
C1A
|
A:HEM301
|
3.2
|
30.9
|
1.0
|
C4D
|
A:HEM301
|
3.2
|
28.3
|
1.0
|
CE1
|
A:HIS149
|
3.2
|
24.1
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
17.9
|
1.0
|
CHB
|
A:HEM301
|
3.4
|
19.7
|
1.0
|
CHC
|
A:HEM301
|
3.5
|
21.9
|
1.0
|
CHA
|
A:HEM301
|
3.5
|
28.4
|
1.0
|
CG
|
A:HIS149
|
4.2
|
18.3
|
1.0
|
ND1
|
A:HIS149
|
4.3
|
23.2
|
1.0
|
C3A
|
A:HEM301
|
4.3
|
24.6
|
1.0
|
C2A
|
A:HEM301
|
4.3
|
29.4
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
25.5
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
24.1
|
1.0
|
C3C
|
A:HEM301
|
4.3
|
24.5
|
1.0
|
C2C
|
A:HEM301
|
4.4
|
22.3
|
1.0
|
C2D
|
A:HEM301
|
4.4
|
23.4
|
1.0
|
C3D
|
A:HEM301
|
4.4
|
21.7
|
1.0
|
CD1
|
A:ILE121
|
4.6
|
44.3
|
0.5
|
CZ
|
A:PHE98
|
4.9
|
34.5
|
1.0
|
|
Iron binding site 2 out
of 2 in 4ynr
Go back to
Iron Binding Sites List in 4ynr
Iron binding site 2 out
of 2 in the Doss Gafa Domain Reduced Co Bound Crystal Structure
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Doss Gafa Domain Reduced Co Bound Crystal Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:30.9
occ:1.00
|
FE
|
B:HEM301
|
0.0
|
30.9
|
1.0
|
C
|
B:CMO302
|
1.8
|
18.9
|
1.0
|
NE2
|
B:HIS149
|
2.1
|
30.5
|
1.0
|
NC
|
B:HEM301
|
2.2
|
25.9
|
1.0
|
NB
|
B:HEM301
|
2.2
|
30.8
|
1.0
|
NA
|
B:HEM301
|
2.2
|
27.5
|
1.0
|
ND
|
B:HEM301
|
2.2
|
37.2
|
1.0
|
CD2
|
B:HIS149
|
3.0
|
30.3
|
1.0
|
O
|
B:CMO302
|
3.0
|
35.9
|
1.0
|
C4C
|
B:HEM301
|
3.1
|
35.2
|
1.0
|
C1C
|
B:HEM301
|
3.1
|
30.2
|
1.0
|
C1D
|
B:HEM301
|
3.1
|
40.7
|
1.0
|
C1B
|
B:HEM301
|
3.1
|
28.9
|
1.0
|
C4B
|
B:HEM301
|
3.1
|
33.6
|
1.0
|
CE1
|
B:HIS149
|
3.1
|
31.6
|
1.0
|
C4A
|
B:HEM301
|
3.2
|
34.9
|
1.0
|
C4D
|
B:HEM301
|
3.2
|
40.6
|
1.0
|
C1A
|
B:HEM301
|
3.2
|
38.5
|
1.0
|
CHD
|
B:HEM301
|
3.4
|
33.2
|
1.0
|
CHC
|
B:HEM301
|
3.5
|
31.7
|
1.0
|
CHB
|
B:HEM301
|
3.5
|
32.0
|
1.0
|
CHA
|
B:HEM301
|
3.5
|
34.9
|
1.0
|
CG
|
B:HIS149
|
4.2
|
32.8
|
1.0
|
ND1
|
B:HIS149
|
4.2
|
29.6
|
1.0
|
C3C
|
B:HEM301
|
4.3
|
28.4
|
1.0
|
C2C
|
B:HEM301
|
4.3
|
30.2
|
1.0
|
C3B
|
B:HEM301
|
4.3
|
30.9
|
1.0
|
C2B
|
B:HEM301
|
4.3
|
27.7
|
1.0
|
C2D
|
B:HEM301
|
4.4
|
34.9
|
1.0
|
C3A
|
B:HEM301
|
4.4
|
36.8
|
1.0
|
C3D
|
B:HEM301
|
4.4
|
37.2
|
1.0
|
C2A
|
B:HEM301
|
4.4
|
42.1
|
1.0
|
CD1
|
B:ILE121
|
4.5
|
43.7
|
0.5
|
CZ
|
B:PHE98
|
4.8
|
31.0
|
1.0
|
|
Reference:
D.Basudhar,
Y.Madrona,
P.R.Ortiz De Montellano.
Mycobacterium Tuberculosis Doss; Kinetics and Structure of Ligand Binding. To Be Published.
Page generated: Sun Dec 13 15:53:12 2020
|