Iron in PDB 6qk2: R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
Enzymatic activity of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
All present enzymatic activity of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;
Protein crystallography data
The structure of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk2
was solved by
J.J.Griese,
M.Hogbom,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.59 /
1.60
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
129.119,
97.794,
55.994,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.3 /
19
|
Other elements in 6qk2:
The structure of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
(pdb code 6qk2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk2:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6qk2
Go back to
Iron Binding Sites List in 6qk2
Iron binding site 1 out
of 4 in the R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:22.6
occ:1.00
|
O1
|
A:PLM404
|
1.8
|
22.5
|
1.0
|
OE2
|
A:GLU167
|
2.0
|
24.4
|
1.0
|
OE2
|
A:GLU102
|
2.0
|
22.6
|
1.0
|
ND1
|
A:HIS205
|
2.1
|
20.8
|
1.0
|
OE1
|
A:GLU202
|
2.1
|
24.8
|
1.0
|
OE2
|
A:GLU202
|
2.3
|
22.5
|
1.0
|
CD
|
A:GLU202
|
2.5
|
23.0
|
1.0
|
C1
|
A:PLM404
|
3.0
|
30.2
|
1.0
|
CE1
|
A:HIS205
|
3.0
|
21.4
|
1.0
|
CD
|
A:GLU102
|
3.0
|
20.0
|
1.0
|
CD
|
A:GLU167
|
3.1
|
28.1
|
1.0
|
HE1
|
A:HIS205
|
3.1
|
25.7
|
1.0
|
CG
|
A:HIS205
|
3.2
|
18.0
|
1.0
|
HB3
|
A:HIS205
|
3.4
|
27.3
|
1.0
|
OE1
|
A:GLU102
|
3.4
|
19.2
|
1.0
|
HG2
|
A:GLU167
|
3.5
|
31.6
|
1.0
|
HB2
|
A:HIS205
|
3.5
|
27.3
|
1.0
|
O2
|
A:PLM404
|
3.5
|
36.4
|
1.0
|
CB
|
A:HIS205
|
3.6
|
22.8
|
1.0
|
MN
|
A:MN403
|
3.7
|
18.4
|
1.0
|
HE2
|
A:PHE98
|
3.8
|
28.8
|
1.0
|
CG
|
A:GLU167
|
3.8
|
26.4
|
1.0
|
HA
|
A:GLU202
|
3.9
|
26.1
|
1.0
|
HZ
|
A:PHE98
|
3.9
|
24.9
|
1.0
|
HE2
|
A:TYR162
|
3.9
|
26.1
|
1.0
|
OE1
|
A:GLU167
|
4.0
|
34.5
|
1.0
|
CE2
|
A:PHE98
|
4.0
|
24.0
|
1.0
|
CG
|
A:GLU202
|
4.0
|
24.7
|
1.0
|
CZ
|
A:PHE98
|
4.0
|
20.7
|
1.0
|
NE2
|
A:HIS205
|
4.2
|
18.9
|
1.0
|
CD2
|
A:HIS205
|
4.3
|
18.3
|
1.0
|
CG
|
A:GLU102
|
4.3
|
16.0
|
1.0
|
HE1
|
A:HIS105
|
4.3
|
24.6
|
1.0
|
HG2
|
A:GLU102
|
4.3
|
19.2
|
1.0
|
HB3
|
A:GLU167
|
4.4
|
27.0
|
1.0
|
HG21
|
A:VAL72
|
4.4
|
24.9
|
1.0
|
C2
|
A:PLM404
|
4.4
|
44.0
|
1.0
|
HG2
|
A:GLU202
|
4.4
|
29.7
|
1.0
|
HG3
|
A:GLU202
|
4.5
|
29.7
|
1.0
|
HG3
|
A:GLU102
|
4.5
|
19.2
|
1.0
|
HG3
|
A:GLU167
|
4.6
|
31.6
|
1.0
|
H22
|
A:PLM404
|
4.6
|
52.9
|
1.0
|
H21
|
A:PLM404
|
4.7
|
52.9
|
1.0
|
HB3
|
A:GLU202
|
4.7
|
24.7
|
1.0
|
CD2
|
A:PHE98
|
4.7
|
20.8
|
1.0
|
CB
|
A:GLU167
|
4.7
|
22.5
|
1.0
|
CA
|
A:GLU202
|
4.7
|
21.7
|
1.0
|
CB
|
A:GLU202
|
4.7
|
20.6
|
1.0
|
CE2
|
A:TYR162
|
4.8
|
21.8
|
1.0
|
CE1
|
A:PHE98
|
4.8
|
23.0
|
1.0
|
CE1
|
A:HIS105
|
4.9
|
20.5
|
1.0
|
HE2
|
A:HIS205
|
4.9
|
22.7
|
1.0
|
O
|
A:HOH502
|
5.0
|
28.0
|
1.0
|
ND1
|
A:HIS105
|
5.0
|
17.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 6qk2
Go back to
Iron Binding Sites List in 6qk2
Iron binding site 2 out
of 4 in the R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:37.7
occ:0.66
|
O
|
A:HOH612
|
1.9
|
45.6
|
1.0
|
O
|
A:HOH561
|
1.9
|
39.1
|
1.0
|
O
|
A:HOH584
|
2.0
|
40.8
|
1.0
|
O
|
A:HOH573
|
2.0
|
43.2
|
1.0
|
NE2
|
A:HIS130
|
2.1
|
28.8
|
1.0
|
CE1
|
A:HIS130
|
3.1
|
32.5
|
1.0
|
CD2
|
A:HIS130
|
3.1
|
32.5
|
1.0
|
HE1
|
A:HIS130
|
3.2
|
39.0
|
1.0
|
HD2
|
A:HIS130
|
3.3
|
39.0
|
1.0
|
O
|
A:HOH533
|
4.1
|
38.4
|
1.0
|
OD2
|
A:ASP129
|
4.2
|
43.2
|
1.0
|
ND1
|
A:HIS130
|
4.2
|
32.1
|
1.0
|
CG
|
A:HIS130
|
4.3
|
29.2
|
1.0
|
OD1
|
A:ASP129
|
4.3
|
35.3
|
1.0
|
O
|
A:HOH636
|
4.4
|
51.3
|
1.0
|
HA3
|
A:GLY240
|
4.7
|
34.9
|
1.0
|
CG
|
A:ASP129
|
4.7
|
34.5
|
1.0
|
O
|
A:HOH596
|
4.8
|
36.2
|
1.0
|
HD1
|
A:HIS130
|
5.0
|
38.5
|
1.0
|
O
|
A:HOH529
|
5.0
|
37.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 6qk2
Go back to
Iron Binding Sites List in 6qk2
Iron binding site 3 out
of 4 in the R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:37.6
occ:0.69
|
O
|
B:HOH613
|
2.0
|
39.2
|
1.0
|
O
|
B:HOH595
|
2.1
|
41.2
|
1.0
|
O
|
B:HOH583
|
2.1
|
39.9
|
1.0
|
O
|
B:HOH651
|
2.2
|
43.2
|
1.0
|
NE2
|
B:HIS130
|
2.2
|
26.9
|
1.0
|
CE1
|
B:HIS130
|
3.1
|
33.8
|
1.0
|
CD2
|
B:HIS130
|
3.1
|
33.2
|
1.0
|
HE1
|
B:HIS130
|
3.3
|
40.6
|
1.0
|
HD2
|
B:HIS130
|
3.3
|
39.8
|
1.0
|
O
|
B:HOH563
|
4.1
|
36.1
|
1.0
|
ND1
|
B:HIS130
|
4.2
|
30.7
|
1.0
|
CG
|
B:HIS130
|
4.3
|
27.1
|
1.0
|
OD1
|
B:ASP129
|
4.3
|
32.3
|
1.0
|
OD2
|
B:ASP129
|
4.3
|
44.5
|
1.0
|
HA3
|
B:GLY240
|
4.7
|
32.2
|
1.0
|
CG
|
B:ASP129
|
4.8
|
35.5
|
1.0
|
O
|
B:HOH593
|
5.0
|
39.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 6qk2
Go back to
Iron Binding Sites List in 6qk2
Iron binding site 4 out
of 4 in the R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:22.8
occ:1.00
|
O1
|
B:PLM404
|
1.9
|
28.9
|
1.0
|
OE2
|
B:GLU167
|
2.0
|
24.8
|
1.0
|
OE2
|
B:GLU102
|
2.1
|
21.4
|
1.0
|
ND1
|
B:HIS205
|
2.1
|
21.9
|
1.0
|
OE1
|
B:GLU202
|
2.1
|
24.0
|
1.0
|
OE2
|
B:GLU202
|
2.2
|
22.0
|
1.0
|
CD
|
B:GLU202
|
2.5
|
20.5
|
1.0
|
C1
|
B:PLM404
|
3.0
|
31.0
|
1.0
|
CD
|
B:GLU167
|
3.0
|
28.0
|
1.0
|
CE1
|
B:HIS205
|
3.0
|
21.1
|
1.0
|
CD
|
B:GLU102
|
3.1
|
21.1
|
1.0
|
CG
|
B:HIS205
|
3.2
|
20.2
|
1.0
|
HE1
|
B:HIS205
|
3.2
|
25.3
|
1.0
|
HB3
|
B:HIS205
|
3.3
|
28.4
|
1.0
|
O2
|
B:PLM404
|
3.4
|
33.6
|
1.0
|
HB2
|
B:HIS205
|
3.4
|
28.4
|
1.0
|
OE1
|
B:GLU102
|
3.4
|
20.4
|
1.0
|
HG2
|
B:GLU167
|
3.4
|
30.8
|
1.0
|
CB
|
B:HIS205
|
3.5
|
23.6
|
1.0
|
MN
|
B:MN403
|
3.6
|
18.1
|
1.0
|
HE2
|
B:PHE98
|
3.7
|
27.4
|
1.0
|
CG
|
B:GLU167
|
3.8
|
25.6
|
1.0
|
HA
|
B:GLU202
|
3.9
|
23.1
|
1.0
|
OE1
|
B:GLU167
|
3.9
|
34.3
|
1.0
|
CE2
|
B:PHE98
|
4.0
|
22.8
|
1.0
|
CG
|
B:GLU202
|
4.0
|
23.4
|
1.0
|
HE2
|
B:TYR162
|
4.0
|
26.7
|
1.0
|
HZ
|
B:PHE98
|
4.0
|
30.9
|
1.0
|
CZ
|
B:PHE98
|
4.2
|
25.7
|
1.0
|
NE2
|
B:HIS205
|
4.2
|
19.3
|
1.0
|
CD2
|
B:HIS205
|
4.3
|
19.4
|
1.0
|
HB3
|
B:GLU167
|
4.3
|
25.9
|
1.0
|
CG
|
B:GLU102
|
4.3
|
16.3
|
1.0
|
HG21
|
B:VAL72
|
4.4
|
24.6
|
1.0
|
HE1
|
B:HIS105
|
4.4
|
20.5
|
1.0
|
HG2
|
B:GLU202
|
4.4
|
28.1
|
1.0
|
HG2
|
B:GLU102
|
4.4
|
19.5
|
1.0
|
HG3
|
B:GLU202
|
4.4
|
28.1
|
1.0
|
C2
|
B:PLM404
|
4.5
|
38.1
|
1.0
|
HG3
|
B:GLU167
|
4.5
|
30.8
|
1.0
|
HG3
|
B:GLU102
|
4.6
|
19.5
|
1.0
|
HB3
|
B:GLU202
|
4.6
|
28.0
|
1.0
|
CB
|
B:GLU167
|
4.7
|
21.6
|
1.0
|
CB
|
B:GLU202
|
4.7
|
23.3
|
1.0
|
H22
|
B:PLM404
|
4.7
|
45.8
|
1.0
|
H21
|
B:PLM404
|
4.7
|
45.8
|
1.0
|
CD2
|
B:PHE98
|
4.7
|
21.4
|
1.0
|
CA
|
B:GLU202
|
4.7
|
19.3
|
1.0
|
O
|
B:HOH501
|
4.8
|
25.3
|
1.0
|
CE2
|
B:TYR162
|
4.9
|
22.2
|
1.0
|
CE1
|
B:HIS105
|
5.0
|
17.0
|
1.0
|
HE2
|
B:HIS205
|
5.0
|
23.2
|
1.0
|
HD2
|
B:PHE98
|
5.0
|
25.6
|
1.0
|
ND1
|
B:HIS105
|
5.0
|
17.2
|
1.0
|
CE1
|
B:PHE98
|
5.0
|
23.4
|
1.0
|
|
Reference:
J.J.Griese,
M.Hogbom.
R2-Like Ligand-Binding Oxidase Y175F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor To Be Published.
Page generated: Wed Aug 7 07:53:12 2024
|