Iron in PDB 6qk0: R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
Enzymatic activity of R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
All present enzymatic activity of R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;
Protein crystallography data
The structure of R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk0
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)
|
48.60 /
2.09
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
160.808,
55.963,
98.059,
90.00,
126.23,
90.00
|
R / Rfree (%)
|
20.9 /
26.3
|
Other elements in 6qk0:
The structure of R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor
(pdb code 6qk0). 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk0:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6qk0
Go back to
Iron Binding Sites List in 6qk0
Iron binding site 1 out
of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:45.1
occ:1.00
|
OE2
|
A:GLU167
|
2.0
|
41.0
|
1.0
|
OE2
|
A:GLU202
|
2.2
|
51.5
|
1.0
|
OE2
|
A:GLU102
|
2.2
|
39.7
|
1.0
|
O1
|
A:PLM403
|
2.3
|
49.4
|
1.0
|
ND1
|
A:HIS205
|
2.4
|
36.6
|
1.0
|
OE1
|
A:GLU202
|
2.5
|
50.4
|
1.0
|
CD
|
A:GLU202
|
2.5
|
58.2
|
1.0
|
HG2
|
A:GLU167
|
2.8
|
53.4
|
1.0
|
CD
|
A:GLU167
|
2.9
|
37.2
|
1.0
|
CD
|
A:GLU102
|
3.2
|
39.2
|
1.0
|
CE1
|
A:HIS205
|
3.3
|
39.7
|
1.0
|
CG
|
A:GLU167
|
3.3
|
44.5
|
1.0
|
HE1
|
A:HIS205
|
3.4
|
47.6
|
1.0
|
C1
|
A:PLM403
|
3.4
|
62.0
|
1.0
|
MN
|
A:MN401
|
3.5
|
38.6
|
1.0
|
CG
|
A:HIS205
|
3.5
|
40.6
|
1.0
|
OE1
|
A:GLU102
|
3.5
|
38.6
|
1.0
|
HB2
|
A:HIS205
|
3.6
|
37.1
|
1.0
|
HB3
|
A:HIS205
|
3.7
|
37.1
|
1.0
|
HE2
|
A:PHE98
|
3.8
|
48.6
|
1.0
|
CB
|
A:HIS205
|
3.8
|
30.9
|
1.0
|
OE1
|
A:GLU167
|
3.9
|
41.8
|
1.0
|
HA
|
A:GLU202
|
3.9
|
45.1
|
1.0
|
HE2
|
A:TYR162
|
3.9
|
52.0
|
1.0
|
CG
|
A:GLU202
|
3.9
|
54.3
|
1.0
|
HG3
|
A:GLU167
|
4.0
|
53.4
|
1.0
|
HE1
|
A:HIS105
|
4.0
|
50.0
|
1.0
|
O2
|
A:PLM403
|
4.1
|
67.6
|
1.0
|
HG2
|
A:GLU202
|
4.1
|
65.1
|
1.0
|
HB3
|
A:GLU167
|
4.1
|
40.2
|
1.0
|
HH
|
A:TYR162
|
4.3
|
54.9
|
1.0
|
CE2
|
A:PHE98
|
4.3
|
40.5
|
1.0
|
CB
|
A:GLU167
|
4.4
|
33.5
|
1.0
|
H22
|
A:PLM403
|
4.4
|
66.7
|
1.0
|
NE2
|
A:HIS205
|
4.5
|
36.1
|
1.0
|
C2
|
A:PLM403
|
4.5
|
55.6
|
1.0
|
HB3
|
A:GLU202
|
4.5
|
49.6
|
1.0
|
HG21
|
A:VAL72
|
4.5
|
55.8
|
1.0
|
HG3
|
A:GLU202
|
4.6
|
65.1
|
1.0
|
CG
|
A:GLU102
|
4.6
|
35.2
|
1.0
|
CD2
|
A:HIS205
|
4.6
|
35.5
|
1.0
|
HZ
|
A:PHE98
|
4.6
|
54.2
|
1.0
|
CB
|
A:GLU202
|
4.6
|
41.4
|
1.0
|
CE1
|
A:HIS105
|
4.6
|
41.6
|
1.0
|
ND1
|
A:HIS105
|
4.7
|
36.8
|
1.0
|
H21
|
A:PLM403
|
4.7
|
66.7
|
1.0
|
CA
|
A:GLU202
|
4.7
|
37.6
|
1.0
|
HG2
|
A:GLU102
|
4.7
|
42.2
|
1.0
|
CZ
|
A:PHE98
|
4.8
|
45.1
|
1.0
|
CE2
|
A:TYR162
|
4.8
|
43.4
|
1.0
|
HG3
|
A:GLU102
|
4.8
|
42.2
|
1.0
|
HB2
|
A:GLU167
|
5.0
|
40.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 6qk0
Go back to
Iron Binding Sites List in 6qk0
Iron binding site 2 out
of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe404
b:78.2
occ:1.00
|
NE2
|
A:HIS130
|
2.4
|
61.0
|
1.0
|
CE1
|
A:HIS130
|
3.3
|
59.1
|
1.0
|
CD2
|
A:HIS130
|
3.4
|
52.2
|
1.0
|
HE1
|
A:HIS130
|
3.4
|
70.9
|
1.0
|
HD2
|
A:HIS130
|
3.5
|
62.6
|
1.0
|
OD2
|
A:ASP129
|
3.8
|
70.6
|
1.0
|
ND1
|
A:HIS130
|
4.4
|
53.9
|
1.0
|
OD1
|
A:ASP129
|
4.5
|
57.7
|
1.0
|
CG
|
A:HIS130
|
4.5
|
52.9
|
1.0
|
CG
|
A:ASP129
|
4.6
|
55.4
|
1.0
|
O
|
A:HOH501
|
4.7
|
52.0
|
1.0
|
HA3
|
A:GLY240
|
4.8
|
55.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 6qk0
Go back to
Iron Binding Sites List in 6qk0
Iron binding site 3 out
of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:44.7
occ:0.61
|
HD1
|
B:HIS205
|
1.8
|
44.3
|
1.0
|
OE2
|
B:GLU167
|
1.8
|
43.4
|
1.0
|
OE1
|
B:GLU202
|
2.2
|
59.7
|
1.0
|
OE2
|
B:GLU102
|
2.2
|
58.4
|
1.0
|
CD
|
B:GLU202
|
2.3
|
57.9
|
1.0
|
OE2
|
B:GLU202
|
2.5
|
64.2
|
1.0
|
ND1
|
B:HIS205
|
2.6
|
37.0
|
1.0
|
HG2
|
B:GLU167
|
2.7
|
48.4
|
1.0
|
CD
|
B:GLU167
|
2.7
|
41.0
|
1.0
|
MN
|
B:MN401
|
3.1
|
62.0
|
0.9
|
HG3
|
B:GLU202
|
3.1
|
59.7
|
1.0
|
CG
|
B:GLU167
|
3.2
|
40.4
|
1.0
|
CG
|
B:GLU202
|
3.3
|
49.7
|
1.0
|
HE1
|
B:HIS205
|
3.3
|
46.9
|
1.0
|
CE1
|
B:HIS205
|
3.3
|
39.1
|
1.0
|
CD
|
B:GLU102
|
3.4
|
47.0
|
1.0
|
CG
|
B:HIS205
|
3.7
|
34.8
|
1.0
|
OE1
|
B:GLU167
|
3.8
|
41.6
|
1.0
|
HA
|
B:GLU202
|
3.8
|
48.0
|
1.0
|
HG3
|
B:GLU167
|
3.8
|
48.4
|
1.0
|
HG2
|
B:GLU202
|
3.9
|
59.7
|
1.0
|
HB2
|
B:HIS205
|
3.9
|
39.8
|
1.0
|
HE2
|
B:PHE98
|
4.0
|
50.2
|
1.0
|
HE1
|
B:HIS105
|
4.0
|
55.6
|
1.0
|
HB3
|
B:HIS205
|
4.0
|
39.8
|
1.0
|
OE1
|
B:GLU102
|
4.1
|
62.7
|
1.0
|
CB
|
B:HIS205
|
4.2
|
33.2
|
1.0
|
HB3
|
B:GLU167
|
4.2
|
39.5
|
1.0
|
HZ
|
B:PHE98
|
4.3
|
42.5
|
1.0
|
OH
|
B:TYR162
|
4.3
|
41.7
|
1.0
|
CE2
|
B:PHE98
|
4.3
|
41.8
|
1.0
|
CB
|
B:GLU167
|
4.4
|
32.9
|
1.0
|
HH
|
B:TYR162
|
4.4
|
50.0
|
1.0
|
CB
|
B:GLU202
|
4.5
|
47.0
|
1.0
|
CG
|
B:GLU102
|
4.5
|
51.1
|
1.0
|
ND1
|
B:HIS105
|
4.5
|
49.6
|
1.0
|
HG2
|
B:GLU102
|
4.5
|
61.4
|
1.0
|
CZ
|
B:PHE98
|
4.5
|
35.5
|
1.0
|
CE1
|
B:HIS105
|
4.6
|
46.4
|
1.0
|
NE2
|
B:HIS205
|
4.6
|
38.8
|
1.0
|
CA
|
B:GLU202
|
4.6
|
40.0
|
1.0
|
HG3
|
B:GLU102
|
4.6
|
61.4
|
1.0
|
O1
|
B:PLM403
|
4.8
|
64.5
|
1.0
|
CD2
|
B:HIS205
|
4.8
|
36.1
|
1.0
|
CZ
|
B:TYR162
|
4.8
|
44.8
|
1.0
|
HB2
|
B:GLU167
|
4.9
|
39.5
|
1.0
|
HB2
|
B:GLU202
|
5.0
|
56.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 6qk0
Go back to
Iron Binding Sites List in 6qk0
Iron binding site 4 out
of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe404
b:76.8
occ:0.99
|
NE2
|
B:HIS130
|
2.2
|
66.0
|
1.0
|
O
|
B:HOH532
|
2.6
|
50.5
|
1.0
|
CD2
|
B:HIS130
|
3.0
|
57.4
|
1.0
|
HD2
|
B:HIS130
|
3.1
|
68.9
|
1.0
|
CE1
|
B:HIS130
|
3.3
|
64.3
|
1.0
|
OD2
|
B:ASP129
|
3.4
|
69.4
|
1.0
|
HE1
|
B:HIS130
|
3.5
|
77.2
|
1.0
|
CG
|
B:HIS130
|
4.2
|
63.0
|
1.0
|
ND1
|
B:HIS130
|
4.3
|
66.3
|
1.0
|
CG
|
B:ASP129
|
4.3
|
69.9
|
1.0
|
OD1
|
B:ASP129
|
4.4
|
65.7
|
1.0
|
HA3
|
B:GLY240
|
4.7
|
59.4
|
1.0
|
|
Reference:
J.J.Griese,
M.Hogbom.
R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor To Be Published.
Page generated: Wed Aug 7 07:53:12 2024
|