Manganese 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:
Manganese Binding Sites:
The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the
R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk2:
Jump to Manganese binding site number:
1;
2;
Manganese binding site 1 out
of 2 in 6qk2
Go back to
Manganese Binding Sites List in 6qk2
Manganese binding site 1 out
of 2 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 Manganese with other atoms in the Mn 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:Mn403
b:18.4
occ:1.00
|
O2
|
A:PLM404
|
1.8
|
36.4
|
1.0
|
OE1
|
A:GLU102
|
2.1
|
19.2
|
1.0
|
OE1
|
A:GLU69
|
2.1
|
21.4
|
1.0
|
ND1
|
A:HIS105
|
2.1
|
17.3
|
1.0
|
O
|
A:HOH502
|
2.2
|
28.0
|
1.0
|
OE2
|
A:GLU202
|
2.2
|
22.5
|
1.0
|
C1
|
A:PLM404
|
2.8
|
30.2
|
1.0
|
CE1
|
A:HIS105
|
3.0
|
20.5
|
1.0
|
HE1
|
A:HIS105
|
3.0
|
24.6
|
1.0
|
CD
|
A:GLU69
|
3.1
|
24.4
|
1.0
|
CD
|
A:GLU102
|
3.2
|
20.0
|
1.0
|
CG
|
A:HIS105
|
3.3
|
15.5
|
1.0
|
CD
|
A:GLU202
|
3.3
|
23.0
|
1.0
|
OE2
|
A:GLU69
|
3.3
|
25.5
|
1.0
|
O1
|
A:PLM404
|
3.4
|
22.5
|
1.0
|
HB2
|
A:HIS105
|
3.5
|
19.9
|
1.0
|
OE2
|
A:GLU102
|
3.6
|
22.6
|
1.0
|
HB3
|
A:HIS105
|
3.6
|
19.9
|
1.0
|
HA
|
A:GLU102
|
3.7
|
18.6
|
1.0
|
FE
|
A:FE2401
|
3.7
|
22.6
|
1.0
|
CB
|
A:HIS105
|
3.7
|
16.6
|
1.0
|
HG21
|
A:VAL72
|
3.8
|
24.9
|
1.0
|
H32
|
A:PLM404
|
3.9
|
39.5
|
1.0
|
H31
|
A:PLM404
|
4.0
|
39.5
|
1.0
|
HG2
|
A:GLU202
|
4.0
|
29.7
|
1.0
|
HG3
|
A:GLU202
|
4.0
|
29.7
|
1.0
|
CG
|
A:GLU202
|
4.1
|
24.7
|
1.0
|
C2
|
A:PLM404
|
4.1
|
44.0
|
1.0
|
NE2
|
A:HIS105
|
4.2
|
17.4
|
1.0
|
OE1
|
A:GLU202
|
4.2
|
24.8
|
1.0
|
HG
|
A:LEU198
|
4.3
|
25.9
|
1.0
|
C3
|
A:PLM404
|
4.3
|
33.0
|
1.0
|
CD2
|
A:HIS105
|
4.3
|
20.3
|
1.0
|
HE1
|
A:HIS205
|
4.3
|
25.7
|
1.0
|
HA
|
A:GLU69
|
4.4
|
21.2
|
1.0
|
CG
|
A:GLU69
|
4.5
|
22.4
|
1.0
|
CG
|
A:GLU102
|
4.5
|
16.0
|
1.0
|
CA
|
A:GLU102
|
4.6
|
15.5
|
1.0
|
HG23
|
A:VAL72
|
4.6
|
24.9
|
1.0
|
HD23
|
A:LEU198
|
4.6
|
25.5
|
1.0
|
CG2
|
A:VAL72
|
4.6
|
20.7
|
1.0
|
HB3
|
A:GLU102
|
4.6
|
20.8
|
1.0
|
HB3
|
A:GLU69
|
4.7
|
23.1
|
1.0
|
H22
|
A:PLM404
|
4.8
|
52.9
|
1.0
|
CB
|
A:GLU102
|
4.8
|
17.3
|
1.0
|
HG22
|
A:VAL72
|
4.8
|
24.9
|
1.0
|
HZ
|
A:PHE175
|
4.8
|
26.8
|
1.0
|
HG3
|
A:GLU69
|
4.8
|
26.8
|
1.0
|
H21
|
A:PLM404
|
4.8
|
52.9
|
1.0
|
HE2
|
A:HIS105
|
4.9
|
20.8
|
1.0
|
CE1
|
A:HIS205
|
4.9
|
21.4
|
1.0
|
ND1
|
A:HIS205
|
4.9
|
20.8
|
1.0
|
HG2
|
A:GLU102
|
4.9
|
19.2
|
1.0
|
CB
|
A:GLU69
|
5.0
|
19.2
|
1.0
|
|
Manganese binding site 2 out
of 2 in 6qk2
Go back to
Manganese Binding Sites List in 6qk2
Manganese binding site 2 out
of 2 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 Manganese with other atoms in the Mn 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
|
B:Mn403
b:18.1
occ:1.00
|
O2
|
B:PLM404
|
1.8
|
33.6
|
1.0
|
OE1
|
B:GLU102
|
2.1
|
20.4
|
1.0
|
OE1
|
B:GLU69
|
2.1
|
21.4
|
1.0
|
ND1
|
B:HIS105
|
2.2
|
17.2
|
1.0
|
O
|
B:HOH501
|
2.2
|
25.3
|
1.0
|
OE2
|
B:GLU202
|
2.2
|
22.0
|
1.0
|
C1
|
B:PLM404
|
2.9
|
31.0
|
1.0
|
CE1
|
B:HIS105
|
3.0
|
17.0
|
1.0
|
CD
|
B:GLU69
|
3.1
|
24.7
|
1.0
|
HE1
|
B:HIS105
|
3.1
|
20.5
|
1.0
|
CD
|
B:GLU102
|
3.2
|
21.1
|
1.0
|
CG
|
B:HIS105
|
3.3
|
15.4
|
1.0
|
OE2
|
B:GLU69
|
3.3
|
24.3
|
1.0
|
CD
|
B:GLU202
|
3.3
|
20.5
|
1.0
|
O1
|
B:PLM404
|
3.5
|
28.9
|
1.0
|
HB2
|
B:HIS105
|
3.5
|
19.4
|
1.0
|
HB3
|
B:HIS105
|
3.5
|
19.4
|
1.0
|
OE2
|
B:GLU102
|
3.5
|
21.4
|
1.0
|
FE
|
B:FE2402
|
3.6
|
22.8
|
1.0
|
CB
|
B:HIS105
|
3.7
|
16.1
|
1.0
|
HA
|
B:GLU102
|
3.7
|
19.8
|
1.0
|
HG21
|
B:VAL72
|
3.8
|
24.6
|
1.0
|
H31
|
B:PLM404
|
3.9
|
37.9
|
1.0
|
HG2
|
B:GLU202
|
4.0
|
28.1
|
1.0
|
HG3
|
B:GLU202
|
4.1
|
28.1
|
1.0
|
CG
|
B:GLU202
|
4.1
|
23.4
|
1.0
|
C2
|
B:PLM404
|
4.2
|
38.1
|
1.0
|
NE2
|
B:HIS105
|
4.2
|
18.3
|
1.0
|
HG
|
B:LEU198
|
4.2
|
22.0
|
1.0
|
OE1
|
B:GLU202
|
4.2
|
24.0
|
1.0
|
HE1
|
B:HIS205
|
4.3
|
25.3
|
1.0
|
H32
|
B:PLM404
|
4.3
|
37.9
|
1.0
|
CD2
|
B:HIS105
|
4.3
|
17.1
|
1.0
|
HA
|
B:GLU69
|
4.4
|
20.5
|
1.0
|
C3
|
B:PLM404
|
4.4
|
31.5
|
1.0
|
CG
|
B:GLU69
|
4.5
|
19.9
|
1.0
|
CG
|
B:GLU102
|
4.5
|
16.3
|
1.0
|
HG23
|
B:VAL72
|
4.5
|
24.6
|
1.0
|
CG2
|
B:VAL72
|
4.6
|
20.5
|
1.0
|
CA
|
B:GLU102
|
4.6
|
16.5
|
1.0
|
HB3
|
B:GLU69
|
4.6
|
24.5
|
1.0
|
HB3
|
B:GLU102
|
4.7
|
21.2
|
1.0
|
HD23
|
B:LEU198
|
4.7
|
26.3
|
1.0
|
CB
|
B:GLU102
|
4.8
|
17.7
|
1.0
|
HG22
|
B:VAL72
|
4.8
|
24.6
|
1.0
|
H21
|
B:PLM404
|
4.8
|
45.8
|
1.0
|
CE1
|
B:HIS205
|
4.8
|
21.1
|
1.0
|
H22
|
B:PLM404
|
4.8
|
45.8
|
1.0
|
ND1
|
B:HIS205
|
4.9
|
21.9
|
1.0
|
HG3
|
B:GLU69
|
4.9
|
23.9
|
1.0
|
HZ
|
B:PHE175
|
4.9
|
26.2
|
1.0
|
CB
|
B:GLU69
|
4.9
|
20.4
|
1.0
|
HG2
|
B:GLU102
|
4.9
|
19.5
|
1.0
|
HE2
|
B:HIS105
|
4.9
|
22.0
|
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: Sun Oct 6 06:01:06 2024
|