Calcium in PDB 6muj: Formylglycine Generating Enzyme Bound to Copper
Enzymatic activity of Formylglycine Generating Enzyme Bound to Copper
All present enzymatic activity of Formylglycine Generating Enzyme Bound to Copper:
1.8.3.7;
Protein crystallography data
The structure of Formylglycine Generating Enzyme Bound to Copper, PDB code: 6muj
was solved by
J.Lafrance-Vanasse,
M.J.Appel,
C.-L.Tsai,
C.Bertozzi,
J.A.Tainer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.74 /
2.25
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
140.008,
140.008,
217.508,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.2 /
24.6
|
Other elements in 6muj:
The structure of Formylglycine Generating Enzyme Bound to Copper also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Formylglycine Generating Enzyme Bound to Copper
(pdb code 6muj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Formylglycine Generating Enzyme Bound to Copper, PDB code: 6muj:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 6muj
Go back to
Calcium Binding Sites List in 6muj
Calcium binding site 1 out
of 5 in the Formylglycine Generating Enzyme Bound to Copper
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:43.4
occ:1.00
|
O
|
A:ILE195
|
2.3
|
48.1
|
1.0
|
OD1
|
A:ASP208
|
2.3
|
47.8
|
1.0
|
O
|
A:HOH623
|
2.3
|
50.0
|
1.0
|
O
|
A:HIS210
|
2.3
|
43.6
|
1.0
|
OD1
|
A:ASN194
|
2.3
|
43.3
|
1.0
|
O
|
A:HOH634
|
2.4
|
46.0
|
1.0
|
OD2
|
A:ASP208
|
2.4
|
46.1
|
1.0
|
CG
|
A:ASP208
|
2.7
|
50.6
|
1.0
|
C
|
A:ILE195
|
3.5
|
45.6
|
1.0
|
C
|
A:HIS210
|
3.5
|
45.8
|
1.0
|
CG
|
A:ASN194
|
3.6
|
43.2
|
1.0
|
N
|
A:ILE195
|
3.9
|
39.9
|
1.0
|
OE1
|
A:GLN197
|
4.2
|
53.0
|
1.0
|
CB
|
A:ASP208
|
4.2
|
47.7
|
1.0
|
CA
|
A:HIS210
|
4.2
|
44.5
|
1.0
|
N
|
A:HIS210
|
4.3
|
46.2
|
1.0
|
C
|
A:ASN194
|
4.3
|
42.9
|
1.0
|
CA
|
A:ILE195
|
4.3
|
37.9
|
1.0
|
CB
|
A:HIS210
|
4.3
|
48.6
|
1.0
|
CA
|
A:ASN194
|
4.4
|
42.5
|
1.0
|
O
|
A:LEU211
|
4.4
|
44.5
|
1.0
|
ND2
|
A:ASN194
|
4.4
|
43.1
|
1.0
|
N
|
A:TRP196
|
4.5
|
45.6
|
1.0
|
CB
|
A:ASN194
|
4.5
|
40.1
|
1.0
|
N
|
A:LEU211
|
4.6
|
45.0
|
1.0
|
ND2
|
A:ASN204
|
4.6
|
55.7
|
1.0
|
OD1
|
A:ASN204
|
4.6
|
57.6
|
1.0
|
O
|
A:TYR270
|
4.6
|
43.7
|
1.0
|
CA
|
A:TRP196
|
4.6
|
49.6
|
1.0
|
NE2
|
A:GLN197
|
4.7
|
50.5
|
1.0
|
CA
|
A:LEU211
|
4.8
|
47.6
|
1.0
|
CB
|
A:TYR270
|
4.8
|
43.0
|
1.0
|
CD
|
A:GLN197
|
4.8
|
50.9
|
1.0
|
C
|
A:LEU211
|
4.8
|
51.3
|
1.0
|
O
|
A:ASN194
|
5.0
|
43.9
|
1.0
|
|
Calcium binding site 2 out
of 5 in 6muj
Go back to
Calcium Binding Sites List in 6muj
Calcium binding site 2 out
of 5 in the Formylglycine Generating Enzyme Bound to Copper
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:41.2
occ:1.00
|
OD1
|
B:ASN194
|
2.3
|
34.4
|
1.0
|
O
|
B:ILE195
|
2.3
|
49.3
|
1.0
|
O
|
B:HOH631
|
2.4
|
42.4
|
1.0
|
O
|
B:HOH629
|
2.4
|
43.5
|
1.0
|
OD1
|
B:ASP208
|
2.4
|
43.0
|
1.0
|
O
|
B:HIS210
|
2.4
|
42.7
|
1.0
|
OD2
|
B:ASP208
|
2.5
|
47.9
|
1.0
|
CG
|
B:ASP208
|
2.8
|
49.2
|
1.0
|
C
|
B:ILE195
|
3.5
|
43.8
|
1.0
|
CG
|
B:ASN194
|
3.5
|
39.8
|
1.0
|
C
|
B:HIS210
|
3.6
|
44.1
|
1.0
|
N
|
B:ILE195
|
3.7
|
39.9
|
1.0
|
C
|
B:ASN194
|
4.1
|
37.9
|
1.0
|
CA
|
B:ILE195
|
4.2
|
43.0
|
1.0
|
CB
|
B:ASP208
|
4.3
|
46.4
|
1.0
|
CA
|
B:ASN194
|
4.3
|
38.7
|
1.0
|
OE1
|
B:GLN197
|
4.3
|
49.6
|
1.0
|
ND2
|
B:ASN194
|
4.4
|
35.7
|
1.0
|
O
|
B:TYR270
|
4.4
|
42.0
|
1.0
|
N
|
B:HIS210
|
4.4
|
47.7
|
1.0
|
CA
|
B:HIS210
|
4.4
|
43.2
|
1.0
|
CB
|
B:ASN194
|
4.4
|
40.5
|
1.0
|
N
|
B:TRP196
|
4.5
|
44.9
|
1.0
|
NE2
|
B:GLN197
|
4.5
|
46.8
|
1.0
|
CB
|
B:HIS210
|
4.6
|
45.3
|
1.0
|
CA
|
B:TRP196
|
4.6
|
46.0
|
1.0
|
OD1
|
B:ASN204
|
4.6
|
50.4
|
1.0
|
N
|
B:LEU211
|
4.6
|
44.0
|
1.0
|
O
|
B:LEU211
|
4.7
|
44.8
|
1.0
|
ND2
|
B:ASN204
|
4.7
|
50.0
|
1.0
|
CB
|
B:TYR270
|
4.7
|
42.8
|
1.0
|
CA
|
B:LEU211
|
4.7
|
44.5
|
1.0
|
CD
|
B:GLN197
|
4.8
|
51.6
|
1.0
|
C
|
B:LEU211
|
4.8
|
43.0
|
1.0
|
O
|
B:ASN194
|
4.9
|
37.5
|
1.0
|
|
Calcium binding site 3 out
of 5 in 6muj
Go back to
Calcium Binding Sites List in 6muj
Calcium binding site 3 out
of 5 in the Formylglycine Generating Enzyme Bound to Copper
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca502
b:40.8
occ:1.00
|
O
|
C:ILE195
|
2.2
|
37.2
|
1.0
|
OD1
|
C:ASN194
|
2.3
|
39.1
|
1.0
|
OD1
|
C:ASP208
|
2.4
|
36.5
|
1.0
|
OD2
|
C:ASP208
|
2.4
|
41.4
|
1.0
|
O
|
C:HOH649
|
2.4
|
38.8
|
1.0
|
O
|
C:HOH623
|
2.4
|
37.5
|
1.0
|
O
|
C:HIS210
|
2.5
|
41.2
|
1.0
|
CG
|
C:ASP208
|
2.8
|
39.0
|
1.0
|
C
|
C:ILE195
|
3.4
|
40.0
|
1.0
|
CG
|
C:ASN194
|
3.5
|
42.9
|
1.0
|
N
|
C:ILE195
|
3.6
|
34.0
|
1.0
|
C
|
C:HIS210
|
3.7
|
37.9
|
1.0
|
C
|
C:ASN194
|
4.0
|
39.1
|
1.0
|
CA
|
C:ILE195
|
4.1
|
35.2
|
1.0
|
CA
|
C:ASN194
|
4.2
|
39.9
|
1.0
|
OE1
|
C:GLN197
|
4.3
|
41.7
|
1.0
|
CB
|
C:ASP208
|
4.3
|
41.0
|
1.0
|
N
|
C:HIS210
|
4.4
|
42.1
|
1.0
|
N
|
C:TRP196
|
4.4
|
40.4
|
1.0
|
ND2
|
C:ASN194
|
4.4
|
41.0
|
1.0
|
CA
|
C:HIS210
|
4.4
|
39.7
|
1.0
|
CB
|
C:ASN194
|
4.4
|
32.8
|
1.0
|
NE2
|
C:GLN197
|
4.5
|
39.6
|
1.0
|
ND2
|
C:ASN204
|
4.5
|
39.0
|
1.0
|
CB
|
C:HIS210
|
4.6
|
38.6
|
1.0
|
OD1
|
C:ASN204
|
4.6
|
34.7
|
1.0
|
O
|
C:TYR270
|
4.6
|
39.0
|
1.0
|
CA
|
C:TRP196
|
4.6
|
39.1
|
1.0
|
O
|
C:LEU211
|
4.7
|
34.9
|
1.0
|
N
|
C:LEU211
|
4.7
|
39.9
|
1.0
|
CD
|
C:GLN197
|
4.7
|
42.9
|
1.0
|
O
|
C:ASN194
|
4.8
|
40.8
|
1.0
|
CB
|
C:TYR270
|
4.8
|
40.0
|
1.0
|
CA
|
C:LEU211
|
4.9
|
37.2
|
1.0
|
|
Calcium binding site 4 out
of 5 in 6muj
Go back to
Calcium Binding Sites List in 6muj
Calcium binding site 4 out
of 5 in the Formylglycine Generating Enzyme Bound to Copper
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca403
b:50.8
occ:1.00
|
O
|
D:ILE195
|
2.3
|
43.0
|
1.0
|
O
|
D:HOH545
|
2.3
|
43.5
|
1.0
|
O
|
D:HIS210
|
2.4
|
53.8
|
1.0
|
OD1
|
D:ASN194
|
2.4
|
52.5
|
1.0
|
OD1
|
D:ASP208
|
2.4
|
47.5
|
1.0
|
OD2
|
D:ASP208
|
2.5
|
50.0
|
1.0
|
O
|
D:HOH536
|
2.5
|
51.2
|
1.0
|
CG
|
D:ASP208
|
2.8
|
49.0
|
1.0
|
C
|
D:ILE195
|
3.5
|
48.5
|
1.0
|
C
|
D:HIS210
|
3.5
|
52.9
|
1.0
|
CG
|
D:ASN194
|
3.6
|
45.4
|
1.0
|
N
|
D:ILE195
|
3.9
|
38.5
|
1.0
|
N
|
D:HIS210
|
4.1
|
50.0
|
1.0
|
C
|
D:ASN194
|
4.1
|
44.1
|
1.0
|
CA
|
D:HIS210
|
4.1
|
52.2
|
1.0
|
CA
|
D:ASN194
|
4.3
|
49.7
|
1.0
|
CA
|
D:ILE195
|
4.3
|
50.5
|
1.0
|
CB
|
D:HIS210
|
4.3
|
52.0
|
1.0
|
OE1
|
D:GLN197
|
4.3
|
53.8
|
1.0
|
CB
|
D:ASP208
|
4.3
|
49.7
|
1.0
|
N
|
D:TRP196
|
4.5
|
46.1
|
1.0
|
ND2
|
D:ASN194
|
4.5
|
40.4
|
1.0
|
CB
|
D:ASN194
|
4.5
|
45.0
|
1.0
|
N
|
D:LEU211
|
4.6
|
48.1
|
1.0
|
O
|
D:LEU211
|
4.6
|
43.9
|
1.0
|
OD1
|
D:ASN204
|
4.6
|
46.9
|
1.0
|
ND2
|
D:ASN204
|
4.6
|
54.8
|
1.0
|
CA
|
D:TRP196
|
4.6
|
49.7
|
1.0
|
NE2
|
D:GLN197
|
4.6
|
52.2
|
1.0
|
O
|
D:TYR270
|
4.6
|
46.3
|
1.0
|
CB
|
D:TYR270
|
4.7
|
45.6
|
1.0
|
O
|
D:ASN194
|
4.8
|
46.7
|
1.0
|
CA
|
D:LEU211
|
4.8
|
49.2
|
1.0
|
CD
|
D:GLN197
|
4.9
|
54.4
|
1.0
|
C
|
D:LEU211
|
4.9
|
48.0
|
1.0
|
|
Calcium binding site 5 out
of 5 in 6muj
Go back to
Calcium Binding Sites List in 6muj
Calcium binding site 5 out
of 5 in the Formylglycine Generating Enzyme Bound to Copper
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca401
b:34.8
occ:1.00
|
O
|
E:ILE195
|
2.2
|
36.4
|
1.0
|
O
|
E:HOH560
|
2.3
|
33.2
|
1.0
|
O
|
E:HOH539
|
2.3
|
37.0
|
1.0
|
OD1
|
E:ASN194
|
2.3
|
35.7
|
1.0
|
O
|
E:HIS210
|
2.3
|
38.8
|
1.0
|
OD2
|
E:ASP208
|
2.5
|
37.1
|
1.0
|
OD1
|
E:ASP208
|
2.5
|
38.3
|
1.0
|
CG
|
E:ASP208
|
2.8
|
41.6
|
1.0
|
C
|
E:ILE195
|
3.4
|
36.0
|
1.0
|
C
|
E:HIS210
|
3.5
|
39.1
|
1.0
|
CG
|
E:ASN194
|
3.5
|
39.2
|
1.0
|
N
|
E:ILE195
|
3.7
|
30.6
|
1.0
|
C
|
E:ASN194
|
4.1
|
35.3
|
1.0
|
CA
|
E:ILE195
|
4.2
|
31.7
|
1.0
|
CA
|
E:ASN194
|
4.2
|
34.8
|
1.0
|
NE2
|
E:GLN197
|
4.3
|
40.0
|
1.0
|
OE1
|
E:GLN197
|
4.3
|
39.0
|
1.0
|
CA
|
E:HIS210
|
4.3
|
37.0
|
1.0
|
CB
|
E:ASP208
|
4.4
|
37.4
|
1.0
|
N
|
E:HIS210
|
4.4
|
38.4
|
1.0
|
ND2
|
E:ASN194
|
4.4
|
31.1
|
1.0
|
N
|
E:TRP196
|
4.4
|
32.9
|
1.0
|
CB
|
E:ASN194
|
4.5
|
33.0
|
1.0
|
N
|
E:LEU211
|
4.5
|
37.7
|
1.0
|
CB
|
E:HIS210
|
4.5
|
37.2
|
1.0
|
O
|
E:TYR270
|
4.5
|
32.9
|
1.0
|
CA
|
E:LEU211
|
4.6
|
28.9
|
1.0
|
CA
|
E:TRP196
|
4.6
|
37.3
|
1.0
|
OD1
|
E:ASN204
|
4.6
|
35.2
|
1.0
|
ND2
|
E:ASN204
|
4.7
|
35.5
|
1.0
|
O
|
E:LEU211
|
4.7
|
30.2
|
1.0
|
CB
|
E:TYR270
|
4.7
|
35.3
|
1.0
|
CD
|
E:GLN197
|
4.7
|
38.1
|
1.0
|
O
|
E:ASN194
|
4.8
|
36.9
|
1.0
|
C
|
E:LEU211
|
4.9
|
30.0
|
1.0
|
CA
|
E:ALA206
|
5.0
|
39.8
|
1.0
|
|
Reference:
M.J.Appel,
K.K.Meier,
J.Lafrance-Vanasse,
H.Lim,
C.L.Tsai,
B.Hedman,
K.O.Hodgson,
J.A.Tainer,
E.I.Solomon,
C.R.Bertozzi.
Formylglycine-Generating Enzyme Binds Substrate Directly at A Mononuclear Cu(I) Center to Initiate O2ACTIVATION. Proc. Natl. Acad. Sci. V. 116 5370 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30824597
DOI: 10.1073/PNAS.1818274116
Page generated: Tue Jul 16 11:27:48 2024
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