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:

Copper (Cu) 20 atoms

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

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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

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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

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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

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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

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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: Sat Dec 12 07:12:02 2020

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