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Copper 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 (Ca) 5 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Copper atom in the Formylglycine Generating Enzyme Bound to Copper (pdb code 6muj). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 20 binding sites of Copper where determined in the Formylglycine Generating Enzyme Bound to Copper, PDB code: 6muj:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 20 in 6muj

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Copper binding site 1 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:51.6
occ:0.84
SG A:CYS272 2.1 48.9 1.0
SG A:CYS277 2.1 53.8 1.0
O A:CYS277 2.8 54.3 1.0
CB A:CYS277 3.1 54.0 1.0
CB A:CYS272 3.1 43.8 1.0
C A:CYS277 3.4 57.3 1.0
O A:HOH680 3.5 46.8 1.0
N A:ARG279 3.6 49.4 1.0
CA A:CYS272 3.6 49.9 1.0
CZ2 A:TRP234 3.9 43.9 1.0
CA A:CYS277 3.9 54.9 1.0
CB A:ARG279 3.9 48.0 1.0
CA A:ARG279 4.2 48.2 1.0
N A:ASN278 4.3 53.9 1.0
CH2 A:TRP234 4.4 46.2 1.0
CG A:ARG279 4.5 51.3 1.0
N A:CYS272 4.5 44.1 1.0
C A:ASN278 4.6 49.3 1.0
CA A:ASN278 4.7 47.9 1.0
C A:ARG279 4.7 47.1 1.0
C A:CYS272 4.7 49.4 1.0
CA A:GLY268 4.8 44.6 1.0
N A:HIS273 4.8 52.3 1.0
CE2 A:TRP234 4.8 42.1 1.0
N A:TYR280 4.9 48.8 1.0
CD A:ARG279 5.0 48.5 1.0

Copper binding site 2 out of 20 in 6muj

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Copper binding site 2 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:68.5
occ:0.64
ND1 A:HIS210 2.4 44.2 1.0
O A:HOH681 3.2 44.0 1.0
CE1 A:HIS210 3.2 44.9 1.0
CG A:HIS210 3.4 46.9 1.0
O A:THR213 3.5 46.8 1.0
CB A:HIS210 3.8 48.6 1.0
CA A:HIS210 4.2 44.5 1.0
CA A:ALA214 4.3 41.0 1.0
NE2 A:HIS210 4.4 45.8 1.0
CE1 A:HIS139 4.4 46.5 1.0
CD A:PRO215 4.4 42.9 1.0
O A:GLY209 4.4 47.4 1.0
C A:THR213 4.5 44.1 1.0
CD2 A:HIS210 4.5 46.2 1.0
N A:ALA214 4.8 37.4 1.0
CB A:ALA214 4.9 43.4 1.0
NE2 A:HIS139 4.9 41.6 1.0

Copper binding site 3 out of 20 in 6muj

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Copper binding site 3 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:67.7
occ:0.60
ND1 A:HIS81 2.2 51.0 1.0
CG A:HIS81 3.1 54.5 1.0
CE1 A:HIS81 3.2 54.5 1.0
CB A:HIS81 3.4 52.9 1.0
CA A:HIS81 3.9 53.8 1.0
OG1 A:THR79 4.2 64.0 1.0
CD2 A:HIS81 4.3 53.5 1.0
NE2 A:HIS81 4.3 54.1 1.0
CZ A:PHE75 4.4 49.7 1.0
CB A:ALA151 4.6 53.3 1.0
N A:HIS81 4.7 53.9 1.0
CE1 A:PHE75 4.8 52.6 1.0
CB A:THR79 4.9 59.0 1.0

Copper binding site 4 out of 20 in 6muj

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Copper binding site 4 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu505

b:0.8
occ:1.00
NE2 A:HIS95 2.4 59.5 1.0
ND1 A:HIS202 2.8 73.4 1.0
O A:HOH689 3.2 59.2 1.0
CE1 A:HIS95 3.3 60.2 1.0
CA A:HIS202 3.4 58.5 1.0
CD2 A:HIS95 3.5 59.2 1.0
CG A:HIS202 3.6 72.9 1.0
O A:PRO201 3.7 56.6 1.0
CE1 A:HIS202 3.7 73.7 1.0
CD2 A:LEU96 3.7 53.5 1.0
CB A:HIS202 3.8 65.8 1.0
C A:PRO201 4.2 58.7 1.0
N A:HIS202 4.2 61.4 1.0
O A:HIS202 4.2 63.5 1.0
C A:HIS202 4.3 61.2 1.0
ND1 A:HIS95 4.5 61.0 1.0
CG A:LEU96 4.5 51.0 1.0
CG A:HIS95 4.6 59.5 1.0
CD2 A:HIS202 4.7 76.0 1.0
NE2 A:HIS202 4.7 71.7 1.0

Copper binding site 5 out of 20 in 6muj

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Copper binding site 5 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:52.8
occ:0.97
SG B:CYS272 2.2 47.0 1.0
SG B:CYS277 2.2 53.1 1.0
O B:CYS277 2.9 48.3 1.0
CB B:CYS272 3.2 44.1 1.0
CB B:CYS277 3.3 48.5 1.0
C B:CYS277 3.5 52.9 1.0
N B:ARG279 3.6 46.4 1.0
O B:HOH670 3.7 43.7 1.0
CA B:CYS272 3.7 49.2 1.0
CZ2 B:TRP234 3.8 46.0 1.0
CB B:ARG279 3.9 41.6 1.0
CA B:CYS277 4.1 49.3 1.0
CA B:ARG279 4.2 43.4 1.0
N B:ASN278 4.4 51.8 1.0
CH2 B:TRP234 4.4 39.8 1.0
N B:CYS272 4.6 42.8 1.0
C B:ASN278 4.6 50.0 1.0
CA B:GLY268 4.6 44.8 1.0
C B:ARG279 4.6 43.9 1.0
CG B:ARG279 4.7 50.8 1.0
CA B:ASN278 4.7 46.7 1.0
CE2 B:TRP234 4.7 43.6 1.0
C B:CYS272 4.8 47.3 1.0
N B:HIS273 4.8 47.5 1.0
N B:TYR280 4.8 45.7 1.0
CD B:ARG279 5.0 57.9 1.0
CD1 B:TYR280 5.0 45.8 1.0
OH B:TYR276 5.0 53.0 1.0

Copper binding site 6 out of 20 in 6muj

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Copper binding site 6 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu504

b:70.9
occ:0.76
ND1 B:HIS210 2.3 48.5 1.0
O B:HOH705 3.0 46.6 1.0
CG B:HIS210 3.3 48.5 1.0
CE1 B:HIS210 3.3 44.3 1.0
O B:THR213 3.4 40.8 1.0
CB B:HIS210 3.5 45.3 1.0
O B:HOH694 4.0 41.6 1.0
CA B:HIS210 4.1 43.2 1.0
CA B:ALA214 4.2 40.4 1.0
CE1 B:HIS139 4.3 43.0 1.0
C B:THR213 4.3 40.3 1.0
NE2 B:HIS210 4.4 45.1 1.0
CD2 B:HIS210 4.4 42.0 1.0
O B:GLY209 4.5 50.0 1.0
N B:ALA214 4.6 40.0 1.0
CD B:PRO215 4.8 38.4 1.0
CB B:ALA214 4.9 43.5 1.0
O B:SER212 4.9 42.1 1.0
NE2 B:HIS139 4.9 41.5 1.0
N B:LEU211 5.0 44.0 1.0

Copper binding site 7 out of 20 in 6muj

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Copper binding site 7 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu505

b:0.8
occ:1.00
NE2 B:HIS95 2.5 60.9 1.0
ND1 B:HIS202 2.7 78.5 1.0
CE1 B:HIS95 3.4 57.7 1.0
CA B:HIS202 3.4 56.9 1.0
CD2 B:HIS95 3.5 62.2 1.0
O B:PRO201 3.5 52.2 1.0
CG B:HIS202 3.6 73.4 1.0
CE1 B:HIS202 3.6 76.5 1.0
CD2 B:LEU96 3.7 58.7 1.0
CB B:HIS202 3.8 60.8 1.0
C B:PRO201 4.1 54.4 1.0
O B:HIS202 4.2 57.8 1.0
N1 A:IMD506 4.2 75.0 1.0
N B:HIS202 4.2 55.6 1.0
C B:HIS202 4.3 58.0 1.0
CG B:LEU96 4.4 56.1 1.0
ND1 B:HIS95 4.5 58.1 1.0
C5 A:IMD506 4.6 68.2 1.0
CG B:HIS95 4.6 56.7 1.0
NE2 B:HIS202 4.7 73.4 1.0
CD2 B:HIS202 4.7 75.1 1.0
CD1 B:LEU96 4.8 53.6 1.0

Copper binding site 8 out of 20 in 6muj

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Copper binding site 8 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu503

b:45.8
occ:0.87
SG C:CYS272 2.1 44.9 1.0
SG C:CYS277 2.1 50.0 1.0
O C:CYS277 2.7 39.0 1.0
CB C:CYS272 3.1 36.1 1.0
CB C:CYS277 3.2 46.6 1.0
C C:CYS277 3.4 42.9 1.0
N C:ARG279 3.5 43.4 1.0
O C:HOH652 3.6 37.9 1.0
CA C:CYS272 3.6 38.0 1.0
CB C:ARG279 3.8 47.8 1.0
CA C:CYS277 3.9 47.5 1.0
CZ2 C:TRP234 4.0 40.6 1.0
CA C:ARG279 4.1 43.7 1.0
N C:ASN278 4.3 45.1 1.0
N C:CYS272 4.4 38.2 1.0
CH2 C:TRP234 4.4 41.9 1.0
CG C:ARG279 4.5 44.6 1.0
C C:ASN278 4.5 42.8 1.0
CA C:ASN278 4.7 43.9 1.0
C C:ARG279 4.7 40.5 1.0
CA C:GLY268 4.8 36.6 1.0
C C:CYS272 4.8 41.7 1.0
CD C:ARG279 4.8 42.1 1.0
N C:TYR280 4.9 39.0 1.0
CE2 C:TRP234 4.9 40.0 1.0
N C:HIS273 5.0 42.8 1.0
O C:HOH716 5.0 45.4 1.0

Copper binding site 9 out of 20 in 6muj

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Copper binding site 9 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu504

b:83.3
occ:0.56
ND1 C:HIS81 2.1 61.2 1.0
O C:HOH729 2.6 62.5 1.0
CE1 C:HIS81 3.0 59.0 1.0
CG C:HIS81 3.1 55.8 1.0
O C:HOH709 3.2 54.1 1.0
CB C:HIS81 3.4 56.2 1.0
CA C:HIS81 3.6 60.6 1.0
NE2 C:HIS81 4.1 56.0 1.0
CD2 C:HIS81 4.2 52.8 1.0
N C:VAL82 4.5 54.8 1.0
N C:HIS81 4.6 60.0 1.0
C C:HIS81 4.6 58.0 1.0
OG1 C:THR79 4.8 53.4 1.0
CZ C:PHE75 4.9 52.1 1.0

Copper binding site 10 out of 20 in 6muj

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Copper binding site 10 out of 20 in the Formylglycine Generating Enzyme Bound to Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Formylglycine Generating Enzyme Bound to Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu505

b:80.0
occ:0.62
NE2 C:HIS210 2.4 49.9 1.0
O A:HOH696 2.8 61.4 1.0
O C:HOH737 3.0 56.2 1.0
O C:HOH670 3.3 52.2 1.0
CE1 C:HIS210 3.3 50.2 1.0
CD2 C:HIS210 3.4 38.8 1.0
O A:GLY135 3.7 60.2 1.0
CB C:SER218 3.9 41.0 1.0
OG C:SER218 4.1 45.3 1.0
ND1 C:HIS210 4.5 44.0 1.0
CG C:HIS210 4.5 41.4 1.0
C A:GLY135 4.6 58.3 1.0
CA C:SER218 4.8 42.7 1.0
O C:ASP208 4.8 41.7 1.0
CA A:GLY135 4.9 50.6 1.0
CZ C:TYR219 5.0 42.8 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: Sun Dec 13 11:24:21 2020

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