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Copper in PDB 6xto: Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex

Enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex

All present enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex:
1.8.3.7;

Protein crystallography data

The structure of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex, PDB code: 6xto was solved by F.Leisinger, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.94 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.216, 71.925, 76.476, 90, 90, 90
R / Rfree (%) 18.3 / 19.7

Other elements in 6xto:

The structure of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex (pdb code 6xto). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex, PDB code: 6xto:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6xto

Go back to Copper Binding Sites List in 6xto
Copper binding site 1 out of 2 in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:11.2
occ:0.45
 CU A:CU1401 0.0 11.2 0.5
CU A:CU1401 1.2 10.9 0.6
SG A:CYS269 2.0 14.2 1.0
SG A:CYS274 2.1 10.6 0.5
SG A:CYS274 2.1 14.2 0.5
O A:CYS274 2.8 14.9 0.5
CB A:CYS269 2.9 12.8 1.0
SG C:CYS7 3.3 14.1 0.6
CB A:CYS274 3.4 13.2 0.5
CB A:CYS274 3.4 13.3 0.5
N A:ARG276 3.5 15.0 1.0
CB A:ARG276 3.5 14.3 1.0
CA A:CYS269 3.5 10.6 1.0
C A:CYS274 3.6 15.0 0.5
N A:NO404 3.6 11.2 1.0
CZ2 A:TRP228 3.9 8.9 1.0
CA A:ARG276 3.9 16.9 1.0
CA A:CYS274 4.1 14.6 0.5
O A:NO404 4.2 19.8 1.0
N A:ASN275 4.2 17.4 0.5
CG A:ARG276 4.3 14.6 1.0
C A:ARG276 4.4 15.1 1.0
N A:CYS269 4.4 10.0 1.0
C A:CYS274 4.5 13.4 0.5
CA A:CYS274 4.5 14.3 0.5
N A:ASN275 4.5 17.4 0.5
CB C:CYS7 4.6 10.2 0.6
O A:HOH505 4.6 18.3 1.0
C A:ASN275 4.6 18.8 0.5
N A:TYR277 4.6 16.2 1.0
C A:CYS269 4.6 10.4 1.0
CH2 A:TRP228 4.7 9.2 1.0
CE2 A:TRP228 4.7 8.1 1.0
CA A:GLY265 4.7 8.6 1.0
C A:ASN275 4.7 18.8 0.5
N A:HIS270 4.7 13.4 1.0
NE1 A:TRP228 4.8 8.5 1.0
CD A:ARG276 4.8 12.9 1.0
CA A:ASN275 4.8 18.8 0.5
OH A:TYR273 4.9 13.0 0.5
O A:ARG276 4.9 18.8 1.0

Copper binding site 2 out of 2 in 6xto

Go back to Copper Binding Sites List in 6xto
Copper binding site 2 out of 2 in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:No Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:10.9
occ:0.55
 CU A:CU1401 0.0 10.9 0.6
CU A:CU1401 1.2 11.2 0.5
SG A:CYS274 2.0 14.2 0.5
SG A:CYS274 2.3 10.6 0.5
SG C:CYS7 2.4 14.1 0.6
SG A:CYS269 2.6 14.2 1.0
N A:NO404 3.0 11.2 1.0
CB A:CYS274 3.2 13.3 0.5
CB A:CYS274 3.2 13.2 0.5
O A:NO404 3.3 19.8 1.0
O A:CYS274 3.5 14.9 0.5
O A:HOH505 3.5 18.3 1.0
CB A:CYS269 3.6 12.8 1.0
CB C:CYS7 3.6 10.2 0.6
CZ2 A:TRP228 3.7 8.9 1.0
CA A:CYS269 3.8 10.6 1.0
C A:CYS274 4.1 15.0 0.5
OH A:TYR273 4.2 13.0 0.5
CB A:ARG276 4.2 14.3 1.0
CA A:CYS274 4.3 14.6 0.5
NE1 A:TRP228 4.3 8.5 1.0
CE2 A:TRP228 4.4 8.1 1.0
N A:CYS269 4.5 10.0 1.0
CZ A:TYR273 4.5 10.9 0.5
N A:ARG276 4.5 15.0 1.0
CA A:CYS274 4.6 14.3 0.5
CA C:CYS7 4.7 13.8 0.6
CE1 A:TYR273 4.7 12.8 0.5
CH2 A:TRP228 4.8 9.2 1.0
CG A:ARG276 4.8 14.6 1.0
CA A:ARG276 4.9 16.9 1.0
C A:CYS274 4.9 13.4 0.5
N A:ASN275 4.9 17.4 0.5
CD A:ARG276 5.0 12.9 1.0

Reference:

F.Leisinger, D.A.Miarzlou, F.P.Seebeck. Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme To Be Published.
Page generated: Wed Mar 3 13:07:52 2021

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