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Silver in PDB 6xtm: Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 Complex

Enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 Complex

All present enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 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:Ag:S:O2 Complex, PDB code: 6xtm 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) 46.36 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.161, 71.909, 76.769, 90, 90, 90
R / Rfree (%) 16.8 / 18.1

Other elements in 6xtm:

The structure of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 Complex also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Calcium (Ca) 2 atoms

Silver Binding Sites:

The binding sites of Silver atom in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 Complex (pdb code 6xtm). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 2 binding sites of Silver where determined in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 Complex, PDB code: 6xtm:
Jump to Silver binding site number: 1; 2;

Silver binding site 1 out of 2 in 6xtm

Go back to Silver Binding Sites List in 6xtm
Silver 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:Ag:S:O2 Complex


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag407

b:10.0
occ:0.80
AG A:AG407 0.0 10.0 0.8
AG A:AG407 1.1 10.6 0.2
SG A:CYS274 2.0 15.0 0.1
SG C:CYS7 2.4 10.4 0.9
SG A:CYS269 2.5 12.0 1.0
SG A:CYS274 2.5 11.3 0.8
O1 A:OXY401 3.0 9.5 0.7
O2 A:OXY401 3.2 17.7 0.7
CB A:CYS274 3.3 11.2 0.1
CB A:CYS274 3.3 10.1 0.8
CB A:CYS269 3.5 11.8 1.0
O A:HOH505 3.5 14.1 1.0
O A:CYS274 3.5 12.3 0.1
CB C:CYS7 3.6 10.0 0.9
CZ2 A:TRP228 3.7 10.3 1.0
CA A:CYS269 3.8 10.5 1.0
CB A:ARG276 3.9 12.4 1.0
O A:HOH667 4.0 16.0 1.0
NE1 A:TRP228 4.2 9.7 1.0
C A:CYS274 4.3 12.8 0.1
CE2 A:TRP228 4.3 8.7 1.0
CA A:CYS274 4.5 12.9 0.1
N A:CYS269 4.5 10.9 1.0
N A:ARG276 4.5 12.4 1.0
CA A:ARG276 4.6 12.4 1.0
CG A:ARG276 4.7 12.3 1.0
CD A:ARG276 4.7 12.2 1.0
CH2 A:TRP228 4.7 10.2 1.0
CA A:CYS274 4.8 12.4 0.8
CA C:CYS7 4.8 9.9 0.9
C A:ARG276 5.0 14.0 1.0

Silver binding site 2 out of 2 in 6xtm

Go back to Silver Binding Sites List in 6xtm
Silver 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:Ag:S:O2 Complex


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag:S:O2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag407

b:10.6
occ:0.19
AG A:AG407 0.0 10.6 0.2
AG A:AG407 1.1 10.0 0.8
SG A:CYS269 2.0 12.0 1.0
SG A:CYS274 2.1 15.0 0.1
SG A:CYS274 2.3 11.3 0.8
CB A:CYS269 2.8 11.8 1.0
O A:CYS274 2.9 12.3 0.1
CB A:ARG276 3.3 12.4 1.0
SG C:CYS7 3.3 10.4 0.9
CB A:CYS274 3.4 10.1 0.8
CB A:CYS274 3.5 11.2 0.1
CA A:CYS269 3.5 10.5 1.0
O1 A:OXY401 3.6 9.5 0.7
N A:ARG276 3.6 12.4 1.0
CA A:ARG276 3.7 12.4 1.0
C A:CYS274 3.8 12.8 0.1
CZ2 A:TRP228 3.8 10.3 1.0
C A:ARG276 4.0 14.0 1.0
O2 A:OXY401 4.0 17.7 0.7
O A:ARG276 4.3 13.8 1.0
CG A:ARG276 4.3 12.3 1.0
CA A:CYS274 4.3 12.9 0.1
N A:CYS269 4.4 10.9 1.0
N A:TYR277 4.5 13.2 1.0
O A:HOH505 4.5 14.1 1.0
CB C:CYS7 4.5 10.0 0.9
CE2 A:TRP228 4.6 8.7 1.0
O A:HOH667 4.6 16.0 1.0
C A:CYS269 4.6 10.8 1.0
CH2 A:TRP228 4.7 10.2 1.0
CD A:ARG276 4.7 12.2 1.0
CA A:CYS274 4.7 12.4 0.8
N A:HIS270 4.7 12.3 1.0
NE1 A:TRP228 4.7 9.7 1.0
CA A:GLY265 4.8 9.3 1.0
C A:CYS274 4.8 10.7 0.8
C A:ASN275 4.9 12.3 1.0
N A:ASN275 5.0 12.5 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: Sat Apr 17 13:21:34 2021

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