Chlorine 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:

Silver (Ag) 2 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6xtm

Go back to Chlorine Binding Sites List in 6xtm
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl404

b:19.1
occ:0.83
 N A:ASN132 3.2 12.3 1.0
CD A:PRO131 3.4 16.8 1.0
CD2 A:HIS133 3.5 12.5 1.0
CB A:ASN132 3.6 16.7 1.0
N A:PRO131 3.7 13.7 1.0
CA A:ASN132 3.7 13.2 1.0
CG A:PRO131 3.8 15.9 1.0
C A:ARG130 3.9 14.5 1.0
CA A:ARG130 4.0 13.5 1.0
O A:ASP129 4.0 18.5 1.0
C A:ASN132 4.0 12.1 1.0
N A:HIS133 4.1 11.6 1.0
NE2 A:HIS133 4.2 13.0 1.0
C A:PRO131 4.2 12.4 1.0
CA A:PRO131 4.4 13.9 1.0
O A:ARG130 4.5 13.6 1.0
CG A:PRO209 4.6 13.1 1.0
C A:ASP129 4.6 16.9 1.0
O A:HOH710 4.6 26.1 1.0
N A:ARG130 4.6 15.5 1.0
CG A:HIS133 4.7 12.3 1.0
O A:ASN132 4.8 12.2 1.0
CB A:PRO131 4.8 16.7 1.0
CB A:PRO209 4.8 12.3 1.0

Chlorine binding site 2 out of 3 in 6xtm

Go back to Chlorine Binding Sites List in 6xtm
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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:Cl405

b:32.9
occ:1.00
 N A:GLU40 3.1 20.1 1.0
OG1 C:THR4 3.1 16.6 1.0
CG A:GLU40 3.3 28.5 1.0
N A:PRO39 3.3 20.7 1.0
CD A:PRO39 3.4 19.8 1.0
CB A:GLU40 3.5 22.7 1.0
CB A:PHE38 3.6 15.2 1.0
C A:PHE38 3.7 18.9 1.0
CA A:PHE38 3.9 15.9 1.0
CA A:GLU40 3.9 18.9 1.0
C A:PRO39 4.0 18.8 1.0
CA A:PRO39 4.0 18.3 1.0
CD A:GLU40 4.1 37.4 1.0
CB A:PRO39 4.1 22.2 1.0
CG A:PRO39 4.2 22.6 1.0
CB C:THR4 4.2 14.3 1.0
CG2 C:THR4 4.3 18.1 1.0
O A:PHE38 4.4 16.4 1.0
OE2 A:GLU40 4.5 33.9 1.0
CG A:PHE38 4.6 15.6 1.0
OE1 A:GLU40 4.7 41.6 1.0
C A:GLU40 4.9 16.6 1.0
CA C:THR4 4.9 13.4 1.0
N A:ASP41 5.0 14.9 1.0

Chlorine binding site 3 out of 3 in 6xtm

Go back to Chlorine Binding Sites List in 6xtm
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl406

b:27.2
occ:1.00
 O A:HOH723 3.3 29.1 1.0
N A:GLU178 3.4 15.8 1.0
CG A:PRO181 3.4 22.2 1.0
N A:ASN177 3.5 15.5 1.0
CB A:GLU178 3.7 19.8 1.0
CA A:GLY176 3.8 15.4 1.0
O A:GLU178 3.9 17.2 1.0
CB A:PRO181 3.9 21.4 1.0
C A:GLY176 3.9 14.5 1.0
CA A:GLU178 4.0 17.5 1.0
CD1 A:TRP175 4.0 16.2 1.0
CG A:GLU178 4.1 26.8 1.0
O A:TRP175 4.2 17.0 1.0
O A:HOH860 4.3 35.7 1.0
C A:ASN177 4.4 17.6 1.0
C A:GLU178 4.4 17.1 1.0
N A:GLY176 4.5 13.4 1.0
CA A:ASN177 4.5 15.2 1.0
C A:TRP175 4.6 14.3 1.0
NE1 A:TRP175 4.6 15.1 1.0
CD A:GLU178 4.6 32.8 1.0
CD A:PRO181 4.7 17.6 1.0
O A:GLY176 4.9 14.7 1.0
OE2 A:GLU178 5.0 33.1 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 12:54:17 2021

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