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

Enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Ag: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:Ag: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:Ag:S:No Complex, PDB code: 6xtn 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) 46.46 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.299, 71.898, 76.919, 90, 90, 90
R / Rfree (%) 16.9 / 19.6

Other elements in 6xtn:

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

Silver (Ag) 2 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 6xtn

Go back to Calcium Binding Sites List in 6xtn
Calcium 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:No Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:No Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.4
occ:1.00
 O A:GLY225 2.5 10.8 1.0
O A:VAL227 2.6 9.7 1.0
O A:VAL223 2.9 15.0 1.0
O A:ASN222 3.2 11.9 1.0
O A:GLY265 3.2 11.1 1.0
O A:HOH632 3.2 11.7 1.0
OE2 A:GLU229 3.4 13.0 1.0
C A:VAL223 3.5 13.7 1.0
O A:GLY264 3.6 15.4 1.0
C A:GLY225 3.6 9.7 1.0
C A:VAL227 3.6 9.6 1.0
C A:GLY264 3.7 11.5 1.0
N A:GLY225 3.8 10.6 1.0
CA A:GLY264 3.8 11.3 1.0
CD A:GLU229 4.0 11.1 1.0
C A:ALA224 4.0 11.6 1.0
N A:VAL227 4.0 11.0 1.0
CA A:VAL223 4.2 12.5 1.0
CG A:GLU229 4.2 10.7 1.0
C A:ASN222 4.2 11.3 1.0
N A:ALA224 4.2 11.7 1.0
CA A:GLY225 4.2 10.4 1.0
C A:GLY265 4.3 10.8 1.0
O A:LYS263 4.3 10.5 1.0
CA A:ALA224 4.3 10.9 1.0
N A:GLY265 4.4 9.9 1.0
CA A:VAL227 4.5 11.4 1.0
N A:TRP228 4.5 9.5 1.0
O A:ALA224 4.6 11.7 1.0
N A:VAL223 4.7 11.5 1.0
N A:ASN226 4.7 10.2 1.0
CA A:TRP228 4.7 8.7 1.0
OE1 A:GLU229 4.8 11.6 1.0
N A:GLY264 4.9 9.8 1.0
C A:ASN226 4.9 9.7 1.0
CA A:GLY265 4.9 11.4 1.0
CZ2 A:TRP160 5.0 9.8 1.0
C A:TRP228 5.0 9.6 1.0

Calcium binding site 2 out of 2 in 6xtn

Go back to Calcium Binding Sites List in 6xtn
Calcium 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:No Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:No Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.5
occ:1.00
 O A:HOH543 2.3 15.1 1.0
OD1 A:ASN188 2.3 12.5 1.0
O A:TYR204 2.4 15.0 1.0
O A:ILE189 2.4 13.0 1.0
O A:HOH559 2.4 12.9 1.0
OD1 A:ASP202 2.5 14.6 1.0
OD2 A:ASP202 2.5 13.1 1.0
CG A:ASP202 2.8 13.9 1.0
C A:TYR204 3.5 12.5 1.0
C A:ILE189 3.5 12.3 1.0
CG A:ASN188 3.6 11.7 1.0
N A:ILE189 3.7 12.2 1.0
C A:ASN188 4.1 11.8 1.0
OE1 A:GLN191 4.2 14.2 1.0
CA A:ASN188 4.2 11.0 1.0
CA A:ILE189 4.3 11.1 1.0
CA A:TYR204 4.3 12.9 1.0
N A:TYR204 4.3 14.4 1.0
OD2 A:ASP198 4.3 15.2 1.0
CB A:ASP202 4.3 16.7 1.0
CB A:TYR204 4.4 15.6 1.0
ND2 A:ASN188 4.5 11.6 1.0
NE2 A:GLN191 4.5 15.4 1.0
CB A:ASN188 4.5 12.2 1.0
O A:PHE267 4.5 12.6 1.0
OD1 A:ASP198 4.5 14.6 1.0
N A:THR205 4.5 13.7 1.0
N A:TRP190 4.5 12.2 1.0
CA A:THR205 4.6 14.9 1.0
CA A:TRP190 4.7 13.1 1.0
CD A:GLN191 4.7 13.8 1.0
CB A:PHE267 4.8 10.7 1.0
CG A:ASP198 4.9 14.0 1.0
O A:ASN188 4.9 12.0 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: Tue Jul 16 18:14:11 2024

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