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Calcium 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
Silver (Ag) 2 atoms

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:O2 Complex (pdb code 6xtm). 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:O2 Complex, PDB code: 6xtm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6xtm

Go back to Calcium Binding Sites List in 6xtm
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:O2 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:O2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:15.7
occ:1.00
 O A:VAL227 2.6 8.4 1.0
O A:GLY225 2.6 9.4 1.0
O A:VAL223 2.8 12.4 1.0
O A:ASN222 3.1 9.9 1.0
O A:HOH660 3.2 9.8 1.0
O A:GLY265 3.2 10.9 1.0
OE2 A:GLU229 3.4 10.8 1.0
C A:VAL223 3.5 10.8 1.0
O A:GLY264 3.5 14.3 1.0
C A:VAL227 3.7 8.3 1.0
C A:GLY225 3.7 9.3 1.0
C A:GLY264 3.7 9.8 1.0
N A:GLY225 3.8 9.9 1.0
CA A:GLY264 3.8 10.8 1.0
CD A:GLU229 3.9 9.5 1.0
C A:ALA224 4.0 10.5 1.0
N A:VAL227 4.1 9.3 1.0
CA A:VAL223 4.1 10.6 1.0
CG A:GLU229 4.2 8.7 1.0
C A:ASN222 4.2 9.6 1.0
N A:ALA224 4.2 10.0 1.0
CA A:GLY225 4.3 9.4 1.0
O A:LYS263 4.3 9.1 1.0
C A:GLY265 4.3 9.0 1.0
CA A:ALA224 4.3 9.8 1.0
N A:GLY265 4.4 9.6 1.0
CA A:VAL227 4.5 8.5 1.0
N A:TRP228 4.6 8.0 1.0
O A:ALA224 4.6 10.3 1.0
N A:VAL223 4.7 9.9 1.0
CA A:TRP228 4.7 8.4 1.0
N A:ASN226 4.8 9.2 1.0
OE1 A:GLU229 4.8 9.4 1.0
N A:GLY264 4.9 8.5 1.0
CZ2 A:TRP160 4.9 9.4 1.0
C A:ASN226 4.9 8.9 1.0
CA A:GLY265 5.0 9.3 1.0
C A:TRP228 5.0 8.1 1.0

Calcium binding site 2 out of 2 in 6xtm

Go back to Calcium Binding Sites List in 6xtm
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:O2 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:O2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:10.8
occ:1.00
 OD1 A:ASN188 2.3 11.3 1.0
O A:HOH555 2.3 13.2 1.0
O A:HOH579 2.3 10.9 1.0
O A:ILE189 2.4 11.6 1.0
O A:TYR204 2.4 12.8 1.0
OD2 A:ASP202 2.5 11.5 1.0
OD1 A:ASP202 2.5 12.6 1.0
CG A:ASP202 2.8 12.1 1.0
C A:ILE189 3.5 10.7 1.0
C A:TYR204 3.5 11.6 1.0
CG A:ASN188 3.6 10.3 1.0
N A:ILE189 3.8 10.7 1.0
C A:ASN188 4.1 10.6 1.0
OE1 A:GLN191 4.2 13.0 1.0
CA A:ASN188 4.2 10.1 1.0
CA A:ILE189 4.2 10.3 1.0
OD2 A:ASP198 4.3 12.7 1.0
CA A:TYR204 4.3 11.6 1.0
CB A:ASP202 4.3 14.7 1.0
N A:TYR204 4.3 12.1 1.0
CB A:TYR204 4.4 12.7 1.0
CB A:ASN188 4.5 10.4 1.0
ND2 A:ASN188 4.5 9.9 1.0
O A:PHE267 4.5 11.1 1.0
N A:TRP190 4.5 11.5 1.0
NE2 A:GLN191 4.5 13.7 1.0
OD1 A:ASP198 4.5 12.1 1.0
N A:THR205 4.5 11.7 1.0
CA A:TRP190 4.6 10.9 1.0
CA A:THR205 4.7 13.1 1.0
CD A:GLN191 4.7 12.4 1.0
CB A:PHE267 4.8 10.6 1.0
CG A:ASP198 4.9 13.2 1.0
O A:ASN188 4.9 10.3 1.0
CA A:GLY200 5.0 15.3 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 Jul 9 20:05:11 2025

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