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Calcium in PDB 6xts: Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1D Complex

Enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1D 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:O2-1D 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:O2-1D Complex, PDB code: 6xts 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 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.104, 72.222, 76.886, 90, 90, 90
R / Rfree (%) 20 / 21.6

Other elements in 6xts:

The structure of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1D Complex also contains other interesting chemical elements:

Copper (Cu) 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:Cu:S:O2-1D Complex (pdb code 6xts). 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:Cu:S:O2-1D Complex, PDB code: 6xts:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6xts

Go back to Calcium Binding Sites List in 6xts
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:Cu:S:O2-1D 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:Cu:S:O2-1D Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.1
occ:1.00
 O A:VAL227 2.5 6.9 1.0
O A:GLY225 2.5 9.1 1.0
O A:VAL223 2.8 12.1 1.0
O A:ASN222 3.1 9.1 1.0
O A:HOH654 3.1 8.6 1.0
O A:GLY265 3.2 8.9 1.0
OE2 A:GLU229 3.3 9.9 1.0
C A:VAL223 3.5 10.4 1.0
C A:VAL227 3.6 7.5 1.0
C A:GLY225 3.6 8.3 1.0
O A:GLY264 3.7 12.5 1.0
C A:GLY264 3.8 8.3 1.0
N A:GLY225 3.8 8.7 1.0
CA A:GLY264 3.9 9.4 1.0
CD A:GLU229 3.9 8.7 1.0
N A:VAL227 4.0 8.2 1.0
C A:ALA224 4.1 9.3 1.0
CG A:GLU229 4.1 7.9 1.0
CA A:VAL223 4.2 9.5 1.0
C A:ASN222 4.2 8.2 1.0
N A:ALA224 4.3 9.0 1.0
O A:LYS263 4.3 7.5 1.0
CA A:GLY225 4.3 9.0 1.0
C A:GLY265 4.4 8.1 1.0
CA A:ALA224 4.4 8.9 1.0
CA A:VAL227 4.5 8.2 1.0
N A:GLY265 4.5 8.4 1.0
N A:TRP228 4.5 7.0 1.0
O A:ALA224 4.6 9.8 1.0
N A:VAL223 4.7 8.2 1.0
CA A:TRP228 4.7 7.1 1.0
N A:ASN226 4.7 7.6 1.0
OE1 A:GLU229 4.7 8.8 1.0
C A:ASN226 4.9 7.4 1.0
C A:TRP228 4.9 7.5 1.0
N A:GLY264 4.9 7.0 1.0
CZ2 A:TRP160 5.0 8.4 1.0

Calcium binding site 2 out of 2 in 6xts

Go back to Calcium Binding Sites List in 6xts
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:Cu:S:O2-1D 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:Cu:S:O2-1D Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:9.9
occ:1.00
 O A:TYR204 2.3 11.8 1.0
OD1 A:ASN188 2.3 10.4 1.0
O A:HOH556 2.3 12.2 1.0
O A:HOH594 2.4 10.7 1.0
O A:ILE189 2.4 9.9 1.0
OD1 A:ASP202 2.5 12.0 1.0
OD2 A:ASP202 2.5 10.1 1.0
CG A:ASP202 2.8 11.5 1.0
C A:TYR204 3.5 10.9 1.0
C A:ILE189 3.5 9.7 1.0
CG A:ASN188 3.6 9.8 1.0
N A:ILE189 3.8 9.8 1.0
C A:ASN188 4.1 9.0 1.0
OE1 A:GLN191 4.2 12.2 1.0
CA A:ASN188 4.2 10.1 1.0
CA A:ILE189 4.3 9.6 1.0
CA A:TYR204 4.3 11.6 1.0
OD2 A:ASP198 4.3 12.0 1.0
N A:TYR204 4.3 12.6 1.0
CB A:TYR204 4.3 12.3 1.0
CB A:ASP202 4.4 12.2 1.0
ND2 A:ASN188 4.5 9.4 1.0
N A:THR205 4.5 10.2 1.0
CB A:ASN188 4.5 9.8 1.0
NE2 A:GLN191 4.5 12.2 1.0
O A:PHE267 4.5 10.0 1.0
OD1 A:ASP198 4.5 11.8 1.0
N A:TRP190 4.5 10.1 1.0
CA A:THR205 4.6 11.0 1.0
CA A:TRP190 4.6 10.7 1.0
CD A:GLN191 4.7 10.7 1.0
CB A:PHE267 4.8 9.7 1.0
CG A:ASP198 4.9 11.8 1.0
O A:ASN188 4.9 8.8 1.0
CA A:GLY200 5.0 15.7 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 18:16:40 2024

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