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

Enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1A 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:O2-1A 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:O2-1A Complex, PDB code: 6xtp 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) 45.69 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.327, 70.971, 75.64, 90, 90, 90
R / Rfree (%) 24.3 / 29.1

Other elements in 6xtp:

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

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

Calcium binding site 1 out of 2 in 6xtp

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

b:21.2
occ:1.00
 O A:VAL227 2.6 12.5 1.0
O A:GLY225 2.8 13.3 1.0
O A:VAL223 2.9 17.3 1.0
O A:GLY265 2.9 20.6 1.0
O A:HOH548 3.5 19.1 1.0
O A:ASN222 3.5 14.5 1.0
C A:GLY264 3.5 16.3 1.0
O A:GLY264 3.5 20.2 1.0
CA A:GLY264 3.6 12.6 1.0
C A:VAL223 3.6 14.2 1.0
C A:VAL227 3.6 15.2 1.0
C A:GLY225 3.7 14.9 1.0
N A:GLY225 3.7 19.0 1.0
OE2 A:GLU229 3.7 14.8 1.0
C A:GLY265 4.0 19.6 1.0
N A:VAL227 4.1 20.0 1.0
C A:ALA224 4.1 16.2 1.0
O A:LYS263 4.1 18.3 1.0
N A:GLY265 4.1 16.5 1.0
CA A:GLY225 4.2 16.1 1.0
CD A:GLU229 4.2 15.7 1.0
CA A:VAL223 4.3 13.6 1.0
CG A:GLU229 4.3 15.1 1.0
N A:ALA224 4.3 14.3 1.0
N A:TRP228 4.4 11.9 1.0
CA A:ALA224 4.4 12.7 1.0
CA A:VAL227 4.5 14.6 1.0
C A:ASN222 4.5 13.6 1.0
CA A:TRP228 4.6 13.1 1.0
N A:GLY264 4.6 14.2 1.0
CA A:GLY265 4.7 17.3 1.0
O A:ALA224 4.7 19.8 1.0
N A:ASN226 4.8 19.1 1.0
C A:LYS263 4.8 13.7 1.0
C A:TRP228 4.9 12.8 1.0
CZ2 A:TRP160 4.9 12.3 1.0
N A:GLU229 4.9 11.7 1.0
N A:VAL223 4.9 19.1 1.0

Calcium binding site 2 out of 2 in 6xtp

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

b:18.8
occ:1.00
 OD1 A:ASN188 2.3 17.0 1.0
O A:TYR204 2.4 18.6 1.0
O A:HOH543 2.4 19.9 1.0
O A:ILE189 2.4 14.9 1.0
O A:HOH520 2.5 22.2 1.0
OD2 A:ASP202 2.5 19.8 1.0
OD1 A:ASP202 2.6 19.6 1.0
CG A:ASP202 2.9 19.0 1.0
CG A:ASN188 3.4 17.9 1.0
C A:TYR204 3.5 17.8 1.0
C A:ILE189 3.6 17.2 1.0
N A:ILE189 3.8 21.1 1.0
C A:ASN188 4.1 17.8 1.0
CA A:ASN188 4.2 18.5 1.0
OE1 A:GLN191 4.2 23.5 1.0
CA A:TYR204 4.3 19.4 1.0
CA A:ILE189 4.3 17.7 1.0
N A:TYR204 4.3 20.6 1.0
CB A:TYR204 4.3 21.9 1.0
OD2 A:ASP198 4.3 19.5 1.0
CB A:ASN188 4.3 17.9 1.0
ND2 A:ASN188 4.3 17.9 1.0
CB A:ASP202 4.4 20.4 1.0
O A:PHE267 4.5 18.6 1.0
OD1 A:ASP198 4.5 24.5 1.0
N A:THR205 4.5 19.4 1.0
N A:TRP190 4.6 19.0 1.0
CB A:PHE267 4.7 18.0 1.0
CA A:THR205 4.7 20.6 1.0
NE2 A:GLN191 4.7 25.8 1.0
CA A:TRP190 4.8 18.5 1.0
O A:ASN188 4.8 19.6 1.0
CD A:GLN191 4.8 24.8 1.0
CG A:ASP198 4.9 20.0 1.0
CA A:GLY200 5.0 24.2 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 18:15:24 2024

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