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Calcium in PDB 6s07: Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen.

Enzymatic activity of Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen.

All present enzymatic activity of Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen.:
1.8.3.7;

Protein crystallography data

The structure of Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen., PDB code: 6s07 was solved by F.Leisinger, D.A.Miarzlou, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.48 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.409, 71.939, 76.733, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 18

Other elements in 6s07:

The structure of Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Copper (Cu) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen. (pdb code 6s07). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen., PDB code: 6s07:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6s07

Go back to Calcium Binding Sites List in 6s07
Calcium binding site 1 out of 2 in the Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:12.0
occ:1.00
 O A:VAL227 2.6 6.7 1.0
O A:GLY225 2.6 7.4 1.0
O A:VAL223 2.7 9.5 1.0
HA3 A:GLY264 3.0 10.1 1.0
O A:ASN222 3.1 8.4 1.0
O A:HOH600 3.2 8.1 1.0
O A:GLY265 3.2 8.8 1.0
OE2 A:GLU229 3.3 9.5 1.0
HG3 A:GLU229 3.4 9.3 1.0
H A:VAL227 3.4 8.4 1.0
C A:VAL223 3.4 8.9 1.0
HA A:VAL223 3.6 10.2 1.0
C A:GLY225 3.6 7.7 1.0
C A:VAL227 3.7 6.7 1.0
H A:GLY225 3.7 9.6 1.0
N A:GLY225 3.8 8.0 1.0
C A:GLY264 3.8 8.2 1.0
CA A:GLY264 3.8 8.4 1.0
O A:GLY264 3.8 11.1 1.0
CD A:GLU229 3.9 7.5 1.0
HZ2 A:TRP160 4.0 10.5 1.0
C A:ALA224 4.0 8.4 1.0
N A:VAL227 4.1 7.0 1.0
HA A:ALA224 4.1 10.2 1.0
CA A:VAL223 4.1 8.5 1.0
CG A:GLU229 4.1 7.8 1.0
C A:ASN222 4.2 7.8 1.0
N A:ALA224 4.2 8.3 1.0
HA A:TRP228 4.2 7.6 1.0
HA2 A:GLY264 4.2 10.1 1.0
O A:LYS263 4.3 7.7 1.0
CA A:GLY225 4.3 8.5 1.0
CA A:ALA224 4.3 8.5 1.0
C A:GLY265 4.4 7.1 1.0
N A:GLY265 4.5 7.3 1.0
CA A:VAL227 4.5 6.9 1.0
HB3 A:ASN226 4.5 9.0 1.0
N A:TRP228 4.6 6.4 1.0
O A:ALA224 4.6 9.2 1.0
HG23 A:VAL227 4.6 9.6 1.0
HH21 A:ARG297 4.6 9.4 1.0
HA2 A:GLY225 4.6 10.2 1.0
N A:VAL223 4.6 8.2 1.0
N A:ASN226 4.8 7.8 1.0
OE1 A:GLU229 4.8 7.8 1.0
HG2 A:GLU229 4.8 9.3 1.0
CA A:TRP228 4.8 6.3 1.0
HG22 A:VAL227 4.8 9.6 1.0
HA A:SER266 4.8 9.3 1.0
HB3 A:ASN222 4.8 10.7 1.0
HB2 A:GLU229 4.9 8.3 1.0
H A:GLY265 4.9 8.8 1.0
N A:GLY264 4.9 7.0 1.0
CZ2 A:TRP160 4.9 8.8 1.0
H A:ALA224 4.9 9.9 1.0
C A:ASN226 4.9 7.1 1.0
C A:TRP228 5.0 6.2 1.0
C A:LYS263 5.0 6.8 1.0

Calcium binding site 2 out of 2 in 6s07

Go back to Calcium Binding Sites List in 6s07
Calcium binding site 2 out of 2 in the Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Formylglycine-Generating Enzyme at 1.04 A in Complex with Copper and Substrate Reveals An Acidic Pocket For Binding and Acti- Vation of Molecular Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:9.5
occ:1.00
 OD1 A:ASN188 2.3 9.3 1.0
O A:TYR204 2.4 12.5 1.0
O A:ILE189 2.4 9.9 1.0
O A:HOH539 2.4 9.7 1.0
O A:HOH532 2.4 10.8 1.0
OD2 A:ASP202 2.4 10.4 1.0
OD1 A:ASP202 2.5 12.0 1.0
CG A:ASP202 2.8 11.3 1.0
C A:ILE189 3.5 9.1 1.0
C A:TYR204 3.5 11.4 1.0
HB2 A:TYR204 3.5 13.6 1.0
H A:ILE189 3.6 11.1 1.0
CG A:ASN188 3.6 8.6 1.0
HA A:ASN188 3.7 11.5 1.0
H A:TYR204 3.7 13.5 1.0
N A:ILE189 3.7 9.2 1.0
HA A:THR205 3.9 13.7 1.0
HE22 A:GLN191 3.9 14.4 1.0
HB2 A:PHE267 4.0 11.0 1.0
HA A:TRP190 4.0 10.7 1.0
HA2 A:GLY200 4.1 17.9 1.0
C A:ASN188 4.1 8.7 1.0
OE1 A:GLN191 4.2 13.1 1.0
CA A:ASN188 4.2 9.6 1.0
CA A:ILE189 4.2 8.7 1.0
CA A:TYR204 4.3 11.3 1.0
OD2 A:ASP198 4.3 11.3 1.0
CB A:TYR204 4.3 11.3 1.0
CB A:ASP202 4.3 12.6 1.0
N A:TYR204 4.3 11.3 1.0
HD21 A:ASN188 4.4 10.9 1.0
H A:ASP202 4.4 16.0 1.0
ND2 A:ASN188 4.5 9.1 1.0
CB A:ASN188 4.5 9.7 1.0
O A:PHE267 4.5 9.2 1.0
HA A:PHE267 4.5 10.2 1.0
NE2 A:GLN191 4.5 12.0 1.0
N A:TRP190 4.5 9.0 1.0
N A:THR205 4.5 11.6 1.0
OD1 A:ASP198 4.5 11.6 1.0
HA A:ILE189 4.6 10.4 1.0
CA A:THR205 4.6 11.4 1.0
CA A:TRP190 4.7 8.9 1.0
HB3 A:ASP202 4.7 15.1 1.0
HD2 A:TYR204 4.7 16.3 1.0
CD A:GLN191 4.7 11.4 1.0
H A:GLN191 4.8 12.5 1.0
HB2 A:ASP202 4.8 15.1 1.0
HB3 A:TYR204 4.8 13.6 1.0
CB A:PHE267 4.8 9.2 1.0
HB2 A:ASN188 4.9 11.7 1.0
CG A:ASP198 4.9 11.1 1.0
O A:ASN188 4.9 8.3 1.0
CA A:GLY200 5.0 14.9 1.0

Reference:

D.A.Miarzlou, F.Leisinger, D.Joss, D.Haussinger, F.P.Seebeck. Structure of Formylglycine-Generating Enzyme in Complex with Copper and A Substrate Reveals An Acidic Pocket For Binding and Activation of Molecular Oxygen. Chem Sci V. 10 7049 2019.
ISSN: ISSN 2041-6520
PubMed: 31588272
DOI: 10.1039/C9SC01723B
Page generated: Tue Jul 16 14:29:29 2024

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