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

Enzymatic activity of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B 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:O2-1B 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:O2-1B Complex, PDB code: 6xtq 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) 45.85 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.909, 70.995, 75.057, 90, 90, 90
R / Rfree (%) 17.9 / 19.8

Other elements in 6xtq:

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

Chlorine (Cl) 2 atoms
Copper (Cu) 1 atom
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex (pdb code 6xtq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex, PDB code: 6xtq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6xtq

Go back to Magnesium Binding Sites List in 6xtq
Magnesium binding site 1 out of 4 in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:O2-1B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:28.4
occ:1.00
 O A:HOH591 2.0 23.4 1.0
O A:HOH741 2.1 31.9 1.0
O A:HOH735 2.1 30.0 1.0
O A:HOH639 2.1 29.4 1.0
O A:HOH727 2.2 33.5 1.0
O A:HOH736 2.3 29.9 1.0
O A:HOH681 4.0 24.1 1.0
OG1 A:THR148 4.2 20.5 1.0
O A:HOH516 4.4 30.4 1.0
O A:HOH733 4.4 33.2 1.0
O A:HOH739 4.4 31.0 1.0
O A:LYS152 4.4 18.4 1.0
CB A:ARG153 4.7 16.2 1.0
SD A:MET1 4.7 36.4 0.9
O A:HOH697 4.8 13.9 1.0
O A:HOH737 4.9 35.8 1.0

Magnesium binding site 2 out of 4 in 6xtq

Go back to Magnesium Binding Sites List in 6xtq
Magnesium binding site 2 out of 4 in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:O2-1B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:31.4
occ:1.00
 O A:HOH702 2.0 28.9 1.0
O A:HOH701 2.1 26.9 1.0
O A:HOH712 2.1 33.1 1.0
O A:HOH510 2.1 24.1 1.0
O A:HOH722 2.1 32.2 1.0
O A:LYS18 4.0 22.2 1.0
NZ A:LYS152 4.0 20.6 1.0
O A:HOH685 4.0 31.4 1.0
O A:HOH605 4.0 23.1 1.0
O A:HOH529 4.1 28.8 1.0
O A:HOH708 4.1 32.6 1.0
O A:GLU15 4.3 21.9 1.0
O A:HOH524 4.4 26.6 1.0
NE2 A:GLN65 4.6 22.3 1.0
CE A:LYS152 4.7 19.7 1.0
O A:ILE16 4.8 21.9 1.0
C A:LYS18 5.0 18.7 1.0

Magnesium binding site 3 out of 4 in 6xtq

Go back to Magnesium Binding Sites List in 6xtq
Magnesium binding site 3 out of 4 in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:36.3
occ:1.00
 O A:HOH612 1.5 37.4 1.0
O A:HOH587 2.2 29.3 1.0
OD1 A:ASP7 4.2 28.2 1.0
O A:PHE4 4.2 30.0 1.0
C A:ASP5 4.6 31.1 1.0
O A:ASP5 4.6 36.1 1.0
CA A:ASP5 4.6 25.9 1.0
OD2 A:ASP5 4.6 31.2 0.1
O A:PHE6 4.7 23.5 1.0

Magnesium binding site 4 out of 4 in 6xtq

Go back to Magnesium Binding Sites List in 6xtq
Magnesium binding site 4 out of 4 in the Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Reveals Non-Coordinative Binding of O2 to the Copper Center of the Formylglycine-Generating Enzyme - Fge:Cu:S:O2-1B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:44.9
occ:1.00
 O A:HOH719 1.8 51.5 1.0
O A:HOH650 1.8 34.1 1.0
O A:HOH721 1.9 44.7 1.0
O A:HOH717 2.2 30.6 1.0
O A:HOH693 2.3 35.7 1.0
O A:GLU271 3.8 22.9 1.0
O A:HOH609 3.8 27.3 1.0
OD2 A:ASP36 4.2 45.8 1.0
O A:HOH577 4.3 28.4 1.0
CB A:ASP36 4.5 36.9 1.0
CG A:ASP36 4.7 42.0 1.0
O C:HOH208 4.8 25.6 1.0
ND2 A:ASN275 4.8 27.9 1.0
CG A:GLU271 4.9 28.2 1.0
C A:GLU271 4.9 22.2 1.0
CB A:ASN275 4.9 19.4 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 Oct 1 23:39:51 2024

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