Magnesium in PDB 7cje: Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase

The structure of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase, PDB code: 7cje was solved by D.Ruiz-Carrillo, S.Lamers, Q.Feng, S.Yu, B.Sun, J.Jiang, M.Lukman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 1.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.8, 90.8, 164.5, 90, 90, 120
R / Rfree (%)	18.3 / 20.9

The structure of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase (pdb code 7cje). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase, PDB code: 7cje:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:46.2 occ:1.00 OD1 A:ASP42 2.0 54.6 1.0 O A:PHE44 2.1 45.0 1.0 O A:HOH513 2.1 47.2 1.0 OE2 A:GLU318 2.1 45.9 1.0 OD1 A:ASP314 2.2 45.3 1.0 O A:HOH532 2.2 46.1 1.0 CG A:ASP42 2.9 55.7 1.0 OD2 A:ASP42 3.1 54.7 1.0 CG A:ASP314 3.1 46.9 1.0 CD A:GLU318 3.2 47.5 1.0 C A:PHE44 3.2 45.3 1.0 OD2 A:ASP314 3.4 49.3 1.0 CG A:GLU318 3.8 46.3 1.0 N A:PHE44 3.9 47.6 1.0 CA A:PHE44 4.0 45.8 1.0 N A:ALA46 4.1 46.0 1.0 CB A:PHE44 4.1 43.6 1.0 CB A:ASP42 4.3 58.0 1.0 N A:SER45 4.3 45.4 1.0 OE1 A:GLU318 4.3 49.5 1.0 CD1 A:PHE44 4.4 39.5 1.0 O A:HOH637 4.4 51.5 1.0 CB A:ASP314 4.4 44.4 1.0 CA A:SER45 4.5 44.0 1.0 C A:SER45 4.7 43.0 1.0 CA A:ASP42 4.8 59.5 1.0 CG A:PHE44 4.8 40.6 1.0 C A:ASP42 4.8 58.3 1.0 N A:LEU43 4.9 53.0 1.0 CB A:ALA46 4.9 44.9 1.0

Magnesium binding site 2 out of 2 in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:36.7 occ:1.00 OD1 C:ASP42 2.0 46.0 1.0 OE1 C:GLU318 2.1 35.9 1.0 O C:PHE44 2.1 40.9 1.0 OD1 C:ASP314 2.1 35.0 1.0 O C:HOH515 2.1 37.8 1.0 O C:HOH580 2.2 37.2 1.0 CG C:ASP42 3.0 48.6 1.0 CG C:ASP314 3.1 36.8 1.0 CD C:GLU318 3.2 35.8 1.0 C C:PHE44 3.2 39.9 1.0 OD2 C:ASP314 3.3 37.4 1.0 OD2 C:ASP42 3.5 49.7 1.0 CG C:GLU318 3.6 34.3 1.0 N C:PHE44 3.8 39.4 1.0 CA C:PHE44 3.9 37.7 1.0 CB C:ASP42 4.0 49.9 1.0 CB C:PHE44 4.1 35.0 1.0 N C:ALA46 4.2 41.3 1.0 N C:SER45 4.3 36.5 1.0 OE2 C:GLU318 4.3 38.0 1.0 O C:HOH623 4.3 44.3 1.0 CB C:ASP314 4.4 37.6 1.0 CA C:SER45 4.4 38.5 1.0 CD2 C:PHE44 4.5 33.4 1.0 C C:ASP42 4.6 47.8 1.0 CA C:ASP42 4.6 50.4 1.0 N C:LEU43 4.7 45.6 1.0 C C:SER45 4.7 37.0 1.0 CG C:PHE44 4.8 32.8 1.0 O C:ASP42 4.9 48.5 1.0 CB C:ALA46 4.9 36.9 1.0 C C:LEU43 5.0 41.6 1.0

S.Lamers, Q.Feng, Y.Cheng, S.Yu, B.Sun, M.Lukman, J.Jiang, D.Ruiz-Carrillo. Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase. Biol.Chem. 2021.
ISSN: ISSN 1431-6730
PubMed: 33823093
DOI: 10.1515/HSZ-2020-0298