Magnesium in PDB 8dpb: Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound

All present enzymatic activity of Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound:
5.4.99.2;

The structure of Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound, PDB code: 8dpb was solved by F.A.Vaccaro, D.A.Born, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.99 / 2.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.23, 80.98, 166.38, 90, 90, 90
R / Rfree (%)	21.6 / 23.7

The binding sites of Magnesium atom in the Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound (pdb code 8dpb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound, PDB code: 8dpb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:35.6 occ:1.00 OG A:SER69 2.1 41.6 1.0 O3G A:GCP401 2.1 30.9 1.0 OD1 A:ASP105 2.1 43.2 1.0 O1B A:GCP401 2.1 32.7 1.0 OE1 A:GLU154 2.1 39.9 1.0 O A:HOH506 2.1 37.0 1.0 CG A:ASP105 3.1 38.0 1.0 CD A:GLU154 3.2 38.1 1.0 PG A:GCP401 3.3 34.8 1.0 CB A:SER69 3.3 35.0 1.0 PB A:GCP401 3.3 36.8 1.0 CB A:ASP105 3.6 35.6 1.0 OE2 A:GLU154 3.7 39.8 1.0 O1G A:GCP401 3.7 39.3 1.0 CA A:ASP105 3.7 34.4 1.0 C3B A:GCP401 3.8 31.7 1.0 N A:SER69 4.0 34.1 1.0 O2B A:GCP401 4.1 36.1 1.0 OD2 A:ASP105 4.1 41.0 1.0 NZ B:LYS188 4.1 45.2 1.0 CA A:SER69 4.2 32.5 1.0 O A:GLY104 4.2 30.1 1.0 O2A A:GCP401 4.3 29.0 1.0 CG A:GLU154 4.4 37.3 1.0 N A:ASP105 4.5 33.1 1.0 O3A A:GCP401 4.6 34.1 1.0 O2G A:GCP401 4.7 39.1 1.0 C A:GLY104 4.7 35.4 1.0 CB A:LYS68 4.8 25.1 1.0 PA A:GCP401 4.8 31.6 1.0 C A:ASP105 4.9 37.0 1.0 CE A:LYS68 4.9 34.0 1.0 O A:ASP105 5.0 40.1 1.0

Magnesium binding site 2 out of 2 in the Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Meab in Complex with the Cobalamin-Binding Domain of Its Target Mutase with Gmppcp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:32.0 occ:1.00 O3G B:GCP401 2.1 29.7 1.0 OG B:SER69 2.1 39.2 1.0 OE1 B:GLU154 2.1 36.6 1.0 O B:HOH506 2.1 26.9 1.0 OD1 B:ASP105 2.1 39.2 1.0 O1B B:GCP401 2.1 26.9 1.0 CG B:ASP105 3.1 34.1 1.0 CD B:GLU154 3.2 34.8 1.0 CB B:SER69 3.3 32.5 1.0 PG B:GCP401 3.3 32.5 1.0 PB B:GCP401 3.3 33.6 1.0 CB B:ASP105 3.6 29.0 1.0 C3B B:GCP401 3.6 34.7 1.0 NZ A:LYS188 3.6 40.1 1.0 CA B:ASP105 3.7 32.9 1.0 OE2 B:GLU154 3.8 36.7 1.0 O1A B:GCP401 3.9 31.4 1.0 O1G B:GCP401 3.9 33.2 1.0 N B:SER69 3.9 35.1 1.0 OD2 B:ASP105 4.1 37.9 1.0 CA B:SER69 4.1 34.5 1.0 O2B B:GCP401 4.3 28.6 1.0 O B:GLY104 4.4 39.5 1.0 O3A B:GCP401 4.4 35.2 1.0 CG B:GLU154 4.5 33.4 1.0 N B:ASP105 4.5 34.1 1.0 PA B:GCP401 4.5 32.3 1.0 O2G B:GCP401 4.6 35.6 1.0 C B:GLY104 4.8 35.6 1.0 O2A B:GCP401 4.8 35.9 1.0 C B:ASP105 4.8 34.4 1.0 CB B:LYS68 4.8 30.0 1.0 O B:ASP105 4.9 34.6 1.0 CE B:LYS68 4.9 34.3 1.0 C B:LYS68 5.0 35.6 1.0 CE A:LYS188 5.0 37.5 1.0

F.A.Vaccaro, D.A.Born, C.L.Drennan. Structure of Metallochaperone in Complex with the Cobalamin-Binding Domain of Its Target Mutase Provides Insight Into Cofactor Delivery. Proc.Natl.Acad.Sci.Usa V. 120 85120 2023.
ISSN: ESSN 1091-6490
PubMed: 36787360
DOI: 10.1073/PNAS.2214085120