Magnesium in PDB 6nop: Structure of Cyanothece Mcda(D38A)-Atp Complex

The structure of Structure of Cyanothece Mcda(D38A)-Atp Complex, PDB code: 6nop was solved by M.A.Schumacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.87 / 1.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.658, 115.658, 76.648, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.4

The binding sites of Magnesium atom in the Structure of Cyanothece Mcda(D38A)-Atp Complex (pdb code 6nop). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Cyanothece Mcda(D38A)-Atp Complex, PDB code: 6nop:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Cyanothece Mcda(D38A)-Atp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Cyanothece Mcda(D38A)-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:28.9 occ:1.00 O B:HOH613 2.1 28.5 1.0 O2B B:ATP501 2.1 24.4 1.0 O B:HOH617 2.1 30.5 1.0 O B:HOH702 2.2 29.2 1.0 O3G B:ATP501 2.2 27.3 1.0 OG1 B:THR16 2.2 28.6 1.0 PB B:ATP501 3.2 27.6 1.0 CB B:THR16 3.3 27.9 1.0 PG B:ATP501 3.3 26.9 1.0 O3B B:ATP501 3.4 26.8 1.0 O B:HOH640 3.4 35.4 1.0 N B:THR16 3.8 26.0 1.0 O1G B:ATP501 4.0 30.2 1.0 OD2 B:ASP123 4.0 27.8 1.0 CA B:THR16 4.1 27.1 1.0 OE1 B:GLN40 4.1 37.5 1.0 OD1 B:ASN42 4.2 35.8 1.0 OD1 B:ASP123 4.2 26.2 1.0 O2A B:ATP501 4.2 26.1 1.0 O1B B:ATP501 4.2 25.2 1.0 O B:HOH653 4.4 29.9 1.0 O3A B:ATP501 4.4 25.9 1.0 CG2 B:THR16 4.5 28.8 1.0 O2G B:ATP501 4.5 27.7 1.0 CG B:ASP123 4.5 26.2 1.0 CB B:LYS15 4.5 22.9 1.0 CE B:LYS15 4.6 23.3 1.0 PA B:ATP501 4.7 26.4 1.0 O B:SER124 4.7 28.4 1.0 CD B:GLN40 4.7 37.1 1.0 C B:LYS15 4.8 25.2 1.0 CB B:ASN42 4.9 33.6 1.0 NZ A:LYS151 4.9 28.6 1.0 CG B:ASN42 4.9 34.5 1.0 O1A B:ATP501 4.9 26.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Cyanothece Mcda(D38A)-Atp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Cyanothece Mcda(D38A)-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:29.5 occ:1.00 O3G A:ATP301 2.1 31.2 1.0 O A:HOH417 2.1 27.5 1.0 OG1 A:THR16 2.1 28.0 1.0 O2B A:ATP301 2.2 29.5 1.0 O A:HOH480 2.2 28.3 1.0 O A:HOH428 2.2 27.4 1.0 PG A:ATP301 3.3 30.7 1.0 CB A:THR16 3.3 28.1 1.0 PB A:ATP301 3.4 29.8 1.0 O3B A:ATP301 3.4 30.4 1.0 O A:HOH470 3.7 33.1 1.0 N A:THR16 3.8 31.1 1.0 O1G A:ATP301 4.0 30.1 1.0 OD2 A:ASP123 4.1 33.1 1.0 NE2 A:GLN40 4.1 35.2 1.0 CA A:THR16 4.1 28.9 1.0 OD1 A:ASP123 4.2 32.2 1.0 O2A A:ATP301 4.2 31.7 1.0 OD1 A:ASN42 4.3 39.5 1.0 O1B A:ATP301 4.3 29.2 1.0 CG2 A:THR16 4.4 30.4 1.0 O2G A:ATP301 4.4 31.0 1.0 O3A A:ATP301 4.5 28.2 1.0 CG A:ASP123 4.5 34.3 1.0 CB A:LYS15 4.5 29.6 1.0 O A:SER124 4.6 31.6 1.0 O A:HOH420 4.6 33.0 1.0 CE A:LYS15 4.7 30.1 1.0 CD A:GLN40 4.8 39.0 1.0 PA A:ATP301 4.8 29.3 1.0 C A:LYS15 4.9 33.5 1.0 NZ B:LYS151 4.9 29.8 1.0 CB A:ASN42 5.0 33.3 1.0

M.A.Schumacher, M.Henderson, H.Zhang. Structures of Maintenance of Carboxysome Distribution Walker-Box Mcda and Mcdb Adaptor Homologs. Nucleic Acids Res. V. 47 5950 2019.
ISSN: ESSN 1362-4962
PubMed: 31106331
DOI: 10.1093/NAR/GKZ314