Magnesium in PDB 6gfq: Cyanobacterial Gapdh with Nad and CP12 Bound

The structure of Cyanobacterial Gapdh with Nad and CP12 Bound, PDB code: 6gfq was solved by C.R.Mcfarlane, J.W.Murray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.77 / 1.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.217, 141.217, 76.238, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.4

The binding sites of Magnesium atom in the Cyanobacterial Gapdh with Nad and CP12 Bound (pdb code 6gfq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cyanobacterial Gapdh with Nad and CP12 Bound, PDB code: 6gfq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cyanobacterial Gapdh with Nad and CP12 Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cyanobacterial Gapdh with Nad and CP12 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:34.7 occ:1.00 O A:HOH1296 2.3 32.0 1.0 O A:GLY305 2.4 16.9 1.0 OD1 A:ASN307 2.5 19.7 1.0 C A:GLY305 3.4 15.8 1.0 CG A:ASN307 3.4 17.1 1.0 O A:HOH1142 3.6 29.3 1.0 CB A:ASN307 3.8 15.8 1.0 N A:ASN307 3.9 14.5 1.0 CA A:GLY305 3.9 15.8 1.0 CA A:ASN307 4.4 15.2 1.0 N A:GLY306 4.5 16.0 1.0 O A:HOH1316 4.6 24.3 1.0 ND2 A:ASN307 4.7 17.8 1.0 O A:LEU304 4.7 15.1 1.0 C A:GLY306 4.8 16.7 1.0 CA A:GLY306 4.9 16.6 1.0

Magnesium binding site 2 out of 2 in the Cyanobacterial Gapdh with Nad and CP12 Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cyanobacterial Gapdh with Nad and CP12 Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:35.7 occ:1.00 O B:HOH1285 2.2 39.8 1.0 O B:HOH1291 2.4 30.1 1.0 O B:HOH1303 2.4 33.0 1.0 O B:GLY305 2.6 20.5 1.0 OD1 B:ASN307 2.8 31.3 1.0 C B:GLY305 3.6 19.9 1.0 CG B:ASN307 3.6 28.2 1.0 CB B:ASN307 3.8 24.0 1.0 O B:HOH1155 4.0 47.0 1.0 CA B:GLY305 4.0 20.0 1.0 N B:ASN307 4.1 19.1 1.0 CA B:ASN307 4.6 20.2 1.0 N B:GLY306 4.7 19.5 1.0 O B:HOH1316 4.7 47.9 1.0 O B:LEU304 4.8 18.3 1.0 ND2 B:ASN307 4.9 28.2 1.0

C.R.Mcfarlane, N.R.Shah, B.V.Kabasakal, B.Echeverria, C.A.R.Cotton, D.Bubeck, J.W.Murray. Structural Basis of Light-Induced Redox Regulation in the Calvin-Benson Cycle in Cyanobacteria. Proc.Natl.Acad.Sci.Usa V. 116 20984 2019.
ISSN: ESSN 1091-6490
PubMed: 31570616
DOI: 10.1073/PNAS.1906722116