Magnesium in PDB 6d5k: Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin

All present enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin:
2.5.1.17;

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin, PDB code: 6d5k was solved by G.J.Dodge, G.Campanello, J.L.Smith, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.61 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.252, 112.252, 117.993, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.9

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Magnesium atom in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin (pdb code 6d5k). 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 Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin, PDB code: 6d5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:75.3 occ:1.00 O C:HOH404 2.2 73.2 1.0 O C:HOH401 2.2 77.0 1.0 O C:HOH407 2.3 70.8 1.0 O C:HOH403 2.6 91.7 1.0 O1A C:ATP301 2.7 64.5 1.0 O B:ILE58 3.6 96.5 1.0 OD1 C:ASP218 3.6 95.5 1.0 PA C:ATP301 4.0 67.1 1.0 O2G C:ATP301 4.4 71.5 1.0 CG C:ASP218 4.5 87.1 1.0 O2A C:ATP301 4.5 67.7 1.0 OD2 C:ASP218 4.5 96.8 1.0 C B:ILE58 4.7 90.2 1.0 O3A C:ATP301 4.8 69.2 1.0 O3G C:ATP301 4.8 64.2 1.0 CA B:TYR59 5.0 81.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg306 b:75.6 occ:1.00 O2B C:ATP301 1.8 65.3 1.0 O C:HOH402 1.9 66.4 1.0 O2A C:ATP301 1.9 67.7 1.0 O3G C:ATP301 2.0 64.2 1.0 OD1 C:ASN214 2.0 75.4 1.0 O C:HOH405 2.1 72.1 1.0 PB C:ATP301 3.0 65.0 1.0 CG C:ASN214 3.1 69.9 1.0 PA C:ATP301 3.2 67.1 1.0 PG C:ATP301 3.3 69.4 1.0 O3A C:ATP301 3.4 69.2 1.0 ND2 C:ASN214 3.5 69.1 1.0 O3B C:ATP301 3.6 63.3 1.0 NZ B:LYS78 3.7 62.4 1.0 O C:HOH404 3.8 73.2 1.0 O1G C:ATP301 4.2 68.6 1.0 O C:ASN214 4.2 73.5 1.0 O5' C:ATP301 4.2 62.9 1.0 O1A C:ATP301 4.3 64.5 1.0 NH1 C:ARG190 4.3 70.2 1.0 O1B C:ATP301 4.3 65.8 1.0 N7 C:ATP301 4.4 64.6 1.0 CB C:ASN214 4.4 63.8 1.0 O2G C:ATP301 4.4 71.5 1.0 OE1 C:GLU193 4.5 67.8 1.0 CA C:ASN214 4.7 69.8 1.0 C8 C:ATP301 4.7 63.2 1.0 CE B:LYS78 4.7 65.5 1.0 OD2 C:ASP218 4.7 96.8 1.0 OE2 C:GLU193 4.8 80.3 1.0 C C:ASN214 4.8 73.2 1.0

G.C.Campanello, M.Ruetz, G.J.Dodge, H.Gouda, A.Gupta, U.T.Twahir, M.M.Killian, D.Watkins, D.S.Rosenblatt, T.C.Brunold, K.Warncke, J.L.Smith, R.Banerjee. Sacrificial Cobalt-Carbon Bond Homolysis in Coenzyme B12AS A Cofactor Conservation Strategy. J. Am. Chem. Soc. V. 140 13205 2018.
ISSN: ESSN 1520-5126
PubMed: 30282455
DOI: 10.1021/JACS.8B08659