Magnesium in PDB 4r9u: Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State

All present enzymatic activity of Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State:
3.6.3.33;

The structure of Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State, PDB code: 4r9u was solved by V.M.Korkhov, S.A.Mireku, D.B.Veprintsev, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.51 / 2.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	372.850, 113.210, 69.430, 90.00, 94.92, 90.00
R / Rfree (%)	21.7 / 24.6

The binding sites of Magnesium atom in the Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State (pdb code 4r9u). 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 Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State, PDB code: 4r9u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:44.9 occ:1.00 OG C:SER40 1.9 80.0 1.0 O2B C:ANP301 1.9 93.6 1.0 O3G C:ANP301 2.2 51.4 1.0 NE2 C:GLN80 2.4 81.0 1.0 OE1 C:GLN80 2.8 88.7 1.0 CD C:GLN80 2.9 77.9 1.0 CB C:SER40 2.9 74.7 1.0 PB C:ANP301 3.5 65.8 1.0 PG C:ANP301 3.5 76.8 1.0 O2A C:ANP301 3.5 64.1 1.0 O1G C:ANP301 3.9 81.5 1.0 OE1 C:GLN159 3.9 0.2 1.0 CA C:SER40 3.9 71.1 1.0 N C:SER40 4.0 72.4 1.0 OD1 C:ASP158 4.0 71.4 1.0 N3B C:ANP301 4.1 55.6 1.0 OD2 C:ASP158 4.1 79.1 1.0 CG C:GLN80 4.2 67.5 1.0 O1B C:ANP301 4.3 65.6 1.0 O3A C:ANP301 4.4 45.9 1.0 CG C:ASP158 4.4 75.0 1.0 PA C:ANP301 4.4 77.9 1.0 CB C:GLN80 4.5 71.4 1.0 N D:GLY129 4.8 79.4 1.0 O1A C:ANP301 4.8 81.7 1.0 O2G C:ANP301 4.8 93.7 1.0 CD C:GLN159 4.8 0.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Vitamin B12 Transporter Btucd in A Nucleotide-Bound Outward Facing State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:48.6 occ:1.00 OG D:SER40 1.9 52.0 1.0 O3G D:ANP301 2.0 40.9 1.0 O2B D:ANP301 2.1 70.7 1.0 NE2 D:GLN80 2.3 67.3 1.0 CB D:SER40 2.9 46.5 1.0 CD D:GLN80 3.0 69.2 1.0 OE1 D:GLN80 3.2 78.3 1.0 O2A D:ANP301 3.3 67.7 1.0 PG D:ANP301 3.4 60.0 1.0 PB D:ANP301 3.6 59.3 1.0 O1G D:ANP301 3.7 63.2 1.0 CA D:SER40 3.9 48.9 1.0 N D:SER40 4.0 53.9 1.0 N3B D:ANP301 4.0 52.2 1.0 OD2 D:ASP158 4.1 65.1 1.0 OD1 D:ASP158 4.1 59.9 1.0 CG D:GLN80 4.3 68.3 1.0 PA D:ANP301 4.4 78.8 1.0 O1B D:ANP301 4.5 57.1 1.0 O3A D:ANP301 4.5 20.1 1.0 CG D:ASP158 4.5 59.7 1.0 CB D:GLN80 4.5 67.8 1.0 N C:GLY129 4.6 58.7 1.0 O2G D:ANP301 4.7 63.0 1.0 O1A D:ANP301 4.9 69.6 1.0 CD D:GLN159 5.0 76.0 1.0

V.M.Korkhov, S.A.Mireku, D.B.Veprintsev, K.P.Locher. Structure of Amp-Pnp Bound Btucd and Mechanism of Atp-Powered Vitamin B12 Transport By Btucd F Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
DOI: 10.1038/NSMB.2918