Magnesium in PDB 3kfu: Crystal Structure of the Transamidosome

The structure of Crystal Structure of the Transamidosome, PDB code: 3kfu was solved by M.Blaise, M.Bailly, M.Frechin, S.Thirup, H.D.Becker, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.19 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	115.920, 214.000, 127.840, 90.00, 93.36, 90.00
R / Rfree (%)	19.9 / 25.2

The structure of Crystal Structure of the Transamidosome also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Transamidosome (pdb code 3kfu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Transamidosome, PDB code: 3kfu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Transamidosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Transamidosome within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg674 b:46.2 occ:1.00 O F:HOH675 2.1 46.2 1.0 O F:HOH676 2.1 46.2 1.0 O F:HOH677 2.1 46.2 1.0 OE1 F:GLU120 2.2 41.7 1.0 OE1 F:GLU146 2.2 50.5 1.0 OE2 F:GLU120 2.4 0.6 1.0 NE2 F:HIS11 2.4 45.6 1.0 CD F:GLU120 2.6 81.1 1.0 CD2 F:HIS11 3.0 51.4 1.0 CD F:GLU146 3.3 67.8 1.0 CE1 F:HIS11 3.6 99.3 1.0 CG F:GLU120 4.1 29.5 1.0 OE2 F:GLU146 4.1 64.4 1.0 CG F:GLU146 4.2 29.5 1.0 CG F:HIS11 4.3 54.8 1.0 NE2 F:GLN91 4.3 65.2 1.0 CB F:GLU146 4.4 33.0 1.0 OE1 F:GLN91 4.4 57.0 1.0 ND1 F:HIS11 4.6 62.9 1.0 NZ F:LYS79 4.7 0.2 1.0 CD F:GLN91 4.8 39.5 1.0 CB F:GLU120 4.8 33.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Transamidosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Transamidosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg468 b:46.2 occ:1.00 OE1 I:GLU146 2.0 58.0 1.0 O I:HOH470 2.1 46.2 1.0 O I:HOH471 2.1 46.2 1.0 O I:HOH469 2.1 46.2 1.0 NE2 I:HIS11 2.2 23.1 1.0 OE1 I:GLU120 2.3 39.9 1.0 OE2 I:GLU120 2.5 92.9 1.0 CD I:GLU120 2.7 66.3 1.0 CD2 I:HIS11 2.9 38.6 1.0 CD I:GLU146 3.1 88.9 1.0 CE1 I:HIS11 3.4 97.9 1.0 OE2 I:GLU146 3.8 88.6 1.0 CG I:GLU146 3.9 69.2 1.0 CB I:GLU146 4.2 59.1 1.0 CG I:HIS11 4.2 37.3 1.0 CG I:GLU120 4.3 17.6 1.0 ND1 I:HIS11 4.4 53.8 1.0 NE2 I:GLN91 4.7 56.1 1.0 OE1 I:GLN91 4.7 63.7 1.0 OE2 I:GLU9 4.7 0.9 1.0 NZ I:LYS79 4.8 0.9 1.0

M.Blaise, M.Bailly, M.Frechin, M.A.Behrens, F.Fischer, C.L.Oliveira, H.D.Becker, J.S.Pedersen, S.Thirup, D.Kern. Crystal Structure of A Transfer-Ribonucleoprotein Particle That Promotes Asparagine Formation. Embo J. V. 29 3118 2010.
ISSN: ISSN 0261-4189
PubMed: 20717102
DOI: 10.1038/EMBOJ.2010.192