Magnesium in PDB 5o44: Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.

The structure of Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages., PDB code: 5o44 was solved by P.Padala, M.N.Isupov, R.Wiener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.93 / 3.14
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	110.767, 110.767, 417.004, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 25.4

The binding sites of Magnesium atom in the Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. (pdb code 5o44). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages., PDB code: 5o44:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.


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 Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:93.5 occ:1.00 O A:GLU64 2.9 0.6 1.0 OG1 A:THR66 3.3 0.9 1.0 C A:GLU64 4.1 0.9 1.0 N A:THR66 4.1 0.2 1.0 CA A:SER65 4.3 0.6 1.0 CB A:THR66 4.3 0.1 1.0 C A:SER65 4.3 0.5 1.0 N A:SER65 4.6 0.8 1.0 CA A:THR66 4.8 0.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.


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 Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:0.9 occ:1.00 OG D:SER57 3.1 0.4 1.0 OD1 D:ASP58 3.3 0.8 1.0 OG1 D:THR55 3.4 0.8 1.0 OE2 E:GLU24 3.9 0.7 1.0 CB E:ASP52 4.3 0.2 1.0 O E:ASP52 4.3 0.5 1.0 C E:ASP52 4.3 0.9 1.0 N E:GLY53 4.3 1.0 1.0 CB E:GLU24 4.3 1.0 1.0 CB D:SER57 4.4 0.6 1.0 CA E:GLY53 4.4 0.3 1.0 CG D:ASP58 4.4 0.0 1.0 CG E:GLU24 4.5 0.2 1.0 CB D:THR55 4.5 0.8 1.0 N D:ASP58 4.6 0.4 1.0 CD E:GLU24 4.6 0.7 1.0 CG2 D:THR55 4.6 0.8 1.0 C D:SER57 5.0 0.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg104 b:74.9 occ:1.00 OD2 E:ASP52 2.3 0.5 1.0 OE2 E:GLU24 2.6 0.7 1.0 CB D:SER57 2.8 0.6 1.0 OE1 E:GLU24 3.1 0.7 1.0 CD E:GLU24 3.2 0.7 1.0 CG E:ASP52 3.4 1.0 1.0 OD1 E:ASP39 3.5 0.3 1.0 OG D:SER57 3.6 0.4 1.0 CA D:SER57 3.9 0.2 1.0 OD1 E:ASP52 4.2 0.5 1.0 CB E:ASP52 4.2 0.2 1.0 O D:SER57 4.2 0.9 1.0 C D:SER57 4.4 0.1 1.0 CG E:ASP39 4.6 0.1 1.0 CG E:GLU24 4.8 0.2 1.0 NZ E:LYS27 4.9 0.1 1.0 CB D:PRO19 5.0 0.6 1.0

P.Padala, N.Soudah, M.Giladi, Y.Haitin, M.N.Isupov, R.Wiener. The Crystal Structure and Conformations of An Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. J. Mol. Biol. V. 429 3801 2017.
ISSN: ESSN 1089-8638
PubMed: 29111344
DOI: 10.1016/J.JMB.2017.10.027