Magnesium in PDB 6ild: Crystal Structure of Human Lysrs: P38/AIMP2 Complex II

All present enzymatic activity of Crystal Structure of Human Lysrs: P38/AIMP2 Complex II:
6.1.1.6;

The structure of Crystal Structure of Human Lysrs: P38/AIMP2 Complex II, PDB code: 6ild was solved by Z.Hei, Z.Liu, J.Wang, P.Fang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.42 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	96.511, 100.074, 270.980, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.4

The binding sites of Magnesium atom in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex II (pdb code 6ild). 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 Human Lysrs: P38/AIMP2 Complex II, PDB code: 6ild:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex II


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 Human Lysrs: P38/AIMP2 Complex II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:35.4 occ:1.00 O A:HOH942 2.0 33.2 1.0 OE2 A:GLU487 2.1 34.7 1.0 OE1 A:GLU494 2.1 30.7 1.0 O A:HOH1023 2.1 32.2 1.0 O A:HOH782 2.2 32.2 1.0 O A:HOH1020 2.4 35.7 1.0 CD A:GLU494 3.1 27.5 1.0 CD A:GLU487 3.3 25.5 1.0 OE2 A:GLU494 3.5 26.3 1.0 OE1 A:GLU487 3.9 26.5 1.0 O A:HOH1019 4.0 52.4 1.0 O A:HOH1015 4.0 41.1 1.0 NH2 A:ARG485 4.1 16.4 1.0 CG A:GLU487 4.4 17.8 1.0 CG A:GLU494 4.4 19.4 1.0 O A:HOH1126 4.6 54.3 1.0 O A:HOH1054 4.6 48.0 1.0 CB A:GLU494 4.7 16.7 1.0 O A:HOH711 5.0 39.9 1.0 O A:HOH990 5.0 32.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex II


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 Human Lysrs: P38/AIMP2 Complex II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:32.7 occ:1.00 OE2 B:GLU487 2.0 32.9 1.0 OP2 B:45A605 2.1 39.6 1.0 O B:HOH763 2.1 29.9 1.0 O B:HOH962 2.1 26.8 1.0 OE1 B:GLU494 2.1 30.9 1.0 O B:HOH740 2.2 23.9 1.0 CD B:GLU494 3.1 28.5 1.0 CD B:GLU487 3.2 25.9 1.0 OE2 B:GLU494 3.4 27.9 1.0 P B:45A605 3.7 50.5 1.0 NH2 B:ARG485 3.9 21.2 1.0 OE1 B:GLU487 3.9 30.0 1.0 O B:HOH1041 3.9 36.9 1.0 C5' B:45A605 4.2 46.7 1.0 CG B:GLU487 4.2 20.8 1.0 O5' B:45A605 4.4 49.8 1.0 O B:HOH746 4.4 29.2 1.0 CG B:GLU494 4.4 19.3 1.0 O1 B:45A605 4.4 56.1 1.0 O B:HOH783 4.5 47.2 1.0 O B:HOH999 4.6 55.0 1.0 C31 B:45A605 4.7 52.5 1.0 CB B:GLU494 4.8 18.3 1.0

Z.Hei, S.Wu, Z.Liu, J.Wang, P.Fang. Retractile Lysyl-Trna Synthetase-AIMP2 Assembly in the Human Multi-Aminoacyl-Trna Synthetase Complex. J. Biol. Chem. V. 294 4775 2019.
ISSN: ESSN 1083-351X
PubMed: 30733335
DOI: 10.1074/JBC.RA118.006356