Magnesium in PDB 5ujj: Crystal Structure of Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp

All present enzymatic activity of Crystal Structure of Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp:
6.1.1.2;

The structure of Crystal Structure of Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp, PDB code: 5ujj was solved by X.Xu, X.-L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.352, 95.277, 99.623, 90.00, 130.46, 90.00
R / Rfree (%)	21.6 / 23.2

The binding sites of Magnesium atom in the Crystal Structure of Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp (pdb code 5ujj). 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 Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp, PDB code: 5ujj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp


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 H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.1 occ:1.00 O1P A:TYM501 2.5 15.7 1.0 O A:HOH635 2.5 22.3 1.0 MG A:MG503 3.0 42.9 1.0 O A:TYM501 3.2 15.3 1.0 NZ A:LYS200 3.6 19.6 1.0 P A:TYM501 3.7 15.7 1.0 O A:HOH633 3.9 20.5 1.0 C A:TYM501 4.0 15.2 1.0 O A:PRO87 4.1 22.5 1.0 O A:HOH602 4.1 23.6 1.0 OPP A:TYM501 4.2 15.6 1.0 O2P A:TYM501 4.3 15.8 1.0 O A:HOH610 4.6 17.9 1.0 OE2 A:GLU199 4.8 17.1 1.0 O5' A:TYM501 5.0 15.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp


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 H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:42.9 occ:1.00 OG A:SER165 2.9 31.0 1.0 MG A:MG502 3.0 49.1 1.0 O A:GLY163 3.0 21.1 1.0 O A:HOH602 3.0 23.6 1.0 O1P A:TYM501 3.2 15.7 1.0 O2P A:TYM501 3.2 15.8 1.0 NH1 A:ARG162 3.2 19.4 1.0 CB A:SER165 3.6 30.1 1.0 P A:TYM501 3.7 15.7 1.0 NZ A:LYS200 3.8 19.6 1.0 C A:GLY163 4.0 21.1 1.0 O A:TYM501 4.1 15.3 1.0 O A:HOH657 4.1 25.9 1.0 CA A:GLY163 4.3 20.2 1.0 CZ A:ARG162 4.3 19.3 1.0 N A:SER165 4.4 27.6 1.0 CA A:SER165 4.7 29.8 1.0 CE A:LYS200 4.7 19.5 1.0 N A:GLY163 4.7 19.2 1.0 OPP A:TYM501 4.8 15.6 1.0 O5' A:TYM501 4.9 15.9 1.0 C A:TYM501 4.9 15.2 1.0 NH2 A:ARG162 4.9 19.6 1.0 CD A:LYS200 4.9 19.3 1.0 O A:HOH658 5.0 13.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp


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 Human H130R Tryptophanyl-Trna Synthetase in Complex with Trpamp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.6 occ:1.00 OD1 B:ASP312 2.4 17.1 1.0 O2P B:TYM501 2.7 15.5 1.0 O B:HOH614 3.4 17.8 1.0 C8 B:TYM501 3.5 16.9 1.0 NE2 B:GLN313 3.5 16.1 1.0 CG B:ASP312 3.6 16.8 1.0 P B:TYM501 3.8 15.7 1.0 O5' B:TYM501 3.8 15.9 1.0 O B:HOH633 3.9 23.1 1.0 O B:PRO87 3.9 22.5 1.0 NZ B:LYS349 4.0 27.8 1.0 CE B:LYS349 4.0 27.7 1.0 C2' B:TYM501 4.0 16.4 1.0 OD2 B:ASP312 4.2 17.3 1.0 N7 B:TYM501 4.2 16.9 1.0 OPP B:TYM501 4.3 15.4 1.0 N9 B:TYM501 4.4 16.6 1.0 O2' B:TYM501 4.5 16.4 1.0 C1' B:TYM501 4.7 16.5 1.0 CB B:ASP312 4.8 16.4 1.0 CD B:GLN313 4.8 15.9 1.0 C B:PRO87 4.9 22.5 1.0 C3' B:TYM501 4.9 16.2 1.0

X.Xu, H.Zhou, Q.Zhou, F.Hong, M.N.Vo, W.Niu, Z.Wang, X.Xiong, K.Nakamura, K.Wakasugi, P.Schimmel, X.L.Yang. An Alternative Conformation of Human Trprs Suggests A Role of Zinc in Activating Non-Enzymatic Function. Rna Biol V. 15 649 2018.
ISSN: ESSN 1555-8584
PubMed: 28910573
DOI: 10.1080/15476286.2017.1377868