Magnesium in PDB 5y8v: Crystal Structure of GAS41

The structure of Crystal Structure of GAS41, PDB code: 5y8v was solved by Y.Wang, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.50 / 2.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.467, 57.212, 205.854, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 28

The binding sites of Magnesium atom in the Crystal Structure of GAS41 (pdb code 5y8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of GAS41, PDB code: 5y8v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of GAS41


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 GAS41 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:40.3 occ:1.00 N B:LYS132 3.5 52.1 1.0 OG1 B:THR133 3.5 44.9 1.0 NZ B:LYS131 3.8 51.0 1.0 N B:THR133 3.8 46.5 1.0 CA B:LYS131 4.1 57.4 1.0 CB B:THR133 4.1 42.9 1.0 C B:LYS131 4.3 54.3 1.0 CA B:LYS132 4.3 51.3 1.0 CB B:LYS131 4.4 57.6 1.0 C B:LYS132 4.5 47.4 1.0 CE B:LYS131 4.6 53.7 1.0 CB B:LYS132 4.6 54.1 1.0 CA B:THR133 4.6 43.4 1.0 NH2 B:ARG32 4.7 78.5 1.0 CG B:LYS131 4.8 59.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of GAS41


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 GAS41 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:52.0 occ:1.00 CE A:LYS131 3.5 60.9 1.0 N A:LYS132 3.5 59.6 1.0 OG1 A:THR133 3.6 49.4 1.0 N A:THR133 3.9 52.5 1.0 NZ A:LYS131 4.0 55.6 1.0 CB A:THR133 4.0 49.5 1.0 CB A:LYS132 4.2 56.5 1.0 CA A:LYS132 4.2 56.3 1.0 CA A:LYS131 4.3 65.5 1.0 C A:LYS131 4.5 63.6 1.0 C A:LYS132 4.5 52.4 1.0 CA A:THR133 4.6 48.9 1.0 CB A:LYS131 4.7 64.5 1.0 CD A:LYS131 4.8 62.8 1.0 CG A:LYS131 4.9 64.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of GAS41


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 GAS41 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:60.5 occ:1.00 O C:HOH306 1.9 65.2 1.0 O C:HOH322 2.4 65.5 1.0 NH1 C:ARG32 2.9 55.8 1.0 OG1 C:THR133 3.5 57.2 1.0 N C:LYS132 3.6 68.0 1.0 CZ C:ARG32 4.1 54.9 1.0 N C:THR133 4.2 58.6 1.0 CA C:LYS131 4.3 82.3 1.0 CB C:LYS132 4.4 60.4 1.0 CA C:LYS132 4.4 63.0 1.0 C C:LYS131 4.4 73.8 1.0 CB C:LYS131 4.4 78.6 1.0 CB C:THR133 4.7 55.2 1.0 C C:LYS132 4.7 57.9 1.0 CD C:LYS131 4.7 86.6 1.0 NH2 C:ARG32 4.7 54.8 1.0 CE C:LYS131 4.9 85.6 1.0 NE C:ARG32 5.0 53.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of GAS41


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of GAS41 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:52.6 occ:1.00 O D:HOH331 1.9 48.8 1.0 N D:LYS132 3.0 62.0 1.0 OG1 D:THR133 3.5 57.5 1.0 N D:THR133 3.6 52.5 1.0 CA D:LYS132 3.8 55.6 1.0 CB D:LYS132 3.8 52.2 1.0 C D:LYS131 3.9 69.2 1.0 CA D:LYS131 3.9 69.7 1.0 CB D:LYS131 4.1 69.2 1.0 C D:LYS132 4.1 52.8 1.0 NH2 D:ARG32 4.4 47.4 1.0 CB D:THR133 4.5 48.4 1.0 CA D:THR133 4.6 48.8 1.0 CG2 D:THR133 4.8 47.1 1.0 CD D:LYS131 4.9 72.1 1.0 CG D:LYS131 4.9 72.0 1.0 CG D:LYS132 5.0 53.0 1.0

Y.Wang, J.Jin, M.W.H.Chung, L.Feng, H.Sun, Q.Hao. Identification of the Yeats Domain of GAS41 As A pH-Dependent Reader of Histone Succinylation Proc. Natl. Acad. Sci. V. 115 2365 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29463709
DOI: 10.1073/PNAS.1717664115