Magnesium in PDB 8phd: Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp

All present enzymatic activity of Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp:
3.6.5.3;

The structure of Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp, PDB code: 8phd was solved by E.Schmitt, Y.Mechulam, C.Cardenal Peralta, J.Fagart, W.Seufert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.22 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.462, 126.02, 74.644, 90, 90.06, 90
R / Rfree (%)	17.6 / 20.5

The binding sites of Magnesium atom in the Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp (pdb code 8phd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp, PDB code: 8phd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:26.5 occ:1.00 O A:HOH522 2.1 22.9 1.0 O A:HOH514 2.1 27.6 1.0 OD2 A:ASP246 2.1 25.1 1.0 O3G A:ATP401 2.1 25.6 1.0 OD1 A:ASN248 2.2 32.2 1.0 O1B A:ATP401 2.3 26.2 1.0 CG A:ASP246 3.1 26.7 1.0 CG A:ASN248 3.3 26.8 1.0 PG A:ATP401 3.5 29.0 1.0 PB A:ATP401 3.5 22.5 1.0 CB A:ASP246 3.6 22.2 1.0 O3B A:ATP401 3.7 25.2 1.0 ND2 A:ASN248 3.8 27.3 1.0 OD2 A:ASP233 4.0 35.1 1.0 O A:HOH539 4.1 24.4 1.0 OD1 A:ASP246 4.2 25.9 1.0 O1A A:ATP401 4.2 27.1 1.0 O1G A:ATP401 4.3 34.5 1.0 NZ A:LYS104 4.3 23.8 1.0 O A:HOH572 4.4 39.0 1.0 O3A A:ATP401 4.4 21.0 1.0 O A:TRP107 4.4 20.9 1.0 O A:PHE247 4.5 31.6 1.0 O2G A:ATP401 4.5 32.0 1.0 CB A:ASN248 4.6 26.5 1.0 NH2 A:ARG193 4.6 33.2 1.0 O A:HOH526 4.6 37.3 1.0 O2B A:ATP401 4.7 24.4 1.0 PA A:ATP401 4.8 21.2 1.0 NH2 A:ARG179 4.8 25.6 1.0 C A:PHE247 4.9 28.4 1.0 CA A:ASP246 4.9 25.0 1.0 O A:HOH595 5.0 40.2 1.0

Magnesium binding site 2 out of 2 in the Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human CDC123 Complexed with Domain 3 of EIF2 Gamma and Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:21.9 occ:1.00 O C:HOH504 2.1 25.8 1.0 O C:HOH558 2.1 24.5 1.0 OD2 C:ASP246 2.1 25.4 1.0 OD1 C:ASN248 2.2 33.3 1.0 O3G C:ATP401 2.2 30.9 1.0 O1B C:ATP401 2.4 30.6 1.0 O3B C:ATP401 2.8 22.2 1.0 PB C:ATP401 3.1 21.7 1.0 PG C:ATP401 3.1 32.0 1.0 CG C:ASP246 3.3 30.1 1.0 CG C:ASN248 3.3 34.5 1.0 CB C:ASP246 3.8 26.4 1.0 ND2 C:ASN248 3.8 25.8 1.0 O2G C:ATP401 3.9 31.1 1.0 OD2 C:ASP233 4.1 29.6 1.0 O C:HOH545 4.2 32.0 1.0 O3A C:ATP401 4.2 20.7 1.0 O1A C:ATP401 4.2 26.0 1.0 O2B C:ATP401 4.3 19.4 1.0 O C:HOH531 4.3 25.6 1.0 OD1 C:ASP246 4.3 29.2 1.0 O C:TRP107 4.4 25.8 1.0 O1G C:ATP401 4.4 27.3 1.0 O C:HOH555 4.4 39.2 1.0 NH2 C:ARG193 4.6 26.3 1.0 NZ C:LYS104 4.6 21.4 1.0 CB C:ASN248 4.6 28.2 1.0 PA C:ATP401 4.7 18.9 1.0 O C:PHE247 4.8 26.3 1.0 NH2 C:ARG179 4.8 26.1 1.0

C.Cardenal Peralta, P.Vandroux, L.Neumann-Arnold, M.Panvert, J.Fagart, W.Seufert, Y.Mechulam, E.Schmitt. Binding of Human CDC123 to EIF2 Gamma. J.Struct.Biol. V. 215 08006 2023.
ISSN: ESSN 1095-8657
PubMed: 37507029
DOI: 10.1016/J.JSB.2023.108006