Magnesium in PDB 8sgd: Crystal Structure of CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae

The structure of Crystal Structure of CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae, PDB code: 8sgd was solved by G.C.R.Saladino, D.A.Leonardo, H.M.Pereira, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.35 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.277, 154.271, 156.264, 90, 90, 90
R / Rfree (%)	20.6 / 25.5

The structure of Crystal Structure of CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Sodium

(Na)

13 atoms

The binding sites of Magnesium atom in the Crystal Structure of CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae (pdb code 8sgd). 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 CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae, PDB code: 8sgd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae


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 CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:61.6 occ:1.00 O1G B:GTP501 2.1 65.2 1.0 OG1 B:THR133 2.2 60.9 1.0 O B:HOH637 2.2 69.9 1.0 O B:HOH603 2.3 59.4 1.0 O2B B:GTP501 2.6 51.2 1.0 CB B:THR133 3.3 55.0 1.0 PG B:GTP501 3.3 97.5 1.0 OE2 B:GLU146 3.3 81.5 1.0 O3G B:GTP501 3.7 76.2 1.0 PB B:GTP501 3.8 40.7 1.0 O3B B:GTP501 4.0 66.5 1.0 OE1 B:GLU146 4.1 66.1 1.0 OD2 B:ASP204 4.1 85.9 1.0 CD B:GLU146 4.1 75.3 1.0 CG2 B:THR133 4.1 42.9 1.0 O2A B:GTP501 4.3 57.1 1.0 CA B:THR133 4.4 50.0 1.0 N B:THR133 4.4 48.9 1.0 O2G B:GTP501 4.5 85.1 1.0 O3A B:GTP501 4.7 52.2 1.0 PA B:GTP501 4.9 42.5 1.0 O1B B:GTP501 4.9 47.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae


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 CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.1 occ:1.00 OG1 D:THR133 2.0 62.1 1.0 O1G D:GTP501 2.2 83.7 1.0 O2B D:GTP501 2.7 59.1 1.0 CB D:THR133 3.4 63.4 1.0 OD2 D:ASP204 3.4 76.6 1.0 PG D:GTP501 3.6 100.5 1.0 OE2 D:GLU146 3.8 109.2 1.0 PB D:GTP501 3.8 47.4 1.0 N D:THR133 3.8 55.6 1.0 O3B D:GTP501 3.9 59.5 1.0 CA D:THR133 4.0 57.7 1.0 OE1 D:GLU146 4.1 107.5 1.0 CG D:ASP204 4.1 69.1 1.0 CG2 D:THR133 4.2 63.0 1.0 CD D:GLU146 4.4 111.7 1.0 O3G D:GTP501 4.5 85.6 1.0 OD1 D:ASP204 4.5 74.3 1.0 O2G D:GTP501 4.5 82.8 1.0 CB D:LYS132 4.6 38.8 1.0 O1B D:GTP501 4.6 51.3 1.0 O2A D:GTP501 4.7 54.2 1.0 C D:LYS132 4.8 55.3 1.0 CE D:LYS132 4.8 53.5 1.0 NZ D:LYS132 5.0 42.2 1.0

R.Marques Da Silva, G.Christe Dos Reis Saladino, D.Antonio Leonardo, H.D'muniz Pereira, S.Andrea Sculaccio, A.Paula Ulian Araujo, R.Charles Garratt. A Key Piece of the Puzzle: the Central Tetramer of the Saccharomyces Cerevisiae Septin Protofilament and Its Implications For Self-Assembly. J.Struct.Biol. V. 215 07983 2023.
ISSN: ESSN 1095-8657
PubMed: 37315820
DOI: 10.1016/J.JSB.2023.107983