Sodium 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:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 13 binding sites of Sodium where determined in the Crystal Structure of CDC3(G) - CDC10(Delta 1-10) Heterocomplex From Saccharomyces Cerevisiae, PDB code: 8sgd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 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 Sodium with other atoms in the Na 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 A:Na402 b:8.3 occ:1.00 NE A:ARG167 3.8 63.7 1.0 CD A:ARG167 3.8 65.1 1.0 CG A:GLU112 4.0 54.8 1.0 CD1 A:TRP111 4.1 49.3 1.0 CG1 A:VAL115 4.1 42.1 1.0 CB A:VAL115 4.1 41.3 1.0 CG2 A:VAL115 4.2 42.1 1.0 NE1 A:TRP111 4.3 48.5 1.0 CA A:GLU112 4.4 48.6 1.0 CB A:GLU112 4.6 47.2 1.0 CZ A:ARG167 4.8 53.5 1.0 CD A:GLU112 4.9 66.0 1.0 OE2 A:GLU112 5.0 65.5 1.0

Sodium binding site 2 out of 13 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 Sodium with other atoms in the Na 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 A:Na403 b:13.8 occ:1.00 CG A:LYS116 3.8 49.6 1.0 CE A:LYS116 3.9 73.8 1.0 CA A:TYR117 4.0 40.2 1.0 CG A:GLU120 4.2 48.5 1.0 CD1 A:TYR117 4.2 46.6 1.0 CB A:GLU120 4.2 47.2 1.0 CD A:LYS116 4.3 54.4 1.0 N A:TYR117 4.3 48.5 1.0 CB A:TYR117 4.5 39.5 1.0 O A:LYS116 4.5 46.0 1.0 C A:LYS116 4.6 49.0 1.0 CG A:TYR117 4.8 44.2 1.0 CB A:LYS116 5.0 43.1 1.0

Sodium binding site 3 out of 13 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 Sodium with other atoms in the Na binding site number 3 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 A:Na404 b:22.1 occ:1.00 N A:ILE105 3.7 54.1 1.0 CB B:PRO266 3.8 40.7 1.0 CD1 A:PHE104 4.0 56.5 1.0 CG B:PRO266 4.1 40.8 1.0 CB A:ILE105 4.1 51.8 1.0 CG1 A:ILE105 4.1 52.5 1.0 CD1 A:ILE105 4.1 54.4 1.0 CB A:PHE104 4.2 47.0 1.0 CA A:PHE104 4.4 52.3 1.0 CD A:LYS73 4.4 65.2 1.0 CE A:LYS73 4.4 75.2 1.0 CA A:ILE105 4.6 50.0 1.0 C A:PHE104 4.6 55.9 1.0 CG A:PHE104 4.6 55.8 1.0 CG A:LYS73 4.6 62.1 1.0 CE1 A:PHE104 4.9 53.5 1.0 NZ A:LYS73 5.0 93.8 1.0

Sodium binding site 4 out of 13 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 Sodium with other atoms in the Na binding site number 4 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:Na503 b:15.7 occ:1.00 N B:GLN216 3.6 62.0 1.0 CA B:ASP215 3.9 49.9 1.0 CB B:ASP215 4.1 51.4 1.0 CD1 A:ILE105 4.2 54.4 1.0 C B:ASP215 4.2 57.5 1.0 CG B:LYS270 4.3 67.9 1.0 CB B:GLN216 4.3 65.6 1.0 CA B:GLN216 4.5 53.8 1.0 CG2 A:ILE105 4.5 52.9 1.0 CD B:LYS270 4.5 69.5 1.0 CE B:LYS270 4.8 86.3 1.0 CB B:LYS270 4.9 53.7 1.0

Sodium binding site 5 out of 13 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 Sodium with other atoms in the Na binding site number 5 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:Na504 b:17.3 occ:1.00 N B:LEU212 3.6 51.2 1.0 CE1 B:HIS180 3.7 106.5 1.0 ND1 B:HIS180 3.8 96.4 1.0 NE2 B:HIS180 3.9 106.3 1.0 NH1 A:ARG159 3.9 78.8 1.0 CA B:PHE211 4.0 57.9 1.0 CB B:PHE211 4.0 52.2 1.0 CD1 B:PHE211 4.1 66.0 1.0 CG B:HIS180 4.1 89.6 1.0 CG A:ARG159 4.1 58.8 1.0 CD2 B:HIS180 4.1 87.8 1.0 CG B:LEU212 4.2 46.5 1.0 CB B:LEU212 4.3 45.5 1.0 C B:PHE211 4.4 54.3 1.0 CD1 B:LEU212 4.5 48.9 1.0 CG B:PHE211 4.6 62.2 1.0 CB A:ARG159 4.6 46.1 1.0 CA B:LEU212 4.6 50.5 1.0 CZ A:ARG159 4.9 76.3 1.0 CB B:HIS180 4.9 80.0 1.0 CD A:ARG159 4.9 43.8 1.0

Sodium binding site 6 out of 13 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 Sodium with other atoms in the Na binding site number 6 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:Na505 b:20.1 occ:1.00 O B:PRO259 4.1 51.3 1.0 C B:PRO259 4.1 42.8 1.0 CG B:PRO259 4.2 36.7 1.0 CD B:PRO259 4.2 36.0 1.0 O A:GLY42 4.2 54.8 1.0 N B:THR260 4.3 42.4 1.0 CD A:LYS180 4.4 47.5 1.0 N B:PRO259 4.4 48.0 1.0 CA B:THR260 4.5 49.1 1.0 CB B:GLU258 4.5 52.4 1.0 CG2 B:THR260 4.6 51.5 1.0 CD2 A:LEU43 4.6 50.5 1.0 O B:HOH642 4.7 32.8 1.0 NE2 A:GLN151 4.7 79.7 1.0 CA B:PRO259 4.7 42.3 1.0 NZ A:LYS180 4.8 40.7 1.0 C B:GLU258 4.9 50.5 1.0 CB B:PRO259 5.0 38.6 1.0

Sodium binding site 7 out of 13 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 Sodium with other atoms in the Na binding site number 7 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 C:Na402 b:10.7 occ:1.00 O C:HOH517 3.7 66.0 1.0 CD C:ARG167 4.0 61.5 1.0 NE C:ARG167 4.0 62.9 1.0 CG1 C:VAL115 4.1 42.9 1.0 CB C:VAL115 4.2 42.4 1.0 CG C:GLU112 4.2 52.3 1.0 CD1 C:TRP111 4.3 51.9 1.0 CA C:GLU112 4.4 42.2 1.0 CG2 C:VAL115 4.5 45.6 1.0 CB C:GLU112 4.6 42.3 1.0 NE1 C:TRP111 4.6 54.2 1.0 CD C:GLU112 4.9 54.1 1.0

Sodium binding site 8 out of 13 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 Sodium with other atoms in the Na binding site number 8 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 C:Na403 b:26.7 occ:1.00 NE C:ARG25 3.7 54.2 1.0 CD C:ARG25 3.7 52.6 1.0 CB C:ARG25 3.8 38.1 1.0 CD2 C:LEU26 4.0 39.7 1.0 CG C:ARG25 4.4 46.7 1.0 CG2 C:ILE22 4.4 47.1 1.0 O C:ILE22 4.5 50.9 1.0 CG C:LEU26 4.7 41.4 1.0 CA C:ILE22 4.7 51.7 1.0 CZ C:ARG25 4.9 47.0 1.0 CB C:ILE22 5.0 51.9 1.0 CG1 C:ILE22 5.0 43.5 1.0

Sodium binding site 9 out of 13 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 Sodium with other atoms in the Na binding site number 9 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 C:Na404 b:19.7 occ:1.00 OE2 C:GLU285 2.6 79.2 1.0 NE2 C:GLN281 3.4 51.9 1.0 CD C:GLU285 3.6 75.7 1.0 CG C:GLU285 4.1 54.1 1.0 CG C:GLN281 4.2 54.2 1.0 CD C:GLN281 4.2 55.9 1.0 OE1 C:GLU285 4.5 75.0 1.0

Sodium binding site 10 out of 13 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 Sodium with other atoms in the Na binding site number 10 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 C:Na405 b:28.2 occ:1.00 OG1 C:THR278 3.3 56.6 1.0 CG2 C:VAL226 3.4 61.2 1.0 CD2 C:LEU222 3.5 54.1 1.0 CG2 C:THR278 4.0 48.5 1.0 CB C:THR278 4.0 53.6 1.0 CA C:PHE274 4.2 53.4 1.0 CD1 C:PHE274 4.3 47.6 1.0 CG C:LEU222 4.4 63.3 1.0 CB C:PHE274 4.5 54.0 1.0 N C:PHE274 4.5 52.5 1.0 CE1 C:HIS279 4.5 53.6 1.0 ND1 C:HIS279 4.6 52.9 1.0 CB C:VAL226 4.6 52.4 1.0 O C:GLU273 4.7 55.3 1.0 C C:GLU273 4.7 55.8 1.0 CG1 C:VAL226 4.8 45.6 1.0 CG C:PHE274 4.9 49.1 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