Sodium in PDB 6uio: Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic)

The structure of Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic), PDB code: 6uio was solved by M.J.Dominguez, G.A.Cornwall, A.Hewetson, R.B.Sutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.53 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.048, 85.924, 111.677, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.2

The structure of Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic) also contains other interesting chemical elements:

Iodine	(I)	26 atoms
Chlorine	(Cl)	8 atoms

The binding sites of Sodium atom in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic) (pdb code 6uio). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic), PDB code: 6uio:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic)


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 Mouse Cres (Cystatin-Related Epididymal Spermatogenic) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na215 b:31.4 occ:1.00 HD12 C:ILE71 3.3 46.8 1.0 HE3 C:LYS46 3.3 64.4 1.0 HZ1 C:LYS46 3.3 63.2 1.0 HZ2 C:LYS46 3.7 63.2 1.0 HB C:ILE71 3.7 45.0 1.0 NZ C:LYS46 3.8 52.7 1.0 HG13 C:ILE40 3.9 34.6 1.0 CE C:LYS46 4.0 53.7 1.0 HD12 C:ILE40 4.0 49.2 1.0 O2 C:SO4208 4.1 62.4 1.0 O C:ILE40 4.3 42.0 1.0 CD1 C:ILE71 4.3 39.0 1.0 HB C:ILE40 4.4 38.4 1.0 HE2 C:LYS46 4.4 64.4 1.0 HA C:SER41 4.5 44.6 1.0 CB C:ILE71 4.6 37.5 1.0 HG22 B:ILE38 4.6 61.7 1.0 CG1 C:ILE40 4.6 28.8 1.0 HG2 C:LYS46 4.6 42.8 1.0 H C:ILE71 4.6 34.0 1.0 HZ3 C:LYS46 4.7 63.2 1.0 HD13 C:ILE71 4.7 46.8 1.0 CD1 C:ILE40 4.7 41.0 1.0 HD11 C:ILE71 4.7 46.8 1.0 HG13 C:ILE71 4.7 44.9 1.0 CG1 C:ILE71 4.8 37.4 1.0 C C:ILE40 4.8 38.4 1.0 O4 C:SO4208 4.9 53.3 1.0 I C:IOD205 5.0 48.6 1.0 S C:SO4208 5.0 48.4 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic)


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 Mouse Cres (Cystatin-Related Epididymal Spermatogenic) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na216 b:43.2 occ:1.00 HB3 C:ASP80 3.6 61.1 1.0 HA C:ASP80 4.1 50.4 1.0 CB C:ASP80 4.4 50.9 1.0 H C:ASP80 4.4 50.4 1.0 N C:ASP80 4.5 42.0 1.0 CA C:ASP80 4.5 42.0 1.0 HB2 C:ASP80 4.9 61.1 1.0 C C:THR79 4.9 35.3 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic)


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 Mouse Cres (Cystatin-Related Epididymal Spermatogenic) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na216 b:38.9 occ:1.00 HB2 D:SER136 3.1 52.7 1.0 O D:SER120 3.1 33.8 1.0 HB3 D:SER120 3.4 56.9 1.0 HB3 D:SER136 3.5 52.7 1.0 C D:SER120 3.7 35.2 1.0 CB D:SER136 3.7 43.9 1.0 HA D:LYS137 3.8 44.0 1.0 C D:SER136 3.9 29.1 1.0 HA D:PHE121 3.9 32.6 1.0 HB2 D:LEU122 3.9 34.0 1.0 HB2 D:GLU138 3.9 50.5 1.0 H D:LEU122 4.0 36.7 1.0 O D:SER136 4.0 30.9 1.0 N D:LYS137 4.0 35.6 1.0 HB3 D:GLU138 4.1 50.5 1.0 H D:GLU138 4.1 40.6 1.0 C D:LYS137 4.1 39.0 1.0 CB D:SER120 4.2 47.4 1.0 N D:GLU138 4.2 33.8 1.0 CA D:LYS137 4.2 36.7 1.0 N D:LEU122 4.2 30.6 1.0 OG D:SER120 4.3 60.0 1.0 N D:PHE121 4.3 26.3 1.0 CA D:PHE121 4.4 27.1 1.0 C D:PHE121 4.4 32.7 1.0 CB D:GLU138 4.4 42.1 1.0 H D:LYS137 4.4 42.7 1.0 CA D:SER136 4.4 32.6 1.0 HB3 D:LEU122 4.5 34.0 1.0 CA D:SER120 4.5 38.9 1.0 CB D:LEU122 4.6 28.4 1.0 O D:LYS137 4.6 39.7 1.0 HG D:SER136 4.8 75.7 1.0 OG D:SER136 4.9 63.1 1.0 H D:PHE121 4.9 31.5 1.0 CA D:GLU138 5.0 35.2 1.0 HB2 D:SER120 5.0 56.9 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic)


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 Mouse Cres (Cystatin-Related Epididymal Spermatogenic) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na217 b:23.5 occ:1.00 OG D:SER37 3.0 60.1 1.0 HZ1 D:LYS75 3.1 76.9 1.0 HZ3 D:LYS75 3.2 76.9 1.0 NZ D:LYS75 3.4 64.1 1.0 HZ2 D:LYS75 3.5 76.9 1.0 HB2 D:SER37 3.5 71.3 1.0 HG D:SER37 3.6 72.2 1.0 CB D:SER37 3.8 59.4 1.0 H D:SER37 4.3 54.0 1.0 HB3 D:SER37 4.4 71.3 1.0 HE1 D:HIS73 4.4 56.8 1.0 NE2 D:HIS73 4.5 47.2 1.0 CE1 D:HIS73 4.8 47.3 1.0 CE D:LYS75 4.9 58.9 1.0 N D:SER37 4.9 45.0 1.0 CA D:SER37 4.9 55.2 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic)


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 Mouse Cres (Cystatin-Related Epididymal Spermatogenic) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na218 b:45.6 occ:1.00 HB1 D:ALA43 3.4 41.5 1.0 CB D:ALA43 4.2 34.6 1.0 HB3 D:ALA43 4.3 41.5 1.0 HB2 D:ALA43 4.6 41.5 1.0 OE1 D:GLN47 4.8 27.1 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Mouse Cres (Cystatin-Related Epididymal Spermatogenic)


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 Mouse Cres (Cystatin-Related Epididymal Spermatogenic) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na219 b:86.6 occ:1.00 HE21 D:GLN77 2.2 45.1 1.0 OG1 D:THR79 2.3 41.2 1.0 HG3 D:GLU83 2.5 43.4 1.0 HG23 D:THR79 2.7 55.4 1.0 HB2 D:GLU83 2.8 34.5 1.0 H D:THR79 2.9 38.1 1.0 NE2 D:GLN77 3.0 37.5 1.0 HG2 D:GLN77 3.0 37.8 1.0 CG D:GLU83 3.1 36.1 1.0 CD D:GLU83 3.1 49.1 1.0 O D:GLN77 3.2 28.3 1.0 O D:ARG81 3.2 30.1 0.3 O D:ARG81 3.2 30.2 0.7 CG2 D:THR79 3.2 46.2 1.0 CB D:THR79 3.2 38.8 1.0 HG21 D:THR79 3.3 55.4 1.0 OE2 D:GLU83 3.3 47.5 1.0 N D:THR79 3.3 31.7 1.0 CB D:GLU83 3.4 28.8 1.0 HE22 D:GLN77 3.5 45.1 1.0 HB3 D:GLN77 3.5 34.6 1.0 HG2 D:ARG81 3.6 44.1 0.3 H D:GLU83 3.6 36.4 1.0 OE1 D:GLU83 3.6 47.1 1.0 CG D:GLN77 3.7 31.5 1.0 C D:GLN77 3.8 33.2 1.0 CD D:GLN77 3.8 33.7 1.0 N D:GLU83 3.8 30.3 1.0 CA D:THR79 3.9 36.8 1.0 HG3 D:ARG81 3.9 44.1 0.7 HG2 D:GLU83 4.0 43.4 1.0 CB D:GLN77 4.0 28.8 1.0 HB D:THR79 4.0 46.5 1.0 C D:ILE78 4.1 31.5 1.0 HE D:ARG81 4.1 42.3 0.3 HG22 D:THR79 4.1 55.4 1.0 H D:ARG81 4.1 37.0 0.3 H D:ARG81 4.1 36.8 0.7 HB3 D:GLU83 4.1 34.5 1.0 C D:ARG81 4.2 30.2 0.3 C D:ARG81 4.2 30.6 0.7 HA D:ILE78 4.2 41.8 1.0 CA D:GLU83 4.2 28.6 1.0 HG3 D:ARG81 4.3 44.1 0.3 HG2 D:ARG81 4.3 44.1 0.7 N D:ILE78 4.3 32.8 1.0 CG D:ARG81 4.4 36.8 0.3 C D:MET82 4.4 34.1 1.0 HA D:MET82 4.4 31.1 1.0 CA D:ILE78 4.5 34.9 1.0 CA D:GLN77 4.5 31.5 1.0 CG D:ARG81 4.5 36.7 0.7 HG3 D:GLN77 4.6 37.8 1.0 HA D:THR79 4.6 44.1 1.0 C D:THR79 4.7 38.6 1.0 CA D:MET82 4.8 25.9 1.0 HA D:GLU83 4.8 34.3 1.0 NE D:ARG81 4.9 35.3 0.3 O D:ILE78 4.9 31.6 1.0 N D:ARG81 4.9 30.9 0.3 N D:ARG81 4.9 30.6 0.7 HB2 D:GLN77 4.9 34.6 1.0 N D:MET82 4.9 31.5 1.0 OE1 D:GLN77 4.9 36.6 1.0 H D:GLN77 5.0 32.9 1.0 H D:ILE78 5.0 39.4 1.0 O D:MET82 5.0 29.4 1.0

A.Hewetson, N.H.Khan, M.J.Dominguez, H.Q.Do, R.E.Kusko, C.G.Borcik, D.J.Rigden, R.M.Keegan, R.B.Sutton, M.P.Latham, B.J.Wylie, G.A.Cornwall. Maturation of the Functional Mouse Cres Amyloid From Globular Form. Proc.Natl.Acad.Sci.Usa V. 117 16363 2020.
ISSN: ESSN 1091-6490
PubMed: 32601205
DOI: 10.1073/PNAS.2006887117