Sodium in PDB 5jyx: Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like

The structure of Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like, PDB code: 5jyx was solved by X.Mei, M.A.Swairjo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	108.56 / 2.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.325, 126.779, 65.083, 90.00, 102.58, 90.00
R / Rfree (%)	17.1 / 25.9

The binding sites of Sodium atom in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like (pdb code 5jyx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like, PDB code: 5jyx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like


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 the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:37.5 occ:1.00 O C:HOH308 2.5 46.9 1.0 OG C:SER33 2.9 37.4 1.0 OE2 C:GLU31 3.2 55.3 1.0 O C:GLU31 3.4 29.1 1.0 O C:THR85 3.5 29.0 1.0 N C:SER33 3.6 30.8 1.0 C C:GLU31 3.7 31.1 1.0 C C:VAL32 3.8 28.3 1.0 CA C:VAL32 3.8 28.4 1.0 N C:VAL32 3.8 29.4 1.0 CG C:GLU31 3.8 47.6 1.0 CD C:GLU31 3.9 54.2 1.0 CE C:LYS87 4.0 47.1 1.0 CD C:LYS87 4.0 42.7 1.0 CG C:LYS87 4.0 38.6 1.0 CB C:SER33 4.2 33.7 1.0 CB C:GLU31 4.2 40.7 1.0 CG2 C:THR85 4.2 32.5 1.0 N C:LYS87 4.2 32.9 1.0 C C:THR85 4.2 30.4 1.0 CB C:LYS87 4.2 35.6 1.0 CB C:THR85 4.3 31.6 1.0 NZ C:LYS87 4.4 49.6 1.0 CA C:SER33 4.5 31.7 1.0 O C:VAL32 4.5 26.7 1.0 CA C:GLU31 4.5 34.9 1.0 CE C:LYS14 4.6 47.1 1.0 C C:VAL86 4.7 31.8 1.0 N C:VAL86 4.8 30.4 1.0 CA C:VAL86 4.8 30.5 1.0 CA C:LYS87 4.9 34.6 1.0 CG C:LYS14 4.9 38.0 1.0 CA C:THR85 5.0 31.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like


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 the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like within 5.0Å range: probe atom residue distance (Å) B Occ E:Na202 b:42.1 occ:1.00 O E:HOH305 2.3 51.8 1.0 OG E:SER33 3.0 39.7 1.0 O E:GLU31 3.5 34.6 1.0 O E:THR85 3.5 36.4 1.0 N E:SER33 3.5 34.1 1.0 CA E:VAL32 3.8 33.9 1.0 CG2 E:THR85 3.8 35.6 1.0 C E:VAL32 3.8 33.5 1.0 C E:GLU31 3.8 34.2 1.0 CB E:SER33 3.8 35.6 1.0 CE E:LYS87 3.8 40.8 1.0 CD E:LYS87 3.9 38.2 1.0 N E:VAL32 3.9 34.3 1.0 CG E:LYS87 4.0 35.9 1.0 OE1 E:GLU31 4.0 58.0 1.0 C E:THR85 4.0 34.6 1.0 CB E:THR85 4.0 35.9 1.0 CG E:GLU31 4.1 49.5 1.0 N E:LYS87 4.2 31.0 1.0 CA E:SER33 4.3 34.2 1.0 CB E:GLU31 4.4 42.4 1.0 N E:VAL86 4.5 33.9 1.0 CE E:LYS14 4.5 52.9 1.0 CA E:VAL86 4.5 32.3 1.0 CD E:GLU31 4.6 55.5 1.0 CB E:LYS87 4.6 33.7 1.0 O E:VAL32 4.6 31.6 1.0 C E:VAL86 4.6 31.5 1.0 CA E:THR85 4.7 35.5 1.0 NZ E:LYS14 4.7 56.4 1.0 CA E:GLU31 4.8 36.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like


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 the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like within 5.0Å range: probe atom residue distance (Å) B Occ L:Na202 b:47.3 occ:1.00 N L:SER33 3.6 52.1 1.0 CB L:SER33 3.7 56.8 1.0 O L:THR85 3.8 51.8 1.0 O L:GLU31 3.8 50.3 1.0 C L:GLU31 3.9 49.5 1.0 CD L:LYS87 3.9 54.9 1.0 N L:VAL32 3.9 49.5 1.0 C L:VAL32 4.0 49.6 1.0 CE L:LYS87 4.0 57.0 1.0 CA L:VAL32 4.0 49.4 1.0 CG L:GLU31 4.0 59.3 1.0 CG L:LYS87 4.0 53.4 1.0 CB L:GLU31 4.1 54.8 1.0 NZ L:LYS87 4.1 57.8 1.0 CG2 L:THR85 4.1 55.0 1.0 CA L:SER33 4.3 54.3 1.0 CB L:THR85 4.3 54.5 1.0 C L:THR85 4.3 50.9 1.0 N L:LYS87 4.4 48.9 1.0 CB L:LYS87 4.4 51.9 1.0 OE2 L:GLU31 4.5 63.9 1.0 CD L:GLU31 4.6 62.1 1.0 CA L:GLU31 4.6 51.1 1.0 C L:VAL86 4.6 47.9 1.0 O L:VAL32 4.8 52.2 1.0 CE L:LYS14 4.8 59.0 1.0 CA L:VAL86 4.8 48.9 1.0 CG L:LYS14 4.9 51.1 1.0 N L:VAL86 4.9 50.1 1.0 OG L:SER33 4.9 62.7 1.0 CA L:THR85 5.0 52.7 1.0

X.Mei, J.Alvarez, A.Bon Ramos, U.Samanta, D.Iwata-Reuyl, M.A.Swairjo. Crystal Structure of the Archaeosine Synthase Quef-Like-Insights Into Amidino Transfer and Trna Recognition By the Tunnel Fold. Proteins V. 85 103 2017.
ISSN: ESSN 1097-0134
PubMed: 27802572
DOI: 10.1002/PROT.25202