Sodium in PDB 5u92: Crystal Structure of Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine

All present enzymatic activity of Crystal Structure of Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine:
2.7.3.3;

The structure of Crystal Structure of Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine, PDB code: 5u92 was solved by A.A.Lopez-Zavala, C.F.Garcia, J.Paredes-Hernandez, V.Stojanoff, R.R.Sotelo-Mundo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.090, 61.450, 60.600, 90.00, 95.75, 90.00
R / Rfree (%)	16.8 / 23.7

The binding sites of Sodium atom in the Crystal Structure of Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine (pdb code 5u92). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine, PDB code: 5u92:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine


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 Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:38.6 occ:1.00 HZ2 A:LYS328 1.9 33.2 0.7 HZ3 A:LYS328 2.3 33.2 0.7 NZ A:LYS328 2.4 33.2 0.7 HD2 A:LYS328 2.5 29.9 0.2 HD3 A:LYS328 2.7 29.9 0.2 CD A:LYS328 2.9 29.9 0.2 HA A:HIS90 3.0 23.5 0.7 O A:TYR89 3.1 22.1 0.9 HZ1 A:LYS328 3.2 33.2 0.7 CE A:LYS328 3.2 32.0 0.6 O A:LYS328 3.7 26.0 1.0 HE3 A:LYS328 3.7 32.0 0.6 CA A:HIS90 3.9 23.5 0.7 HE2 A:LYS328 3.9 32.0 0.6 HE2 A:TYR89 4.0 24.2 1.0 HG3 A:GLU91 4.1 28.6 0.9 C A:TYR89 4.1 23.1 0.7 CE2 A:TYR89 4.1 24.2 1.0 O A:HOH534 4.1 46.7 1.0 HB2 A:GLU91 4.2 28.1 1.0 O A:HOH611 4.3 21.4 0.9 CD2 A:TYR89 4.3 23.6 1.0 HD2 A:TYR89 4.3 23.6 1.0 C A:HIS90 4.4 24.2 0.7 CG A:LYS328 4.4 29.6 0.6 HA A:ARG329 4.4 30.0 1.0 N A:HIS90 4.5 22.5 0.9 HB3 A:LYS328 4.5 26.9 0.9 C A:LYS328 4.5 23.7 1.0 O A:HOH674 4.6 30.4 0.8 ND1 A:HIS90 4.6 22.4 0.9 CZ A:TYR89 4.6 25.9 0.8 O A:HIS90 4.7 23.8 0.8 CD A:GLU91 4.7 31.7 0.7 CG A:GLU91 4.7 28.6 0.9 HG3 A:LYS328 4.8 29.6 0.6 CB A:HIS90 4.9 21.8 1.0 CB A:LYS328 4.9 26.9 0.9 OE1 A:GLU91 4.9 33.9 0.5 N A:GLU91 4.9 24.5 0.9 HG2 A:LYS328 4.9 29.6 0.6 CB A:GLU91 4.9 28.1 1.0 HB3 A:HIS90 4.9 21.8 1.0 CG A:HIS90 5.0 21.7 0.6 OE2 A:GLU91 5.0 34.1 0.2

Sodium binding site 2 out of 2 in the Crystal Structure of Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine


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 Arginine Kinase From the Spider Polybetes Pythagoricus in Complex with Arginine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:48.9 occ:1.00 HG2 A:GLU348 2.8 29.5 0.7 OE1 A:GLU348 2.9 30.1 0.7 HB3 A:ASP344 3.2 24.7 1.0 HA A:ASP344 3.4 25.4 1.0 CG A:GLU348 3.5 29.5 0.7 CD A:GLU348 3.6 29.5 0.7 O A:ASP344 3.6 24.4 0.8 HB2 A:LEU347 3.7 24.4 1.0 HG3 A:GLU348 3.8 29.5 0.7 CB A:ASP344 3.9 24.7 1.0 HD12 A:LEU347 3.9 26.4 1.0 CA A:ASP344 4.0 25.4 1.0 HZ2 A:LYS351 4.1 27.1 0.9 CG A:ASP344 4.2 27.5 0.9 C A:ASP344 4.2 24.3 0.9 HD13 A:LEU347 4.2 26.4 1.0 HB3 A:LEU347 4.2 24.4 1.0 OD1 A:ASP344 4.3 27.5 0.6 HZ1 A:LYS351 4.3 27.1 0.9 CB A:LEU347 4.4 24.4 1.0 H A:GLU348 4.5 26.4 0.8 O A:HOH790 4.5 35.0 0.7 CD1 A:LEU347 4.5 26.4 1.0 NZ A:LYS351 4.6 27.1 0.9 HE3 A:LYS351 4.6 26.4 0.9 OE2 A:GLU348 4.7 28.7 1.0 HB2 A:ASP344 4.8 24.7 1.0 N A:GLU348 4.8 26.4 0.8 OD2 A:ASP344 4.8 27.8 0.8 CB A:GLU348 4.9 30.8 1.0 O A:HOH642 5.0 51.7 1.0

A.Laino, A.A.Lopez-Zavala, K.D.Garcia-Orozco, J.S.Carrasco-Miranda, M.Santana, V.Stojanoff, R.R.Sotelo-Mundo, C.F.Garcia. Biochemical and Structural Characterization of A Novel Arginine Kinase From the Spider Polybetes Pythagoricus. Peerj V. 5 E3787 2017.
ISSN: ESSN 2167-8359
PubMed: 28924503
DOI: 10.7717/PEERJ.3787