Sodium in PDB 4kxh: The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease

All present enzymatic activity of The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease:
3.1.27.5;

The structure of The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease, PDB code: 4kxh was solved by A.Pica, A.Merlino, L.Mazzarella, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.506, 74.319, 128.533, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.6

The structure of The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease (pdb code 4kxh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease, PDB code: 4kxh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:20.0 occ:1.00 O A:HOH306 2.6 4.6 1.0 O B:HOH324 2.7 15.4 1.0 O A:HOH315 2.9 6.5 1.0 N B:LEU51 3.3 14.6 1.0 CD2 C:LEU51 3.6 14.0 1.0 OG A:SER15 3.7 17.3 1.0 CB A:SER15 3.8 18.2 1.0 CA B:PRO50 3.8 12.8 1.0 CB B:LEU51 3.9 15.2 1.0 CB C:LEU51 4.0 13.8 1.0 C B:PRO50 4.0 13.8 1.0 O C:HOH333 4.1 10.4 1.0 CA B:LEU51 4.2 14.8 1.0 O C:HOH320 4.3 5.2 1.0 O A:HOH311 4.3 12.7 1.0 CB B:PRO50 4.3 12.7 1.0 O B:HOH330 4.4 5.9 1.0 CG C:LEU51 4.4 13.7 1.0 O A:HOH312 4.5 4.3 1.0 O D:HOH310 4.9 17.5 1.0 O A:HOH357 4.9 18.2 1.0 O B:GLU49 5.0 12.1 1.0

Sodium binding site 2 out of 3 in the The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ C:Na206 b:12.9 occ:1.00 NE2 C:GLN28 2.8 12.4 1.0 CB C:THR24 3.7 17.5 1.0 CD C:GLN28 3.8 12.6 1.0 OG1 C:THR24 3.9 17.8 1.0 CG C:GLN28 3.9 11.8 1.0 CG2 C:THR24 4.0 17.7 1.0 O C:THR24 4.9 17.4 1.0 OE1 C:GLN28 5.0 14.1 1.0

Sodium binding site 3 out of 3 in the The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The X-Ray Crystal Structure of A Dimeric Variant of Human Pancreatic Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ D:Na203 b:8.3 occ:1.00 O C:HOH337 2.3 15.6 1.0 O D:HOH340 2.8 11.3 1.0 CD2 D:LEU51 3.8 18.6 1.0 CB D:LEU51 4.1 19.2 1.0 O D:HOH336 4.5 8.1 1.0 CG D:LEU51 4.6 19.1 1.0 O C:HOH310 4.7 21.5 1.0

A.Pica, A.Merlino, A.K.Buell, T.P.Knowles, E.Pizzo, G.D'alessio, F.Sica, L.Mazzarella. Three-Dimensional Domain Swapping and Supramolecular Protein Assembly: Insights From the X-Ray Structure of A Dimeric Swapped Variant of Human Pancreatic Rnase. Acta Crystallogr.,Sect.D V. 69 2116 2013.
ISSN: ISSN 0907-4449
PubMed: 24100329
DOI: 10.1107/S0907444913020507