Sodium in PDB 4ith: Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog

All present enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog:
2.7.11.1;

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog, PDB code: 4ith was solved by T.Xie, W.Peng, Y.Liu, C.Yan, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.89 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.128, 93.605, 129.070, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.7

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog also contains other interesting chemical elements:

Iodine	(I)	10 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog (pdb code 4ith). 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 RIP1 Kinase in Complex with Necrostatin-1 Analog, PDB code: 4ith:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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 RIP1 Kinase in Complex with Necrostatin-1 Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:41.6 occ:1.00 N A:GLU234 3.9 54.5 1.0 CA A:GLU234 4.0 53.4 1.0 OH A:TYR191 4.1 34.3 1.0 CB A:GLU234 4.1 54.9 1.0 C A:ALA233 4.2 42.7 1.0 CG A:GLU234 4.3 54.7 1.0 OE2 A:GLU234 4.4 58.7 1.0 CD2 A:LEU237 4.4 27.2 1.0 CD A:GLU234 4.4 56.5 1.0 CB A:ALA231 4.5 43.8 1.0 CA A:ALA233 4.6 45.2 1.0 O A:ALA233 4.6 41.9 1.0 CE1 A:TYR191 4.9 30.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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 RIP1 Kinase in Complex with Necrostatin-1 Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:48.1 occ:1.00 O B:HOH427 3.8 43.5 1.0 O B:PRO287 3.8 40.8 1.0 CA B:PHE288 3.8 38.4 1.0 N B:PHE288 3.9 38.0 1.0 C B:PRO287 4.0 41.0 1.0 CB B:SER291 4.4 50.6 1.0 CB B:PHE288 4.4 38.6 1.0 OG B:SER291 4.6 53.1 1.0 CB B:PRO287 4.6 40.3 1.0 CD2 B:PHE288 4.9 40.0 1.0 CG B:PRO287 4.9 40.6 1.0 CA B:PRO287 5.0 40.4 1.0

T.Xie, W.Peng, Y.Liu, C.Yan, J.Maki, A.Degterev, J.Yuan, Y.Shi. Structural Basis of RIP1 Inhibition By Necrostatins. Structure V. 21 493 2013.
ISSN: ISSN 0969-2126
PubMed: 23473668
DOI: 10.1016/J.STR.2013.01.016