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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4ith:

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

Sodium Binding Sites:

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 4ith

Go back to Sodium Binding Sites List in 4ith
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 4ith

Go back to Sodium Binding Sites List in 4ith
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

Reference:

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
Page generated: Tue Dec 15 06:45:16 2020

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