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Fluorine in PDB 4itj: Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4

Enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4

All present enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4, PDB code: 4itj 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) 35.24 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.841, 97.136, 128.119, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.2

Other elements in 4itj:

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4 also contains other interesting chemical elements:

Iodine (I) 9 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4 (pdb code 4itj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4, PDB code: 4itj:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4itj

Go back to Fluorine Binding Sites List in 4itj
Fluorine binding site 1 out of 2 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:21.0
occ:1.00
F20 A:1HX301 0.0 21.0 1.0
C3 A:1HX301 1.3 20.0 1.0
C2 A:1HX301 2.4 18.1 1.0
C4 A:1HX301 2.4 19.4 1.0
N8 A:1HX301 2.7 17.1 1.0
C7 A:1HX301 2.8 15.8 1.0
O A:HOH415 3.1 20.1 1.0
C10 A:1HX301 3.1 16.8 1.0
CE2 A:PHE162 3.4 21.4 1.0
CZ A:PHE162 3.6 23.6 1.0
C5 A:1HX301 3.6 17.4 1.0
C9 A:1HX301 3.6 17.1 1.0
CB A:MET67 3.6 28.6 1.0
O A:MET67 3.6 25.9 1.0
C1 A:1HX301 3.7 17.7 1.0
CE A:MET67 3.7 31.2 1.0
CD1 A:LEU70 3.9 24.8 1.0
C6 A:1HX301 4.1 19.5 1.0
CA A:MET67 4.2 28.7 1.0
O11 A:1HX301 4.2 17.7 1.0
SD A:MET67 4.2 37.1 1.0
C A:MET67 4.3 31.0 1.0
CG A:MET67 4.3 30.7 1.0
CD2 A:PHE162 4.5 22.6 1.0
C12 A:1HX301 4.5 20.9 1.0
CB A:LEU70 4.6 18.1 1.0
CG A:LEU70 4.7 19.9 1.0
CE1 A:PHE162 4.8 24.9 1.0
C16 A:1HX301 4.9 22.7 1.0

Fluorine binding site 2 out of 2 in 4itj

Go back to Fluorine Binding Sites List in 4itj
Fluorine binding site 2 out of 2 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:17.1
occ:1.00
F20 B:1HX301 0.0 17.1 1.0
C3 B:1HX301 1.3 13.9 1.0
C4 B:1HX301 2.3 13.2 1.0
C2 B:1HX301 2.4 14.2 1.0
N8 B:1HX301 2.6 15.4 1.0
C7 B:1HX301 2.7 12.5 1.0
C10 B:1HX301 3.1 13.6 1.0
O B:HOH407 3.3 12.3 0.9
C9 B:1HX301 3.5 14.1 1.0
C5 B:1HX301 3.6 15.6 1.0
CE2 B:PHE162 3.6 19.5 1.0
CB B:MET67 3.6 21.1 1.0
C1 B:1HX301 3.6 15.2 1.0
CZ B:PHE162 3.7 20.7 1.0
O B:MET67 3.7 16.5 1.0
CD1 B:LEU70 3.8 16.2 1.0
SD B:MET67 4.0 24.7 1.0
C6 B:1HX301 4.1 15.4 1.0
CG B:MET67 4.1 23.1 1.0
O11 B:1HX301 4.1 15.6 1.0
CA B:MET67 4.2 19.9 1.0
C B:MET67 4.3 20.8 1.0
C12 B:1HX301 4.4 13.6 1.0
CB B:LEU70 4.6 14.2 1.0
CD2 B:PHE162 4.7 22.4 1.0
CG B:LEU70 4.8 14.4 1.0
CE1 B:PHE162 4.9 21.5 1.0
C16 B:1HX301 5.0 16.1 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: Sun Dec 13 12:04:48 2020

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