Fluorine in PDB 9jjv: Truncated RNF112, Transition-Like State

The structure of Truncated RNF112, Transition-Like State, PDB code: 9jjv was solved by Y.T.Zhong, L.L.Huang, S.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.01 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.567, 148.057, 71.315, 90, 90, 90
R / Rfree (%)	18.6 / 22.4

The structure of Truncated RNF112, Transition-Like State also contains other interesting chemical elements:

Aluminium	(Al)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the Truncated RNF112, Transition-Like State (pdb code 9jjv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Truncated RNF112, Transition-Like State, PDB code: 9jjv:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Truncated RNF112, Transition-Like State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Truncated RNF112, Transition-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:22.1 occ:1.00 F1 A:ALF602 0.0 22.1 1.0 AL A:ALF602 1.8 24.1 1.0 NZ A:LYS198 2.4 22.5 1.0 O2B A:GDP601 2.5 21.7 1.0 F4 A:ALF602 2.5 21.9 1.0 F3 A:ALF602 2.5 23.4 1.0 O A:HOH754 2.9 21.4 1.0 N A:GLY268 3.0 22.7 1.0 CA A:GLY268 3.2 21.0 1.0 CA A:LYS194 3.3 21.5 1.0 PB A:GDP601 3.4 22.0 1.0 CE A:LYS198 3.4 21.5 1.0 O1B A:GDP601 3.5 20.6 1.0 N A:ARG195 3.5 22.3 1.0 F2 A:ALF602 3.6 24.5 1.0 O3B A:GDP601 3.9 20.6 1.0 CB A:LYS194 3.9 23.1 1.0 C A:LYS194 3.9 23.9 1.0 O A:HOH872 4.0 24.4 1.0 O A:HOH811 4.1 20.9 1.0 MG A:MG604 4.2 21.3 1.0 C A:GLU267 4.2 22.1 1.0 N A:LYS194 4.3 21.3 1.0 O A:GLU193 4.4 21.5 1.0 C A:GLY268 4.4 22.6 1.0 O A:THR266 4.5 23.0 1.0 CA A:GLU267 4.7 24.1 1.0 C A:GLU193 4.7 22.8 1.0 CA A:ARG195 4.7 22.9 1.0 O A:GLY268 4.8 20.1 1.0 CD A:LYS198 4.8 18.1 1.0 O3A A:GDP601 4.9 23.1 1.0

Fluorine binding site 2 out of 4 in the Truncated RNF112, Transition-Like State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Truncated RNF112, Transition-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:24.5 occ:1.00 F2 A:ALF602 0.0 24.5 1.0 AL A:ALF602 1.8 24.1 1.0 F3 A:ALF602 2.4 23.4 1.0 O2B A:GDP601 2.5 21.7 1.0 F4 A:ALF602 2.6 21.9 1.0 N A:THR239 2.6 27.3 1.0 O A:HOH754 2.7 21.4 1.0 NH2 A:ARG195 2.9 23.0 1.0 N A:THR240 3.1 24.2 1.0 CB A:THR239 3.3 28.3 1.0 CA A:THR239 3.3 28.4 1.0 O A:HOH787 3.3 21.6 1.0 NE A:ARG195 3.4 25.4 1.0 F1 A:ALF602 3.6 22.1 1.0 CZ A:ARG195 3.6 26.3 1.0 C A:THR239 3.6 27.0 1.0 C A:THR238 3.7 29.5 1.0 MG A:MG604 3.7 21.3 1.0 CA A:THR238 3.8 29.5 1.0 PB A:GDP601 3.8 22.0 1.0 OG1 A:THR239 3.9 31.6 1.0 O3B A:GDP601 4.1 20.6 1.0 CB A:THR238 4.2 31.6 1.0 OG1 A:THR240 4.2 22.3 1.0 CA A:THR240 4.2 24.0 1.0 CB A:THR240 4.3 24.7 1.0 O1A A:GDP601 4.4 23.2 1.0 O3A A:GDP601 4.5 23.1 1.0 O A:THR240 4.5 22.0 1.0 CG2 A:THR239 4.5 29.1 1.0 CG2 A:THR238 4.7 30.0 1.0 CD A:ARG195 4.7 24.4 1.0 O A:THR238 4.8 28.8 1.0 N A:ARG195 4.8 22.3 1.0 C A:THR240 4.8 26.2 1.0 O A:THR239 4.8 27.9 1.0 O A:GLU237 4.9 29.7 1.0 NH1 A:ARG195 4.9 25.9 1.0 O A:HOH872 4.9 24.4 1.0

Fluorine binding site 3 out of 4 in the Truncated RNF112, Transition-Like State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Truncated RNF112, Transition-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:23.4 occ:1.00 F3 A:ALF602 0.0 23.4 1.0 AL A:ALF602 1.8 24.1 1.0 O2B A:GDP601 2.4 21.7 1.0 F2 A:ALF602 2.4 24.5 1.0 F1 A:ALF602 2.5 22.1 1.0 N A:ARG195 2.8 22.3 1.0 NE A:ARG195 2.8 25.4 1.0 O A:HOH754 2.8 21.4 1.0 CB A:LYS194 3.4 23.1 1.0 CG2 A:THR238 3.5 30.0 1.0 CA A:LYS194 3.5 21.5 1.0 F4 A:ALF602 3.6 21.9 1.0 CG A:ARG195 3.6 25.4 1.0 CA A:ARG195 3.6 22.9 1.0 CD A:ARG195 3.6 24.4 1.0 C A:LYS194 3.6 23.9 1.0 O A:HOH872 3.7 24.4 1.0 CZ A:ARG195 3.7 26.3 1.0 NH2 A:ARG195 3.8 23.0 1.0 CB A:THR238 3.8 31.6 1.0 PB A:GDP601 3.9 22.0 1.0 CA A:THR238 4.0 29.5 1.0 CB A:ARG195 4.2 26.6 1.0 N A:THR239 4.2 27.3 1.0 CG A:LYS194 4.5 24.2 1.0 O1B A:GDP601 4.5 20.6 1.0 NZ A:LYS198 4.6 22.5 1.0 C A:THR238 4.7 29.5 1.0 O3A A:GDP601 4.7 23.1 1.0 O A:LYS194 4.8 22.4 1.0 O3B A:GDP601 4.8 20.6 1.0 N A:GLY268 4.9 22.7 1.0 N A:LYS194 5.0 21.3 1.0 C A:ARG195 5.0 22.8 1.0 NH1 A:ARG195 5.0 25.9 1.0

Fluorine binding site 4 out of 4 in the Truncated RNF112, Transition-Like State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Truncated RNF112, Transition-Like State within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:21.9 occ:1.00 F4 A:ALF602 0.0 21.9 1.0 AL A:ALF602 1.8 24.1 1.0 MG A:MG604 2.0 21.3 1.0 F1 A:ALF602 2.5 22.1 1.0 O2B A:GDP601 2.5 21.7 1.0 F2 A:ALF602 2.6 24.5 1.0 O A:HOH811 2.6 20.9 1.0 OG1 A:THR240 2.8 22.3 1.0 O3B A:GDP601 2.8 20.6 1.0 O A:HOH754 2.8 21.4 1.0 CB A:THR240 2.9 24.7 1.0 O A:HOH787 3.1 21.6 1.0 PB A:GDP601 3.2 22.0 1.0 N A:THR240 3.4 24.2 1.0 F3 A:ALF602 3.6 23.4 1.0 CA A:THR240 3.7 24.0 1.0 OG A:SER199 4.0 23.2 1.0 NZ A:LYS198 4.0 22.5 1.0 O1B A:GDP601 4.1 20.6 1.0 CG2 A:THR240 4.1 23.9 1.0 O A:THR240 4.1 22.0 1.0 O A:THR266 4.3 23.0 1.0 N A:GLY268 4.3 22.7 1.0 C A:THR240 4.4 26.2 1.0 CE A:LYS198 4.5 21.5 1.0 O3A A:GDP601 4.5 23.1 1.0 C A:THR239 4.6 27.0 1.0 CA A:GLU267 4.7 24.1 1.0 NH2 A:ARG195 4.8 23.0 1.0 N A:THR239 4.8 27.3 1.0 C A:GLU267 5.0 22.1 1.0

Y.T.Zhong, L.L.Huang, K.Li, B.Yang, X.Ye, H.R.Zhong, B.Yu, M.Ma, Y.Yuan, Y.Meng, R.Pan, H.Zhang, L.Shi, Y.Wang, R.Tian, S.Gao, X.Bian. Structural and Functional Characterization of the Brain-Specific Dynamin Superfamily Member RNF112. Proc.Natl.Acad.Sci.Usa V. 122 49122 2025.
ISSN: ESSN 1091-6490
PubMed: 40198702
DOI: 10.1073/PNAS.2419449122