Sodium in PDB 7kkh: P1A4 Fab in Complex with ARS1620

The structure of P1A4 Fab in Complex with ARS1620, PDB code: 7kkh was solved by K.Basu, P.J.Rohweder, Z.Zhang, M.-F.Bohn, K.Shokat, C.S.Craik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.77 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.782, 71.302, 86.793, 90, 90.66, 90
R / Rfree (%)	18.5 / 20.4

The structure of P1A4 Fab in Complex with ARS1620 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Fluorine	(F)	2 atoms

The binding sites of Sodium atom in the P1A4 Fab in Complex with ARS1620 (pdb code 7kkh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the P1A4 Fab in Complex with ARS1620, PDB code: 7kkh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the P1A4 Fab in Complex with ARS1620


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of P1A4 Fab in Complex with ARS1620 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:39.7 occ:1.00 OE2 A:GLU99 2.4 40.9 1.0 OH A:TYR191 2.6 39.8 1.0 O A:HOH438 2.7 31.5 1.0 O A:HOH447 2.7 28.7 1.0 CD A:GLU99 3.4 37.5 1.0 CZ A:TYR191 3.4 34.3 1.0 O A:HOH433 3.5 39.1 1.0 CE2 A:TYR191 3.5 33.1 1.0 OE1 A:GLU99 3.6 29.4 1.0 CE1 A:TYR159 3.9 27.2 1.0 CG2 A:THR123 4.3 27.7 1.0 OH A:TYR159 4.5 26.2 1.0 OG1 A:THR123 4.7 26.9 1.0 CE1 A:TYR191 4.7 33.4 1.0 CG A:GLU99 4.7 31.2 1.0 CZ A:TYR159 4.7 28.1 1.0 CD1 A:TYR159 4.8 25.1 1.0 NZ A:LYS121 4.8 46.8 1.0 CD2 A:TYR191 4.8 28.7 1.0 CE A:LYS185 4.8 38.0 1.0 CE A:LYS121 4.8 38.4 1.0

Sodium binding site 2 out of 2 in the P1A4 Fab in Complex with ARS1620


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of P1A4 Fab in Complex with ARS1620 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:48.5 occ:1.00 O B:HOH514 2.5 53.0 1.0 O B:VAL157 2.7 32.9 1.0 OG1 B:THR170 2.8 29.8 1.0 O B:HOH469 3.2 36.1 1.0 CB B:THR170 3.4 27.4 1.0 O B:HOH511 3.5 46.9 1.0 C B:VAL157 3.8 31.8 1.0 CG2 B:THR170 4.2 25.5 1.0 CB B:VAL157 4.3 30.4 1.0 CA B:VAL157 4.4 27.9 1.0 N B:VAL157 4.4 29.6 1.0 CG1 B:VAL168 4.5 31.8 1.0 O B:HOH503 4.6 34.7 1.0 CA B:THR170 4.7 28.3 1.0 N B:THR170 4.8 28.5 1.0 N B:SER158 4.8 27.8 1.0 OG B:SER185 4.9 29.3 1.0 CG1 B:VAL157 5.0 29.5 1.0

Z.Zhang, P.J.Rohweder, C.Ongpipattanakul, K.Basu, M.F.Bohn, E.J.Dugan, V.Steri, B.Hann, K.M.Shokat, C.S.Craik. A Covalent Inhibitor of K-Ras(G12C) Induces Mhc Class I Presentation of Haptenated Peptide Neoepitopes Targetable By Immunotherapy. Cancer Cell V. 40 1060 2022.
ISSN: ISSN 1535-6108
PubMed: 36099883
DOI: 10.1016/J.CCELL.2022.07.005