Sodium in PDB 7kia: Crystal Structure of FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19

All present enzymatic activity of Crystal Structure of FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19:
2.7.10.1;

The structure of Crystal Structure of FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19, PDB code: 7kia was solved by J.Ke, A.S.Wibowo, J.J.Carter, N.A.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.22
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.98, 117.3, 63.81, 90, 90, 90
R / Rfree (%)	19.9 / 22.3

The binding sites of Sodium atom in the Crystal Structure of FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19 (pdb code 7kia). 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 FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19, PDB code: 7kia:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19


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 FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:44.9 occ:1.00 O A:ASP521 2.7 37.8 1.0 O A:ALA523 2.9 35.6 1.0 N B:LYS668 2.9 32.7 1.0 N B:VAL667 3.1 35.3 1.0 N A:ALA523 3.4 36.7 1.0 C A:ASP522 3.4 42.5 1.0 CA A:ASP522 3.4 44.2 1.0 CB B:LYS668 3.6 34.9 1.0 C A:ASP521 3.6 45.0 1.0 C B:PRO666 3.7 35.0 1.0 CG2 B:VAL709 3.7 46.4 1.0 CG B:LYS668 3.7 37.7 1.0 CA B:VAL667 3.8 34.6 1.0 C B:VAL667 3.8 33.4 1.0 CA B:LYS668 3.8 35.3 1.0 C A:ALA523 3.9 34.3 1.0 CB B:VAL667 3.9 35.6 1.0 N A:ASP522 3.9 42.6 1.0 O A:ASP522 4.0 37.9 1.0 CZ3 B:TRP669 4.0 33.8 1.0 CA B:PRO666 4.0 32.0 1.0 CA A:ALA523 4.1 34.3 1.0 CE3 B:TRP669 4.2 32.3 1.0 CB B:PRO666 4.2 29.7 1.0 CD B:LYS668 4.3 39.1 1.0 O B:PRO666 4.5 37.6 1.0 CB A:ASP522 4.6 50.0 1.0 CB A:ALA523 4.7 33.8 1.0 CG1 B:VAL667 4.7 37.6 1.0 C B:LYS668 4.9 36.2 1.0 N B:TRP669 4.9 31.2 1.0 CG2 B:VAL667 4.9 34.9 1.0 CA A:ASP521 5.0 48.1 1.0 CB B:VAL709 5.0 48.3 1.0 O B:VAL667 5.0 36.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19


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 FGFR2 Kinase Domain Gatekeeper Mutant V564F in Complex with Covalent Compound 19 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na803 b:49.1 occ:1.00 O B:ASP521 2.8 44.6 1.0 O B:ALA523 2.8 35.4 1.0 N A:VAL667 3.0 35.4 1.0 N A:LYS668 3.0 34.2 1.0 N B:ALA523 3.3 38.6 1.0 C B:ASP522 3.3 41.1 1.0 CA B:ASP522 3.4 42.9 1.0 C A:PRO666 3.6 36.0 1.0 C B:ASP521 3.7 45.0 1.0 CB A:LYS668 3.7 35.1 1.0 CA A:VAL667 3.7 35.5 1.0 C B:ALA523 3.8 35.8 1.0 CG A:LYS668 3.8 36.4 1.0 O B:ASP522 3.8 37.2 1.0 C A:VAL667 3.9 34.0 1.0 CG2 A:VAL709 3.9 50.4 1.0 CA A:PRO666 3.9 34.5 1.0 CB A:VAL667 3.9 35.8 1.0 CA A:LYS668 4.0 33.7 1.0 CB A:PRO666 4.0 32.6 1.0 N B:ASP522 4.0 42.7 1.0 CA B:ALA523 4.0 36.4 1.0 CZ3 A:TRP669 4.2 31.4 1.0 CE3 A:TRP669 4.3 30.2 1.0 O A:PRO666 4.4 36.0 1.0 CD A:LYS668 4.5 36.8 1.0 CB B:ALA523 4.6 37.5 1.0 CB B:ASP522 4.7 47.0 1.0 CG1 A:VAL709 4.8 45.2 1.0 CG1 A:VAL667 4.9 38.4 1.0 CG2 A:VAL667 4.9 35.6 1.0 CB A:VAL709 5.0 48.9 1.0

R.A.Brawn, A.Cook, K.Omoto, J.Ke, C.Karr, F.Colombo, M.Virrankoski, S.Prajapati, D.Reynolds, D.M.Bolduc, T.V.Nguyen, P.Gee, D.Borrelli, B.Caleb, S.Yao, S.Irwin, N.A.Larsen, A.Selvaraj, X.Zhao, S.Ioannidis. Discovery of Aminopyrazole Derivatives As Potent Inhibitors of Wild-Type and Gatekeeper Mutant FGFR2 and 3. Acs Med.Chem.Lett. V. 12 93 2021.
ISSN: ISSN 1948-5875
PubMed: 33488969
DOI: 10.1021/ACSMEDCHEMLETT.0C00517