Sodium in PDB 8cx5: Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)

Enzymatic activity of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)

All present enzymatic activity of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R):
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R), PDB code: 8cx5 was solved by Z.Zhang, J.Morstein, A.Ecker, K.Z.Guiley, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	59.83 / 1.72
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	41.21, 65.661, 61.13, 90, 101.85, 90
*R / R_free (%)*	18.9 / 22.1

Other elements in 8cx5:

The structure of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Fluorine	(F)	2 atoms
Magnesium	(Mg)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) (pdb code 8cx5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R), PDB code: 8cx5:

Sodium binding site 1 out of 1 in 8cx5

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Sodium Binding Sites List in 8cx5

Sodium binding site 1 out of 1 in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)

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 Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na206 b:52.0 occ:1.00	CD	B:PRO121	2.5	29.7	1.0
	OG	B:SER122	2.6	42.1	1.0
	CG	B:PRO121	2.9	25.7	1.0
	N	B:SER122	3.3	28.0	1.0
	N	B:PRO121	3.5	31.0	1.0
	CB	B:SER122	3.6	39.7	1.0
	CB	B:LEU120	4.1	22.4	1.0
	O	B:HOH321	4.1	29.3	1.0
	CA	B:SER122	4.1	26.5	1.0
	CB	B:PRO121	4.1	31.0	1.0
	CA	B:PRO121	4.2	30.1	1.0
	C	B:PRO121	4.2	32.0	1.0
	C	B:LEU120	4.2	32.8	1.0
	CD2	B:LEU120	4.2	26.8	1.0
	CA	B:LEU120	4.4	25.4	1.0
	CG	B:LEU120	4.7	24.8	1.0

Reference:

Z.Zhang, J.Morstein, A.K.Ecker, K.Z.Guiley, K.M.Shokat. Chemoselective Covalent Modification of K-Ras(G12R) with A Small Molecule Electrophile. J.Am.Chem.Soc. V. 144 15916 2022.
ISSN: ESSN 1520-5126
PubMed: 36001446
DOI: 10.1021/JACS.2C05377

Page generated: Wed Oct 9 11:19:37 2024

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