Sodium in PDB 6sgd: NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24

Enzymatic activity of NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24

All present enzymatic activity of NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24:
2.7.11.1;

Protein crystallography data

The structure of NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24, PDB code: 6sgd was solved by M.W.Richards, C.P.Mas-Droux, R.Bayliss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.35 / 2.00
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	99.670, 56.690, 73.780, 90.00, 129.71, 90.00
*R / R_free (%)*	19.8 / 23.4

Other elements in 6sgd:

The structure of NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24 (pdb code 6sgd). 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 NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24, PDB code: 6sgd:

Sodium binding site 1 out of 1 in 6sgd

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Sodium Binding Sites List in 6sgd

Sodium binding site 1 out of 1 in the NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of NEK2 Kinase Covalently Bound to 2-Arylamino-6-Ethynylpurine Inhibitor 24 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na301 b:49.1 occ:0.50	O13	A:LD5304	3.7	46.9	1.0
	O	A:GLU90	3.8	26.0	1.0
	H091	A:LD5304	4.0	38.0	1.0
	O	A:HOH407	4.1	40.5	1.0
	O	A:HOH437	4.1	30.4	1.0
	C	A:GLY91	4.5	27.7	1.0
	O	A:GLY91	4.5	30.2	1.0
	C09	A:LD5304	4.7	31.7	1.0
	N	A:GLY92	4.7	25.3	1.0
	CA	A:GLY91	4.9	23.4	1.0
	S11	A:LD5304	4.9	42.1	1.0
	C	A:GLU90	4.9	29.5	1.0

Reference:

C.J.Matheson, C.R.Coxon, R.Bayliss, K.Boxall, B.Carbain, A.M.Fry, I.R.Hardcastle, S.J.Harnor, C.P.Mas-Droux, D.R.Newell, D.Turner, M.W.Richards, M.Sivaprakasam, R.J.Griffin, B.T.Golding, C.Cano. 2-Arylamino-6-Ethynylpurines Are Cysteine-Targeting Irreversible Inhibitors of NEK2 Kinase Rsc Med Chem 2020.
ISSN: ESSN 2632-8682
DOI: 10.1039/D0MD00074D

Page generated: Tue Oct 8 13:28:27 2024

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