Sodium in PDB 4twp: The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib

Enzymatic activity of The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib

All present enzymatic activity of The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib:
2.7.10.2;

Protein crystallography data

The structure of The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib, PDB code: 4twp was solved by E.Johnson, M.Mctigue, C.N.Cronin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	52.14 / 2.40
*Space group*	P 2 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.818, 113.801, 131.164, 90.00, 90.00, 90.00
*R / R_free (%)*	21.2 / 24.1

Other elements in 4twp:

The structure of The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib (pdb code 4twp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib, PDB code: 4twp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4twp

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Sodium Binding Sites List in 4twp

Sodium binding site 1 out of 3 in the The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na604 b:58.7 occ:1.00	CD2	A:HIS396	3.4	73.8	1.0
	N	A:HIS396	3.6	59.5	1.0
	NH1	A:ARG362	3.7	54.0	1.0
	CA	A:ALA395	3.8	50.1	1.0
	NH2	A:ARG362	3.9	58.2	1.0
	CB	A:ALA395	3.9	48.6	1.0
	C	A:ALA395	4.2	56.1	1.0
	CG	A:HIS396	4.3	69.7	1.0
	CZ	A:ARG362	4.3	54.2	1.0
	NE2	A:HIS396	4.3	76.6	1.0
	OH	A:TYR393	4.4	62.1	1.0
	CB	A:HIS396	4.5	61.0	1.0
	CE2	A:TYR393	4.6	47.6	1.0
	O	A:HOH825	4.6	58.8	1.0
	NH1	A:ARG386	4.6	59.0	1.0
	CA	A:HIS396	4.7	61.6	1.0
	CB	A:ALA399	4.8	57.8	1.0
	CD2	A:LEU384	4.9	50.5	1.0

Sodium binding site 2 out of 3 in 4twp

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Sodium Binding Sites List in 4twp

Sodium binding site 2 out of 3 in the The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na605 b:59.6 occ:1.00	O	A:HOH786	3.1	39.2	1.0
	O	A:HOH810	3.1	41.0	1.0
	O	A:ARG362	3.3	44.3	1.0
	C	A:ARG362	3.6	42.4	1.0
	O	A:HOH766	3.7	47.0	1.0
	CA	A:ARG362	3.8	37.8	1.0
	CB	A:ALA424	3.8	28.4	1.0
	OD1	A:ASP421	4.2	40.7	1.0
	CE2	A:PHE416	4.3	40.6	1.0
	N	A:ASP363	4.3	39.4	1.0
	O	A:TRP405	4.3	37.2	1.0
	O	A:SER420	4.3	35.4	1.0
	CD2	A:PHE416	4.6	40.6	1.0
	N	A:ARG362	4.6	40.9	1.0
	N	A:LEU364	4.6	36.8	1.0
	CA	A:ASP363	4.8	41.1	1.0
	CA	A:THR406	4.8	33.8	1.0
	C	A:SER420	4.8	35.7	1.0
	CB	A:ARG362	4.9	43.4	1.0
	OG1	A:THR406	4.9	39.8	1.0

Sodium binding site 3 out of 3 in 4twp

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Sodium Binding Sites List in 4twp

Sodium binding site 3 out of 3 in the The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Human ABL1 T315I Gatekeeper Mutant Kinase Domain in Complex with Axitinib within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na604 b:73.8 occ:1.00	OH	B:TYR393	3.1	82.6	1.0
	NH1	B:ARG386	3.6	83.3	1.0
	ND1	B:HIS396	4.1	96.7	1.0
	CZ	B:TYR393	4.1	79.9	1.0
	CE2	B:TYR393	4.2	78.0	1.0
	CE1	B:HIS396	4.4	0.3	1.0
	NH1	B:ARG362	4.4	87.5	1.0
	CZ	B:ARG386	4.7	81.7	1.0
	NH2	B:ARG362	4.7	81.3	1.0
	NH2	B:ARG386	4.8	79.5	1.0
	CB	B:ALA395	4.9	83.2	1.0
	CA	B:ALA395	5.0	81.7	1.0

Reference:

T.Pemovska, E.Johnson, M.Kontro, G.A.Repasky, J.Chen, P.Wells, C.N.Cronin, M.Mctigue, O.Kallioniemi, K.Porkka, B.Murray, K.Wennerberg. Axitinib Effectively Inhibits Bcr-ABL1(T315I) with A Distinct Binding Conformation Nature 2015.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14119

Page generated: Mon Oct 7 18:31:18 2024

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