Sodium in PDB 5cm7: Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)

Enzymatic activity of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)

All present enzymatic activity of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp):
2.7.4.16;

Protein crystallography data

The structure of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), PDB code: 5cm7 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.50 / 1.55
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.750, 117.120, 55.890, 90.00, 108.57, 90.00
*R / R_free (%)*	14.2 / 16.7

Other elements in 5cm7:

The structure of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) (pdb code 5cm7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp), PDB code: 5cm7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5cm7

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Sodium Binding Sites List in 5cm7

Sodium binding site 1 out of 2 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:11.3 occ:1.00	O	A:HOH637	2.3	10.5	1.0
	O	A:ALA42	2.3	8.2	1.0
	O	B:HOH614	2.4	11.2	1.0
	O	B:HOH564	2.4	8.4	1.0
	OD1	A:ASP43	2.5	9.9	1.0
	O	A:HOH762	2.6	9.2	1.0
	C	A:ALA42	3.1	6.9	1.0
	CG	A:ASP43	3.3	10.9	1.0
	OD2	A:ASP71	3.4	9.7	1.0
	MG	B:MG407	3.5	8.5	1.0
	N	A:ALA42	3.5	6.1	1.0
	O3B	B:ADP405	3.7	8.3	1.0
	N	A:ASP43	3.8	6.4	1.0
	CA	A:ALA42	3.9	6.3	1.0
	O	B:GLY117	4.0	8.9	1.0
	CA	A:ASP43	4.0	6.2	1.0
	OD2	A:ASP43	4.1	10.7	1.0
	CB	A:CYS41	4.1	8.4	1.0
	CA	A:CA406	4.1	8.6	1.0
	CB	A:ASP43	4.1	7.8	1.0
	CG	A:ASP71	4.3	9.4	1.0
	C	A:CYS41	4.5	7.3	1.0
	O	B:ASP26	4.5	9.2	1.0
	OD1	A:ASN68	4.6	10.2	1.0
	OD1	B:ASP118	4.6	11.1	1.0
	CA	A:CYS41	4.6	6.0	1.0
	CB	B:ASP118	4.7	10.0	1.0
	CG	B:ASP118	4.9	12.9	1.0
	C	B:GLY117	4.9	7.5	1.0
	PB	B:ADP405	4.9	10.6	1.0
	CB	A:ASP71	5.0	7.7	1.0

Sodium binding site 2 out of 2 in 5cm7

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Sodium Binding Sites List in 5cm7

Sodium binding site 2 out of 2 in the Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Thiamine-Monophosphate Kinase From Acinetobacter Baumannii in Complex with Adenosine Diphosphate (Adp) and Thiamine Diphosphate (Tpp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na408 b:14.6 occ:1.00	O	B:HOH586	2.3	9.8	1.0
	O	B:ALA42	2.3	10.4	1.0
	O	A:HOH582	2.4	10.0	1.0
	O	A:HOH601	2.4	11.8	1.0
	OD1	B:ASP43	2.5	11.1	1.0
	O	B:HOH709	2.6	10.5	1.0
	C	B:ALA42	3.1	8.1	1.0
	CG	B:ASP43	3.4	12.6	1.0
	OD2	B:ASP71	3.5	9.9	1.0
	N	B:ALA42	3.5	7.7	1.0
	MG	A:MG403	3.5	9.1	1.0
	O3B	A:ADP401	3.8	11.1	1.0
	N	B:ASP43	3.8	7.0	1.0
	CA	B:ALA42	3.9	8.5	1.0
	O	A:GLY117	3.9	8.1	1.0
	CA	B:ASP43	4.0	9.0	1.0
	CB	B:CYS41	4.1	8.8	1.0
	OD2	B:ASP43	4.1	10.6	1.0
	CA	B:CA402	4.1	9.3	1.0
	CB	B:ASP43	4.2	12.7	1.0
	CG	B:ASP71	4.4	9.9	1.0
	C	B:CYS41	4.4	8.1	1.0
	O	A:ASP26	4.5	9.1	1.0
	OD1	A:ASP118	4.6	9.6	1.0
	CA	B:CYS41	4.6	7.5	1.0
	OD1	B:ASN68	4.7	12.8	1.0
	CB	A:ASP118	4.7	8.0	1.0
	CG	A:ASP118	4.8	10.8	1.0
	C	A:GLY117	4.9	7.8	1.0
	PB	A:ADP401	5.0	14.2	1.0
	SG	B:CYS41	5.0	11.2	1.0

Reference:

A.H.Sullivan, D.M.Dranow, P.S.Horanyi, D.D.Lorimer, T.E.Edwards, J.Abendroth. Crystal Structures of Thiamine Monophosphate Kinase From Acinetobacter Baumannii in Complex with Substrates and Products. Sci Rep V. 9 4392 2019.
ISSN: ESSN 2045-2322
PubMed: 30867460
DOI: 10.1038/S41598-019-40558-X

Page generated: Mon Oct 7 20:22:58 2024

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