Sodium in PDB 6vnd: Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636

Enzymatic activity of Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636

All present enzymatic activity of Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636:
1.3.5.2;

Protein crystallography data

The structure of Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636, PDB code: 6vnd was solved by A.Padyana, L.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	28.78 / 1.97
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	90.526, 90.526, 123.761, 90.00, 90.00, 120.00
*R / R_free (%)*	15.5 / 19

Other elements in 6vnd:

The structure of Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636 (pdb code 6vnd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636, PDB code: 6vnd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6vnd

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Sodium Binding Sites List in 6vnd

Sodium binding site 1 out of 3 in the Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na407 b:84.3 occ:1.00	O	A:DET402	2.1	78.8	1.0
	OE2	A:GLU52	2.3	32.8	1.0
	NH2	A:ARG56	2.7	72.0	1.0
	C2	A:DET402	3.0	68.5	1.0
	CD	A:GLU52	3.3	32.1	1.0
	N	A:DET402	3.3	63.5	1.0
	CD	A:ARG56	3.3	58.7	1.0
	CG	A:GLU52	3.5	34.8	1.0
	C1	A:DET402	3.5	63.8	1.0
	CG	A:ARG56	3.5	45.1	1.0
	CZ	A:ARG56	3.8	78.3	1.0
	NH2	A:ARG130	3.8	78.3	1.0
	NH2	A:ARG132	3.8	28.9	1.0
	NE	A:ARG56	4.0	73.3	1.0
	CM2	A:DET402	4.1	65.4	1.0
	C3	A:DET402	4.3	66.3	1.0
	CM1	A:DET402	4.3	50.7	1.0
	OE1	A:GLU52	4.4	32.1	1.0
	CE1	A:TYR146	4.4	29.6	1.0
	CZ	A:ARG130	4.5	86.5	1.0
	OH	A:TYR146	4.6	32.4	1.0
	OD1	A:ASN149	4.7	41.7	1.0
	NH1	A:ARG130	4.9	90.1	1.0
	CZ	A:TYR146	5.0	33.0	1.0
	NH1	A:ARG56	5.0	83.8	1.0
	CZ	A:ARG132	5.0	30.1	1.0
	O	A:GLU52	5.0	30.9	1.0

Sodium binding site 2 out of 3 in 6vnd

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Sodium Binding Sites List in 6vnd

Sodium binding site 2 out of 3 in the Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na408 b:62.0 occ:1.00	OE1	A:GLU265	2.2	56.6	1.0
	CG	A:GLU265	2.9	54.5	1.0
	CD	A:GLU265	2.9	43.4	1.0
	O	A:SER261	3.9	29.6	1.0
	CB	A:SER261	4.1	31.4	1.0
	CB	A:GLU265	4.2	31.2	1.0
	OE2	A:GLU265	4.2	41.2	1.0
	C	A:SER261	4.5	30.7	1.0
	CA	A:SER261	4.8	30.3	1.0
	OE2	A:GLU318	4.8	63.2	1.0
	CD2	A:LEU322	4.9	27.9	1.0

Sodium binding site 3 out of 3 in 6vnd

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Sodium Binding Sites List in 6vnd

Sodium binding site 3 out of 3 in the Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Quaternary Complex of Human Dihydroorotate Dehydrogenase (Dhodh) with Flavin Mononucleotide (Fmn), Orotic Acid and Ag-636 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na409 b:70.0 occ:1.00	OE1	A:GLU273	2.3	67.4	1.0
	NH2	A:ARG230	2.9	65.8	1.0
	OG	A:SER269	3.0	35.6	1.0
	CE	A:LYS226	3.4	49.7	1.0
	CD	A:GLU273	3.4	66.7	1.0
	NZ	A:LYS226	3.5	56.8	1.0
	O	A:SER269	3.7	29.9	1.0
	C	A:SER269	3.8	34.2	1.0
	CZ	A:ARG230	3.9	68.0	1.0
	CB	A:GLU273	3.9	38.6	1.0
	CG2	A:VAL270	4.0	36.9	1.0
	N	A:VAL270	4.0	29.8	1.0
	NE	A:ARG230	4.0	68.7	1.0
	CA	A:VAL270	4.0	31.0	1.0
	CB	A:SER269	4.0	28.1	1.0
	CG	A:GLU273	4.2	54.0	1.0
	OE2	A:GLU273	4.3	79.6	1.0
	CA	A:SER269	4.5	30.1	1.0
	CB	A:VAL270	4.6	32.9	1.0
	CD	A:LYS226	4.8	52.2	1.0
	O	A:HOH638	4.8	57.8	1.0

Reference:

G.Mcdonald, V.Chubukov, J.Coco, K.Truskowski, R.Narayanaswamy, S.Choe, M.Steadman, E.Artin, A.K.Padyana, L.Jin, S.Ronseaux, C.Locuson, Z.P.Fan, T.Erdmann, A.Mann, S.Hayes, M.Fletcher, K.Nellore, S.S.Rao, H.Subramanya, S.R.Kunnam, S.K.Panigrahi, T.Anthony, S.Gopinath, Z.Sui, N.Nagaraja, L.Dang, G.Lenz, J.Hurov, S.A.Biller, J.Murtie, K.M.Marks, D.B.Ulanet. Selective Vulnerability to Pyrimidine Starvation in Hematologic Malignancies Revealed By Ag-636, A Novel Clinical-Stage Inhibitor of Dihydroorotate Dehydrogenase. Mol.Cancer Ther. 2020.
ISSN: ESSN 1538-8514
PubMed: 33082276
DOI: 10.1158/1535-7163.MCT-20-0550

Page generated: Tue Oct 8 14:24:42 2024

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