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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 / Rfree (%) 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

Go back to 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

Go back to 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

Go back to 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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