Magnesium in PDB 1umc: Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate

All present enzymatic activity of Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate:
1.2.4.4;

The structure of Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate, PDB code: 1umc was solved by T.Nakai, N.Nakagawa, N.Maoka, R.Masui, S.Kuramitsu, N.Kamiya, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	127.197, 247.216, 137.557, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.6

The binding sites of Magnesium atom in the Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate (pdb code 1umc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate, PDB code: 1umc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:17.3 occ:1.00 O A:TYR206 1.9 21.1 1.0 O12 A:TDP1402 2.1 19.1 1.0 OD1 A:ASP175 2.1 17.4 1.0 OD1 A:ASN204 2.1 17.6 1.0 O A:HOH1428 2.1 18.7 1.0 O23 A:TDP1402 2.1 15.1 1.0 CG A:ASP175 3.0 16.5 1.0 CG A:ASN204 3.0 18.8 1.0 C A:TYR206 3.1 21.9 1.0 P1 A:TDP1402 3.2 18.8 1.0 P2 A:TDP1402 3.3 16.9 1.0 OD2 A:ASP175 3.3 16.1 1.0 O11 A:TDP1402 3.4 17.2 1.0 ND2 A:ASN204 3.5 16.7 1.0 N A:TYR206 3.7 21.1 1.0 N A:ASP175 3.8 14.0 1.0 O21 A:TDP1402 3.8 17.6 1.0 CA A:TYR206 4.0 21.9 1.0 N A:ALA207 4.0 21.5 1.0 O5G A:TDP1402 4.0 19.2 1.0 N A:ASN204 4.2 16.1 1.0 CA A:ALA207 4.2 22.3 1.0 O A:HOH1405 4.2 12.2 1.0 CB A:ASP175 4.2 14.8 1.0 N A:GLY176 4.3 10.8 1.0 CB A:ASN204 4.4 16.6 1.0 O13 A:TDP1402 4.5 20.6 1.0 O22 A:TDP1402 4.5 16.0 1.0 CA A:ASP175 4.5 13.6 1.0 CA A:GLY174 4.5 14.3 1.0 N A:PHE205 4.6 18.1 1.0 C A:GLY174 4.6 13.8 1.0 CA A:ASN204 4.6 16.4 1.0 O A:GLU202 4.6 16.2 1.0 C A:ASN204 4.6 17.2 1.0 CB A:TYR206 4.8 21.6 1.0 C A:PHE205 4.9 21.0 1.0 C A:ASP175 5.0 13.2 1.0

Magnesium binding site 2 out of 2 in the Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methylpentanoate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2401 b:22.7 occ:1.00 O C:TYR206 1.9 22.3 1.0 OD1 C:ASP175 2.0 18.3 1.0 O12 C:TDP2402 2.1 16.2 1.0 OD1 C:ASN204 2.1 20.3 1.0 O C:HOH2430 2.2 18.2 1.0 O23 C:TDP2402 2.2 16.3 1.0 CG C:ASP175 2.9 17.9 1.0 CG C:ASN204 3.0 18.9 1.0 C C:TYR206 3.1 21.6 1.0 P1 C:TDP2402 3.2 18.3 1.0 P2 C:TDP2402 3.3 17.1 1.0 O11 C:TDP2402 3.4 17.1 1.0 OD2 C:ASP175 3.4 17.2 1.0 ND2 C:ASN204 3.4 16.3 1.0 N C:ASP175 3.8 11.8 1.0 N C:TYR206 3.8 21.7 1.0 O21 C:TDP2402 3.9 19.8 1.0 CA C:TYR206 4.0 20.8 1.0 O5G C:TDP2402 4.1 16.7 1.0 N C:ALA207 4.1 21.8 1.0 N C:ASN204 4.1 14.8 1.0 CB C:ASP175 4.2 14.4 1.0 CA C:ALA207 4.3 21.3 1.0 CB C:ASN204 4.3 16.9 1.0 O C:HOH2422 4.4 16.4 1.0 N C:GLY176 4.4 12.1 1.0 O13 C:TDP2402 4.4 18.0 1.0 O22 C:TDP2402 4.5 17.6 1.0 CA C:GLY174 4.5 9.6 1.0 CA C:ASP175 4.5 12.2 1.0 CA C:ASN204 4.5 17.1 1.0 O C:GLU202 4.6 15.8 1.0 C C:ASN204 4.6 18.6 1.0 N C:PHE205 4.6 19.4 1.0 C C:GLY174 4.6 11.7 1.0 CB C:TYR206 4.8 20.9 1.0 C C:PHE205 4.9 21.7 1.0

T.Nakai, N.Nakagawa, N.Maoka, R.Masui, S.Kuramitsu, N.Kamiya. Ligand-Induced Conformational Changes and A Reaction Intermediate in Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8, As Revealed By X-Ray Crystallography J.Mol.Biol. V. 337 1011 2004.
ISSN: ISSN 0022-2836
PubMed: 15033367
DOI: 10.1016/J.JMB.2004.02.011