Magnesium in PDB 1umd: Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methyl-2-Oxopentanoate As An Intermediate

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

The structure of Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methyl-2-Oxopentanoate As An Intermediate, PDB code: 1umd 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)	19.99 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	127.579, 246.503, 137.285, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.5

The binding sites of Magnesium atom in the Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methyl-2-Oxopentanoate As An Intermediate (pdb code 1umd). 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-Methyl-2-Oxopentanoate As An Intermediate, PDB code: 1umd:
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-Methyl-2-Oxopentanoate As An Intermediate


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-Methyl-2-Oxopentanoate As An Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:14.3 occ:1.00 O A:TYR206 1.9 15.3 1.0 O23 A:TDP1402 2.1 11.8 1.0 OD1 A:ASP175 2.1 13.5 1.0 OD1 A:ASN204 2.1 15.2 1.0 O12 A:TDP1402 2.1 14.3 1.0 O A:HOH1435 2.3 15.0 1.0 CG A:ASN204 3.0 15.4 1.0 CG A:ASP175 3.0 14.9 1.0 C A:TYR206 3.1 16.2 1.0 P1 A:TDP1402 3.2 13.6 1.0 P2 A:TDP1402 3.2 13.0 1.0 ND2 A:ASN204 3.3 14.6 1.0 O11 A:TDP1402 3.4 11.2 1.0 OD2 A:ASP175 3.4 14.0 1.0 O21 A:TDP1402 3.8 11.5 1.0 N A:ASP175 3.8 9.5 1.0 N A:TYR206 3.9 15.7 1.0 O5G A:TDP1402 4.0 13.5 1.0 CA A:TYR206 4.1 16.3 1.0 N A:ALA207 4.1 16.1 1.0 N A:ASN204 4.2 11.8 1.0 CA A:ALA207 4.2 16.0 1.0 O A:HOH1434 4.2 14.9 1.0 CB A:ASP175 4.3 11.9 1.0 CB A:ASN204 4.3 14.4 1.0 O22 A:TDP1402 4.4 13.5 1.0 N A:GLY176 4.4 9.7 1.0 O13 A:TDP1402 4.5 13.4 1.0 CA A:GLY174 4.6 11.4 1.0 CA A:ASP175 4.6 11.4 1.0 CA A:ASN204 4.6 13.2 1.0 C A:GLY174 4.6 10.5 1.0 N A:PHE205 4.7 13.6 1.0 O A:GLU202 4.7 11.1 1.0 C A:ASN204 4.7 14.2 1.0 CB A:TYR206 4.8 17.1 1.0

Magnesium binding site 2 out of 2 in the Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus HB8 with 4-Methyl-2-Oxopentanoate As An Intermediate


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-Methyl-2-Oxopentanoate As An Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2401 b:13.2 occ:1.00 OD1 C:ASP175 2.0 15.9 1.0 O C:TYR206 2.1 14.8 1.0 O12 C:TDP2402 2.1 12.5 1.0 O23 C:TDP2402 2.1 12.2 1.0 OD1 C:ASN204 2.1 14.0 1.0 O C:HOH2425 2.2 12.7 1.0 CG C:ASP175 3.0 13.6 1.0 CG C:ASN204 3.0 12.2 1.0 P1 C:TDP2402 3.2 14.2 1.0 P2 C:TDP2402 3.2 12.6 1.0 C C:TYR206 3.2 15.1 1.0 O11 C:TDP2402 3.3 12.2 1.0 OD2 C:ASP175 3.4 14.8 1.0 ND2 C:ASN204 3.4 12.9 1.0 O21 C:TDP2402 3.8 12.4 1.0 N C:ASP175 3.8 8.4 1.0 N C:TYR206 3.9 15.2 1.0 O5G C:TDP2402 4.0 13.9 1.0 N C:ALA207 4.1 14.3 1.0 CA C:TYR206 4.2 15.6 1.0 N C:ASN204 4.2 10.2 1.0 CA C:ALA207 4.3 14.7 1.0 CB C:ASP175 4.3 10.4 1.0 O C:HOH2439 4.3 15.1 1.0 CB C:ASN204 4.4 10.9 1.0 O22 C:TDP2402 4.4 12.5 1.0 N C:GLY176 4.4 9.6 1.0 O13 C:TDP2402 4.4 11.5 1.0 CA C:GLY174 4.5 8.7 1.0 CA C:ASP175 4.6 8.9 1.0 O C:GLU202 4.6 10.2 1.0 C C:GLY174 4.6 8.9 1.0 CA C:ASN204 4.6 12.1 1.0 N C:PHE205 4.7 15.3 1.0 C C:ASN204 4.7 13.1 1.0 CB C:TYR206 5.0 16.0 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