Manganese in PDB 2j9f: Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B

All present enzymatic activity of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B:
1.2.4.4;

The structure of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B, PDB code: 2j9f was solved by L.Jun, M.Machius, J.L.Chuang, R.M.Wynn, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.64 / 1.88
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.342, 145.342, 138.050, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 20

The structure of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Manganese atom in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B (pdb code 2j9f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B, PDB code: 2j9f:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1401 b:17.1 occ:1.00 O3B A:THV1403 2.2 12.0 1.0 O A:TYR224 2.3 11.6 1.0 O2A A:THV1403 2.3 10.0 1.0 OD1 A:ASN222 2.3 14.6 1.0 OE1 A:GLU193 2.3 11.0 1.0 O A:HOH2291 2.5 9.4 1.0 OE2 A:GLU193 2.6 12.5 1.0 CD A:GLU193 2.8 12.4 1.0 CG A:ASN222 3.2 15.6 1.0 C A:TYR224 3.3 12.2 1.0 PA A:THV1403 3.4 9.5 1.0 PB A:THV1403 3.4 10.9 1.0 O3A A:THV1403 3.6 10.4 1.0 ND2 A:ASN222 3.6 15.6 1.0 N A:ALA225 4.1 10.5 1.0 N A:TYR224 4.1 13.2 1.0 CA A:ALA225 4.1 10.3 1.0 O5G A:THV1403 4.2 10.8 1.0 O1B A:THV1403 4.2 14.8 1.0 N A:ASN222 4.3 12.4 1.0 CG A:GLU193 4.3 9.4 1.0 CA A:TYR224 4.3 13.4 1.0 N A:GLU193 4.3 7.7 1.0 N A:GLY194 4.5 8.6 1.0 CB A:ASN222 4.5 13.5 1.0 CB A:ALA225 4.6 9.0 1.0 O A:ARG220 4.6 11.3 1.0 O1A A:THV1403 4.6 9.4 1.0 CA A:ASN222 4.7 13.9 1.0 O2B A:THV1403 4.7 11.5 1.0 O A:HOH2203 4.7 17.9 1.0 C A:ASN222 4.7 14.6 1.0 N A:GLY223 4.8 14.9 1.0 CA A:GLY192 4.9 8.0 1.0 CB A:GLU193 5.0 8.9 1.0 CA A:GLU193 5.0 8.7 1.0 O A:HOH2153 5.0 11.6 1.0

Manganese binding site 2 out of 2 in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1401 b:17.2 occ:1.00 O2A C:THV1403 2.2 7.8 1.0 O3B C:THV1403 2.2 10.0 1.0 OD1 C:ASN222 2.3 13.4 1.0 O C:TYR224 2.3 8.9 1.0 OE1 C:GLU193 2.4 11.1 1.0 O C:HOH2297 2.4 10.3 1.0 OE2 C:GLU193 2.7 10.7 1.0 CD C:GLU193 2.8 12.2 1.0 CG C:ASN222 3.2 13.5 1.0 C C:TYR224 3.3 10.8 1.0 PA C:THV1403 3.3 8.0 1.0 PB C:THV1403 3.4 10.5 1.0 ND2 C:ASN222 3.5 11.3 1.0 O3A C:THV1403 3.6 10.9 1.0 N C:ALA225 4.1 9.4 1.0 N C:TYR224 4.1 11.8 1.0 O5G C:THV1403 4.1 9.3 1.0 O1B C:THV1403 4.1 10.7 1.0 CA C:ALA225 4.2 8.5 1.0 N C:GLU193 4.3 8.0 1.0 N C:ASN222 4.3 10.2 1.0 CA C:TYR224 4.3 11.5 1.0 CG C:GLU193 4.3 8.8 1.0 CB C:ASN222 4.5 11.8 1.0 N C:GLY194 4.5 7.5 1.0 O C:HOH2217 4.5 17.5 1.0 O C:ARG220 4.5 11.2 1.0 O1A C:THV1403 4.6 7.6 1.0 O2B C:THV1403 4.7 10.2 1.0 CA C:ASN222 4.7 11.8 1.0 CB C:ALA225 4.7 7.8 1.0 C C:ASN222 4.8 12.5 1.0 N C:GLY223 4.8 12.9 1.0 CA C:GLY192 4.8 7.2 1.0 CA C:GLU193 5.0 7.9 1.0 CB C:GLU193 5.0 8.6 1.0 C C:GLY192 5.0 7.9 1.0

J.Li, M.Machius, J.L.Chuang, R.M.Wynn, D.T.Chuang. The Two Active Sites in Human Branched-Chain Alpha- Keto Acid Dehydrogenase Operate Independently Without An Obligatory Alternating-Site Mechanism. J.Biol.Chem. V. 282 11904 2007.
ISSN: ISSN 0021-9258
PubMed: 17329260
DOI: 10.1074/JBC.M610843200