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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 2j9f:

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

Manganese (Mn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B, PDB code: 2j9f:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 2j9f

Go back to Potassium Binding Sites List in 2j9f
Potassium binding site 1 out of 4 in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1402

b:17.6
occ:1.00
 O A:PRO163 2.6 8.4 1.0
O A:HOH2078 2.7 10.7 1.0
OE1 A:GLN167 2.8 10.8 1.0
O A:SER161 2.9 8.4 1.0
OG1 A:THR166 3.0 9.1 1.0
OG A:SER161 3.1 10.0 1.0
O A:HOH2081 3.2 13.6 1.0
C A:PRO163 3.8 7.9 1.0
C A:SER161 3.8 8.4 1.0
CD A:GLN167 3.8 10.3 1.0
O B:HOH2096 4.0 8.5 1.0
N A:GLN167 4.1 7.2 1.0
N A:SER161 4.2 7.7 1.0
CB A:SER161 4.2 8.1 1.0
N A:THR166 4.2 6.6 1.0
CA A:SER161 4.3 8.2 1.0
CB A:THR166 4.4 7.4 1.0
CB A:GLN167 4.4 7.7 1.0
O A:HOH2080 4.4 13.8 1.0
O A:HOH2139 4.4 8.7 1.0
N A:PRO163 4.4 7.3 1.0
O A:GLY111 4.5 9.8 1.0
N A:ALA165 4.6 5.7 1.0
C A:SER162 4.6 7.8 1.0
CA A:LEU164 4.6 7.0 1.0
NE2 A:GLN167 4.6 9.2 1.0
CG A:GLN167 4.6 7.2 1.0
N A:LEU164 4.6 8.3 1.0
CA A:PRO163 4.6 6.9 1.0
OE2 B:GLU113 4.7 11.1 1.0
CA A:THR166 4.7 6.2 1.0
C A:LEU164 4.7 6.9 1.0
N A:SER162 4.8 8.2 1.0
C A:THR166 4.8 6.2 1.0
CD A:PRO163 4.8 5.6 1.0
CA A:GLN167 4.9 6.8 1.0
O A:SER162 4.9 9.6 1.0
CB A:PRO163 5.0 6.9 1.0
O A:GLN112 5.0 16.0 1.0

Potassium binding site 2 out of 4 in 2j9f

Go back to Potassium Binding Sites List in 2j9f
Potassium binding site 2 out of 4 in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1343

b:19.3
occ:1.00
 O B:ASN183 2.7 6.7 1.0
O B:GLY128 2.7 10.2 1.0
O B:CYS178 2.9 8.5 1.0
O B:ASP181 2.9 9.8 1.0
O B:LEU130 3.0 7.5 1.0
O B:HOH2136 3.1 10.6 1.0
OG1 B:THR131 3.5 10.0 1.0
C B:ASN183 3.8 7.8 1.0
C B:LEU130 3.8 6.9 1.0
C B:ASP181 3.9 9.8 1.0
C B:GLY128 3.9 8.8 1.0
O B:ILE179 4.0 7.1 1.0
N B:LEU130 4.0 8.7 1.0
C B:CYS178 4.1 9.0 1.0
SG B:CYS185 4.1 10.8 1.0
N B:ASN183 4.2 9.3 1.0
C B:SER129 4.2 8.8 1.0
CB B:ASP181 4.3 9.0 1.0
N B:CYS185 4.3 7.8 1.0
CA B:SER129 4.3 9.1 1.0
C B:ILE179 4.3 7.7 1.0
O B:HOH2145 4.3 19.9 1.0
N B:ASP181 4.3 8.9 1.0
CA B:ASP181 4.4 10.1 1.0
CB B:CYS185 4.5 8.7 1.0
CA B:PRO184 4.5 6.9 1.0
N B:THR131 4.5 7.5 1.0
N B:SER129 4.6 7.8 1.0
CA B:LEU130 4.6 7.8 1.0
N B:PRO184 4.6 7.3 1.0
CA B:ILE179 4.6 7.9 1.0
CA B:ASN183 4.7 8.1 1.0
C B:PRO184 4.7 7.7 1.0
CB B:THR131 4.7 8.6 1.0
CA B:THR131 4.8 7.6 1.0
O B:SER129 4.8 8.8 1.0
N B:ILE179 4.8 7.1 1.0
N B:LYS182 4.9 9.5 1.0
OD2 B:ASP181 4.9 11.7 1.0

Potassium binding site 3 out of 4 in 2j9f

Go back to Potassium Binding Sites List in 2j9f
Potassium binding site 3 out of 4 in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1402

b:18.1
occ:1.00
 O C:PRO163 2.6 8.6 1.0
O C:HOH2094 2.7 6.1 1.0
OE1 C:GLN167 2.8 7.5 1.0
O C:SER161 2.9 8.5 1.0
OG C:SER161 3.0 8.9 1.0
OG1 C:THR166 3.0 8.3 1.0
O C:HOH2096 3.1 11.7 1.0
C C:SER161 3.7 8.4 1.0
C C:PRO163 3.8 7.7 1.0
CD C:GLN167 3.9 5.3 1.0
O D:HOH2103 4.0 8.2 1.0
CB C:SER161 4.1 7.7 1.0
N C:SER161 4.2 7.7 1.0
N C:GLN167 4.2 6.3 1.0
CA C:SER161 4.2 8.0 1.0
N C:THR166 4.3 6.8 1.0
CB C:THR166 4.4 7.4 1.0
N C:PRO163 4.4 7.5 1.0
O C:HOH2095 4.4 12.9 1.0
CB C:GLN167 4.4 5.8 1.0
O C:HOH2144 4.5 9.0 1.0
O C:GLY111 4.6 11.0 1.0
N C:ALA165 4.6 6.6 1.0
C C:SER162 4.6 8.2 1.0
OE2 D:GLU113 4.6 9.6 1.0
CA C:PRO163 4.6 7.1 1.0
N C:LEU164 4.6 7.4 1.0
CA C:LEU164 4.7 7.2 1.0
CG C:GLN167 4.7 4.5 1.0
N C:SER162 4.7 8.1 1.0
NE2 C:GLN167 4.7 4.4 1.0
CA C:THR166 4.7 6.6 1.0
C C:LEU164 4.8 7.3 1.0
CD C:PRO163 4.8 6.6 1.0
O C:SER162 4.9 9.4 1.0
C C:THR166 4.9 6.5 1.0
CB C:PRO163 4.9 8.0 1.0
CA C:GLN167 4.9 5.9 1.0
O C:GLN112 5.0 16.1 1.0

Potassium binding site 4 out of 4 in 2j9f

Go back to Potassium Binding Sites List in 2j9f
Potassium binding site 4 out of 4 in the Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxylase E1B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1343

b:21.3
occ:1.00
 O D:GLY128 2.7 9.7 1.0
O D:ASN183 2.8 9.2 1.0
O D:CYS178 2.8 9.5 1.0
O D:ASP181 2.9 10.8 1.0
O D:HOH2144 3.1 12.2 1.0
O D:LEU130 3.1 7.1 1.0
OG1 D:THR131 3.5 10.8 1.0
C D:ASN183 3.8 9.4 1.0
C D:ASP181 3.8 10.2 1.0
C D:LEU130 3.9 7.5 1.0
O D:ILE179 3.9 10.1 1.0
C D:GLY128 3.9 9.2 1.0
C D:CYS178 4.0 10.3 1.0
SG D:CYS185 4.1 11.9 1.0
N D:LEU130 4.1 8.5 1.0
N D:ASN183 4.2 9.9 1.0
N D:CYS185 4.2 8.1 1.0
CB D:ASP181 4.2 9.8 1.0
N D:ASP181 4.3 10.7 1.0
C D:ILE179 4.3 10.2 1.0
C D:SER129 4.3 9.6 1.0
CB D:CYS185 4.3 8.4 1.0
CA D:ASP181 4.4 10.2 1.0
O D:HOH2150 4.4 26.8 1.0
CA D:SER129 4.4 8.9 1.0
CA D:PRO184 4.5 8.0 1.0
CA D:ILE179 4.6 10.0 1.0
N D:THR131 4.6 7.6 1.0
N D:PRO184 4.6 8.3 1.0
CA D:LEU130 4.6 8.0 1.0
N D:SER129 4.7 8.0 1.0
CB D:THR131 4.7 9.8 1.0
CA D:ASN183 4.7 9.7 1.0
C D:PRO184 4.7 8.1 1.0
CA D:THR131 4.7 8.8 1.0
N D:ILE179 4.7 9.4 1.0
O D:SER129 4.8 9.2 1.0
N D:LYS182 4.9 9.2 1.0
OD2 D:ASP181 4.9 11.9 1.0
CA D:CYS185 5.0 8.4 1.0
CA D:CYS178 5.0 10.3 1.0

Reference:

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
Page generated: Mon Aug 12 06:44:22 2024

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