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Xenon in PDB 1gkz: Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp

Enzymatic activity of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp

All present enzymatic activity of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp:
2.7.1.115;

Protein crystallography data

The structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp, PDB code: 1gkz was solved by M.Machius, J.L.Chuang, R.M.Wynn, D.R.Tomchick, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.77 / 2.20
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.917, 128.917, 74.105, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 26.8

Other elements in 1gkz:

The structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 1 atom
Chlorine (Cl) 3 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp (pdb code 1gkz). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 2 binding sites of Xenon where determined in the Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp, PDB code: 1gkz:
Jump to Xenon binding site number: 1; 2;

Xenon binding site 1 out of 2 in 1gkz

Go back to Xenon Binding Sites List in 1gkz
Xenon binding site 1 out of 2 in the Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe501

b:0.6
occ:1.00
CD1 A:LEU68 3.7 60.3 1.0
XE A:XE502 3.7 0.8 1.0
CG2 A:ILE170 3.8 54.4 1.0
CB A:LEU128 4.1 45.5 1.0
CG1 A:VAL125 4.3 55.9 1.0
CB A:ALA174 4.3 50.4 1.0
CD2 A:LEU129 4.3 50.1 1.0
O A:VAL125 4.3 52.5 1.0
CG A:LEU129 4.4 49.5 1.0
CD1 A:LEU128 4.6 43.3 1.0
N A:LEU129 4.7 52.8 1.0
CA A:VAL125 4.8 51.4 1.0
CD2 A:LEU68 4.8 61.0 1.0
CG A:LEU68 4.8 59.5 1.0
CB A:VAL125 5.0 51.8 1.0

Xenon binding site 2 out of 2 in 1gkz

Go back to Xenon Binding Sites List in 1gkz
Xenon binding site 2 out of 2 in the Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase (Bck) Complxed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe502

b:0.8
occ:1.00
CG A:HIS132 3.5 60.0 1.0
ND1 A:HIS132 3.5 60.8 1.0
O A:HOH2050 3.6 56.2 1.0
XE A:XE501 3.7 0.6 1.0
CD2 A:HIS132 3.8 59.8 1.0
CE1 A:HIS132 3.9 62.4 1.0
CB A:HIS132 4.0 56.6 1.0
NE2 A:HIS132 4.0 62.3 1.0
O A:LEU128 4.0 48.8 1.0
CB A:LEU128 4.2 45.5 1.0
C A:LEU128 4.3 50.4 1.0
O A:HOH2018 4.3 47.4 1.0
CD1 A:ILE72 4.4 50.1 1.0
CG2 A:ILE170 4.6 54.4 1.0
N A:LEU129 4.7 52.8 1.0
CA A:LEU128 4.8 49.7 1.0
CA A:LEU129 4.9 54.1 1.0
CB A:ALA102 5.0 46.9 1.0

Reference:

M.Machius, J.L.Chuang, R.M.Wynn, D.R.Tomchick, D.T.Chuang. Structure of Rat Bckd Kinase: Nucleotide-Induced Domain Communication in A Mitochondrial Protein Kinase. Proc.Natl.Acad.Sci.Usa V. 98 11218 2001.
ISSN: ISSN 0027-8424
PubMed: 11562470
DOI: 10.1073/PNAS.201220098
Page generated: Wed Dec 16 02:39:20 2020

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