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Fluorine in PDB 2bu2: Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands

Enzymatic activity of Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands

All present enzymatic activity of Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands:
2.7.1.99;

Protein crystallography data

The structure of Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands, PDB code: 2bu2 was solved by T.R.Knoechel, A.D.Tucker, C.M.Robinson, C.Phillips, W.Taylor, P.J.Bungay, S.A.Kasten, T.E.Roche, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 108.703, 108.703, 83.855, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 2bu2:

The structure of Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands (pdb code 2bu2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands, PDB code: 2bu2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2bu2

Go back to Fluorine Binding Sites List in 2bu2
Fluorine binding site 1 out of 3 in the Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1387

b:80.2
occ:1.00
F1 A:TF11387 0.0 80.2 1.0
C8 A:TF11387 1.3 80.2 1.0
F3 A:TF11387 2.1 80.3 1.0
F2 A:TF11387 2.1 81.2 1.0
C4 A:TF11387 2.4 80.3 1.0
C9 A:TF11387 2.9 79.4 1.0
C1 A:TF11387 3.0 80.5 1.0
CB A:GLN163 3.2 55.6 1.0
O1 A:TF11387 3.3 81.0 1.0
CE2 A:PHE28 3.4 57.0 1.0
O2 A:TF11387 3.6 79.9 1.0
CD2 A:LEU160 3.6 40.4 1.0
O A:LEU160 3.6 44.9 1.0
CA A:LEU160 3.7 43.5 1.0
CG A:GLN163 3.8 56.1 1.0
N1 A:TF11387 3.9 80.8 1.0
CD2 A:PHE28 3.9 57.3 1.0
C A:LEU160 4.1 44.9 1.0
O A:HOH2091 4.3 58.4 1.0
CB A:LEU160 4.3 42.0 1.0
C3 A:TF11387 4.4 80.8 1.0
CZ A:PHE28 4.5 56.6 1.0
CA A:GLN163 4.6 55.9 1.0
CG A:LEU160 4.6 41.9 1.0
O A:MET159 4.7 41.5 1.0
CD1 A:LEU23 4.7 46.6 1.0
N A:LEU160 4.8 41.9 1.0
N A:HIS164 4.8 57.7 1.0
C A:GLN163 4.9 56.4 1.0
C2 A:TF11387 4.9 80.9 1.0
C6 A:TF11387 4.9 80.3 1.0

Fluorine binding site 2 out of 3 in 2bu2

Go back to Fluorine Binding Sites List in 2bu2
Fluorine binding site 2 out of 3 in the Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1387

b:81.2
occ:1.00
F2 A:TF11387 0.0 81.2 1.0
C8 A:TF11387 1.3 80.2 1.0
F3 A:TF11387 2.1 80.3 1.0
F1 A:TF11387 2.1 80.2 1.0
C4 A:TF11387 2.4 80.3 1.0
O2 A:TF11387 2.8 79.9 1.0
C9 A:TF11387 2.9 79.4 1.0
O A:LEU160 3.0 44.9 1.0
CD2 A:LEU45 3.3 56.5 1.0
CD1 A:LEU45 3.3 57.6 1.0
CG A:LEU45 3.6 57.7 1.0
C A:LEU160 3.6 44.9 1.0
CA A:LEU160 3.8 43.5 1.0
C1 A:TF11387 3.8 80.5 1.0
CB A:LEU160 3.9 42.0 1.0
OG A:SER41 4.1 66.9 1.0
CB A:GLN163 4.2 55.6 1.0
CB A:HIS164 4.3 59.4 1.0
N A:HIS164 4.3 57.7 1.0
CD2 A:LEU160 4.3 40.4 1.0
O1 A:TF11387 4.5 81.0 1.0
N1 A:TF11387 4.6 80.8 1.0
CG A:LEU160 4.6 41.9 1.0
CA A:HIS164 4.7 59.0 1.0
C3 A:TF11387 4.7 80.8 1.0
N A:ILE161 4.8 45.9 1.0
ND1 A:HIS164 4.9 61.4 1.0
C A:GLN163 4.9 56.4 1.0

Fluorine binding site 3 out of 3 in 2bu2

Go back to Fluorine Binding Sites List in 2bu2
Fluorine binding site 3 out of 3 in the Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1387

b:80.3
occ:1.00
F3 A:TF11387 0.0 80.3 1.0
C8 A:TF11387 1.3 80.2 1.0
F2 A:TF11387 2.1 81.2 1.0
F1 A:TF11387 2.1 80.2 1.0
C4 A:TF11387 2.4 80.3 1.0
O2 A:TF11387 2.9 79.9 1.0
C1 A:TF11387 3.0 80.5 1.0
C3 A:TF11387 3.0 80.8 1.0
N1 A:TF11387 3.2 80.8 1.0
CD2 A:LEU160 3.5 40.4 1.0
CD2 A:LEU45 3.6 56.5 1.0
CE2 A:PHE44 3.6 58.5 1.0
C9 A:TF11387 3.7 79.4 1.0
CD2 A:PHE44 3.8 57.4 1.0
CD1 A:LEU23 3.9 46.6 1.0
O1 A:TF11387 4.0 81.0 1.0
CG A:LEU160 4.2 41.9 1.0
CB A:LEU160 4.2 42.0 1.0
CD1 A:LEU160 4.3 40.2 1.0
CG A:LEU45 4.4 57.7 1.0
CA A:LEU160 4.4 43.5 1.0
C7 A:TF11387 4.5 81.2 1.0
C2 A:TF11387 4.5 80.9 1.0
CE2 A:PHE28 4.5 57.0 1.0
C6 A:TF11387 4.6 80.3 1.0
O A:LEU160 4.7 44.9 1.0
CD1 A:LEU45 4.7 57.6 1.0
CZ A:PHE44 4.8 58.3 1.0
C A:LEU160 5.0 44.9 1.0

Reference:

T.R.Knoechel, A.D.Tucker, C.M.Robinson, C.Phillips, W.Taylor, P.J.Bungay, S.A.Kasten, T.E.Roche, D.G.Brown. Regulatory Roles of the N-Terminal Domain Based on Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands. Biochemistry V. 45 402 2006.
ISSN: ISSN 0006-2960
PubMed: 16401071
DOI: 10.1021/BI051402S
Page generated: Wed Jul 31 13:53:19 2024

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