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Fluorine in PDB 6lin: Crystal Structure of Human PDK2 Complexed with GM10030

Enzymatic activity of Crystal Structure of Human PDK2 Complexed with GM10030

All present enzymatic activity of Crystal Structure of Human PDK2 Complexed with GM10030:
2.7.11.2;

Protein crystallography data

The structure of Crystal Structure of Human PDK2 Complexed with GM10030, PDB code: 6lin was solved by J.Kang, J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.08 / 2.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.420, 156.186, 102.012, 90.00, 103.97, 90.00
R / Rfree (%) 22.3 / 28

Other elements in 6lin:

The structure of Crystal Structure of Human PDK2 Complexed with GM10030 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human PDK2 Complexed with GM10030 (pdb code 6lin). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human PDK2 Complexed with GM10030, PDB code: 6lin:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6lin

Go back to Fluorine Binding Sites List in 6lin
Fluorine binding site 1 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:51.6
occ:1.00
 F37 A:EH0403 0.0 51.6 1.0
C17 A:EH0403 1.3 46.7 1.0
C16 A:EH0403 2.3 44.6 1.0
C18 A:EH0403 2.4 46.3 1.0
O21 A:EH0403 2.8 56.2 1.0
CA A:ASN255 3.3 37.9 1.0
O A:ASN255 3.4 35.3 1.0
CD A:ARG258 3.5 69.4 1.0
C22 A:EH0403 3.5 60.0 1.0
CB A:ARG258 3.5 53.1 1.0
CB A:ASN255 3.5 42.2 1.0
C15 A:EH0403 3.6 45.0 1.0
OD1 A:ASN255 3.6 39.8 1.0
C19 A:EH0403 3.6 42.8 1.0
C A:ASN255 3.8 36.0 1.0
CG A:ASN255 3.8 39.7 1.0
CG A:ARG258 3.9 63.7 1.0
NH1 A:ARG258 4.0 84.6 1.0
NE A:ARG258 4.1 75.5 1.0
C20 A:EH0403 4.1 43.8 1.0
CZ A:ARG258 4.3 80.6 1.0
N A:ASN255 4.4 39.3 1.0
N A:ALA259 4.6 40.9 1.0
F41 A:EH0403 4.7 37.8 1.0
CA A:ARG258 4.8 45.1 1.0
O A:LYS254 4.8 39.8 1.0
C11 A:EH0403 4.8 45.8 1.0
C05 A:EH0403 4.9 36.4 1.0
ND2 A:ASN255 4.9 38.3 1.0
C23 A:EH0403 4.9 68.0 1.0
C A:LYS254 5.0 41.5 1.0

Fluorine binding site 2 out of 8 in 6lin

Go back to Fluorine Binding Sites List in 6lin
Fluorine binding site 2 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:37.8
occ:1.00
 F41 A:EH0403 0.0 37.8 1.0
C19 A:EH0403 1.4 42.8 1.0
C18 A:EH0403 2.4 46.3 1.0
C20 A:EH0403 2.4 43.8 1.0
O21 A:EH0403 2.7 56.2 1.0
CD2 A:LEU303 3.2 33.5 1.0
C22 A:EH0403 3.2 60.0 1.0
C17 A:EH0403 3.6 46.7 1.0
C15 A:EH0403 3.6 45.0 1.0
C23 A:EH0403 3.7 68.0 1.0
O40 A:EH0403 3.8 82.3 1.0
C38 A:EH0403 4.1 85.5 1.0
C16 A:EH0403 4.1 44.6 1.0
C39 A:EH0403 4.3 97.8 1.0
C27 A:EH0403 4.6 85.2 1.0
CG A:LEU303 4.7 35.4 1.0
F37 A:EH0403 4.7 51.6 1.0
C11 A:EH0403 4.9 45.8 1.0
NH1 A:ARG258 4.9 84.6 1.0

Fluorine binding site 3 out of 8 in 6lin

Go back to Fluorine Binding Sites List in 6lin
Fluorine binding site 3 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:53.8
occ:1.00
 F37 B:EH0402 0.0 53.8 1.0
C17 B:EH0402 1.4 59.8 1.0
C18 B:EH0402 2.4 58.0 1.0
C16 B:EH0402 2.4 54.7 1.0
O21 B:EH0402 2.7 66.5 1.0
C22 B:EH0402 3.1 82.6 1.0
CD2 B:LEU303 3.3 40.3 1.0
C19 B:EH0402 3.7 57.4 1.0
C15 B:EH0402 3.7 51.0 1.0
OH B:TYR308 4.0 79.6 1.0
C20 B:EH0402 4.2 51.9 1.0
CE1 B:TYR308 4.4 91.7 1.0
C29 B:EH0402 4.6 0.2 1.0
C23 B:EH0402 4.6 0.1 1.0
CZ B:TYR308 4.7 89.3 1.0
N25 B:EH0402 4.7 64.9 1.0
F41 B:EH0402 4.8 66.7 1.0
CG B:LEU303 4.8 41.8 1.0
NH2 B:ARG258 4.9 82.9 1.0
C11 B:EH0402 5.0 51.5 1.0

Fluorine binding site 4 out of 8 in 6lin

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Fluorine binding site 4 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:66.7
occ:1.00
 F41 B:EH0402 0.0 66.7 1.0
C19 B:EH0402 1.4 57.4 1.0
C20 B:EH0402 2.3 51.9 1.0
C18 B:EH0402 2.4 58.0 1.0
O21 B:EH0402 2.8 66.5 1.0
OD1 B:ASN255 3.1 39.8 1.0
CA B:ASN255 3.4 40.7 1.0
CB B:ASN255 3.5 40.2 1.0
CG B:ASN255 3.5 41.3 1.0
C23 B:EH0402 3.5 0.1 1.0
C15 B:EH0402 3.6 51.0 1.0
C22 B:EH0402 3.6 82.6 1.0
C17 B:EH0402 3.6 59.8 1.0
CD B:ARG258 3.7 66.8 1.0
O B:ASN255 3.8 45.6 1.0
C16 B:EH0402 4.1 54.7 1.0
CB B:ARG258 4.1 44.2 1.0
C B:ASN255 4.1 41.0 1.0
NH2 B:ARG258 4.4 82.9 1.0
ND2 B:ASN255 4.5 38.5 1.0
CG B:ARG258 4.5 53.4 1.0
N B:ASN255 4.5 41.6 1.0
C38 B:EH0402 4.7 0.2 1.0
F37 B:EH0402 4.8 53.8 1.0
C05 B:EH0402 4.8 36.1 1.0
C11 B:EH0402 4.8 51.5 1.0
NE B:ARG258 4.8 77.2 1.0

Fluorine binding site 5 out of 8 in 6lin

Go back to Fluorine Binding Sites List in 6lin
Fluorine binding site 5 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:59.4
occ:1.00
 F37 C:EH0402 0.0 59.4 1.0
C17 C:EH0402 1.4 47.4 1.0
C18 C:EH0402 2.3 43.1 1.0
C16 C:EH0402 2.4 47.8 1.0
O21 C:EH0402 2.8 41.0 1.0
C22 C:EH0402 3.1 43.2 1.0
CD2 C:LEU303 3.2 40.0 1.0
C19 C:EH0402 3.6 40.2 1.0
O42 C:EH0402 3.6 72.6 1.0
C15 C:EH0402 3.7 44.3 1.0
C38 C:EH0402 3.8 74.2 1.0
C23 C:EH0402 3.9 54.3 1.0
C39 C:EH0402 4.0 86.9 1.0
C20 C:EH0402 4.1 38.4 1.0
NH1 C:ARG258 4.5 61.3 1.0
F41 C:EH0402 4.7 49.1 1.0
CG C:LEU303 4.7 38.2 1.0
O C:HOH511 4.8 45.6 1.0
N25 C:EH0402 4.9 64.0 1.0
C11 C:EH0402 4.9 49.1 1.0

Fluorine binding site 6 out of 8 in 6lin

Go back to Fluorine Binding Sites List in 6lin
Fluorine binding site 6 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:49.1
occ:1.00
 F41 C:EH0402 0.0 49.1 1.0
C19 C:EH0402 1.3 40.2 1.0
C20 C:EH0402 2.3 38.4 1.0
C18 C:EH0402 2.3 43.1 1.0
O21 C:EH0402 2.8 41.0 1.0
CD C:ARG258 3.2 55.9 1.0
CA C:ASN255 3.4 35.7 1.0
OD1 C:ASN255 3.5 37.9 1.0
CB C:ASN255 3.5 39.4 1.0
C17 C:EH0402 3.6 47.4 1.0
C15 C:EH0402 3.6 44.3 1.0
O C:ASN255 3.7 38.3 1.0
CG C:ASN255 3.7 38.8 1.0
C22 C:EH0402 3.7 43.2 1.0
CB C:ARG258 3.8 51.5 1.0
C C:ASN255 4.0 33.6 1.0
CG C:ARG258 4.0 55.0 1.0
C16 C:EH0402 4.0 47.8 1.0
NH1 C:ARG258 4.2 61.3 1.0
NE C:ARG258 4.3 59.3 1.0
N C:ASN255 4.6 37.9 1.0
ND2 C:ASN255 4.6 38.2 1.0
F37 C:EH0402 4.7 59.4 1.0
CZ C:ARG258 4.7 60.9 1.0
C11 C:EH0402 4.8 49.1 1.0
C05 C:EH0402 4.9 36.3 1.0
N C:ALA259 4.9 48.9 1.0
C23 C:EH0402 5.0 54.3 1.0

Fluorine binding site 7 out of 8 in 6lin

Go back to Fluorine Binding Sites List in 6lin
Fluorine binding site 7 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:52.3
occ:1.00
 F37 D:EH0401 0.0 52.3 1.0
C17 D:EH0401 1.4 46.9 1.0
C18 D:EH0401 2.3 47.0 1.0
C16 D:EH0401 2.4 43.9 1.0
O21 D:EH0401 2.8 53.1 1.0
C22 D:EH0401 3.2 58.5 1.0
OD1 D:ASN255 3.2 34.5 1.0
CA D:ASN255 3.3 36.0 1.0
CB D:ASN255 3.4 37.5 1.0
CG D:ASN255 3.4 39.5 1.0
C19 D:EH0401 3.6 43.2 1.0
C15 D:EH0401 3.6 42.7 1.0
CD D:ARG258 3.7 60.5 1.0
O D:ASN255 3.7 35.9 1.0
CB D:ARG258 3.9 38.4 1.0
C D:ASN255 4.0 35.9 1.0
C20 D:EH0401 4.1 43.9 1.0
C23 D:EH0401 4.3 66.4 1.0
ND2 D:ASN255 4.4 43.3 1.0
CG D:ARG258 4.4 48.0 1.0
NH2 D:ARG258 4.4 84.1 1.0
N D:ASN255 4.5 35.9 1.0
F41 D:EH0401 4.7 43.7 1.0
NE D:ARG258 4.9 72.2 1.0
C05 D:EH0401 4.9 32.5 1.0
C11 D:EH0401 4.9 42.8 1.0

Fluorine binding site 8 out of 8 in 6lin

Go back to Fluorine Binding Sites List in 6lin
Fluorine binding site 8 out of 8 in the Crystal Structure of Human PDK2 Complexed with GM10030


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human PDK2 Complexed with GM10030 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:43.7
occ:1.00
 F41 D:EH0401 0.0 43.7 1.0
C19 D:EH0401 1.3 43.2 1.0
C18 D:EH0401 2.3 47.0 1.0
C20 D:EH0401 2.4 43.9 1.0
O21 D:EH0401 2.7 53.1 1.0
CD2 D:LEU303 3.2 39.9 1.0
C22 D:EH0401 3.4 58.5 1.0
C17 D:EH0401 3.6 46.9 1.0
C15 D:EH0401 3.7 42.7 1.0
C16 D:EH0401 4.1 43.9 1.0
C23 D:EH0401 4.5 66.4 1.0
F37 D:EH0401 4.7 52.3 1.0
CG D:LEU303 4.7 39.9 1.0
O26 D:EH0401 4.8 61.0 1.0
C11 D:EH0401 4.9 42.8 1.0

Reference:

J.Kang, H.S.Pagire, D.Kang, Y.H.Song, I.K.Lee, K.T.Lee, C.J.Park, J.H.Ahn, J.Kim. Structural Basis For the Inhibition of PDK2 By Novel Atp- and Lipoyl-Binding Site Targeting Compounds. Biochem.Biophys.Res.Commun. V. 527 778 2020.
ISSN: ESSN 1090-2104
PubMed: 32444142
DOI: 10.1016/J.BBRC.2020.04.102
Page generated: Thu Aug 1 21:58:01 2024

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