Atomistry » Fluorine » PDB 4olm-4pa0 » 4op2
Atomistry »
  Fluorine »
    PDB 4olm-4pa0 »
      4op2 »

Fluorine in PDB 4op2: Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate

Protein crystallography data

The structure of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate, PDB code: 4op2 was solved by S.R.Jordan, S.Chmait, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.32 / 2.24
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 149.053, 149.053, 131.833, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 27

Other elements in 4op2:

The structure of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Iodine (I) 26 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate (pdb code 4op2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate, PDB code: 4op2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4op2

Go back to Fluorine Binding Sites List in 4op2
Fluorine binding site 1 out of 6 in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:58.4
occ:1.00
F2 A:2UX701 0.0 58.4 1.0
C20 A:2UX701 1.3 55.8 1.0
F1 A:2UX701 2.2 62.3 1.0
F3 A:2UX701 2.2 68.4 1.0
C13 A:2UX701 2.3 47.9 1.0
C14 A:2UX701 2.8 46.2 1.0
CE1 A:HIS504 2.8 43.8 1.0
C9 A:2UX701 2.9 40.3 1.0
C10 A:2UX701 3.0 39.8 1.0
ND1 A:HIS504 3.2 39.5 1.0
O1 A:2UX701 3.4 46.2 1.0
NE2 A:HIS504 3.5 45.4 1.0
CG A:MET522 3.7 34.6 1.0
CG A:HIS504 4.0 43.1 1.0
CD2 A:HIS504 4.2 44.8 1.0
C8 A:2UX701 4.2 37.6 1.0
C11 A:2UX701 4.3 37.4 1.0
CA A:MET522 4.5 37.2 1.0
CB A:MET522 4.7 36.9 1.0
SD A:MET522 4.8 33.0 1.0
O A:HOH817 4.8 27.8 1.0
N A:MET522 4.8 38.7 1.0
CB A:ARG525 4.8 43.4 1.0
CG A:ARG525 5.0 49.3 1.0
CB A:HIS504 5.0 41.6 1.0
O A:ALA521 5.0 32.9 1.0

Fluorine binding site 2 out of 6 in 4op2

Go back to Fluorine Binding Sites List in 4op2
Fluorine binding site 2 out of 6 in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:68.4
occ:1.00
F3 A:2UX701 0.0 68.4 1.0
C20 A:2UX701 1.3 55.8 1.0
F2 A:2UX701 2.2 58.4 1.0
F1 A:2UX701 2.2 62.3 1.0
C13 A:2UX701 2.3 47.9 1.0
O1 A:2UX701 2.6 46.2 1.0
C10 A:2UX701 2.9 39.8 1.0
O A:ALA521 2.9 32.9 1.0
O A:HOH801 3.0 36.9 1.0
C A:ALA521 3.2 38.6 1.0
C9 A:2UX701 3.3 40.3 1.0
CB A:ARG525 3.4 43.4 1.0
CA A:MET522 3.5 37.2 1.0
N A:MET522 3.5 38.7 1.0
C14 A:2UX701 3.7 46.2 1.0
C11 A:2UX701 3.8 37.4 1.0
CG A:MET522 3.9 34.6 1.0
CB A:ALA521 3.9 34.0 1.0
CG A:ARG525 4.1 49.3 1.0
CA A:ALA521 4.2 34.0 1.0
CB A:MET522 4.3 36.9 1.0
NE A:ARG525 4.4 59.9 1.0
C8 A:2UX701 4.5 37.6 1.0
C A:MET522 4.5 41.8 1.0
CA A:ARG525 4.6 46.4 1.0
N A:ARG525 4.7 43.2 1.0
O A:MET522 4.7 46.2 1.0
CE1 A:HIS504 4.8 43.8 1.0
C12 A:2UX701 4.8 36.1 1.0
CD A:ARG525 4.9 49.1 1.0

Fluorine binding site 3 out of 6 in 4op2

Go back to Fluorine Binding Sites List in 4op2
Fluorine binding site 3 out of 6 in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:62.3
occ:1.00
F1 A:2UX701 0.0 62.3 1.0
C20 A:2UX701 1.3 55.8 1.0
F2 A:2UX701 2.2 58.4 1.0
F3 A:2UX701 2.2 68.4 1.0
C13 A:2UX701 2.3 47.9 1.0
O1 A:2UX701 2.5 46.2 1.0
C14 A:2UX701 2.8 46.2 1.0
NE A:ARG525 3.0 59.9 1.0
CG A:ARG525 3.1 49.3 1.0
CB A:ARG525 3.3 43.4 1.0
NE2 A:HIS504 3.4 45.4 1.0
CE1 A:HIS504 3.4 43.8 1.0
CD A:ARG525 3.6 49.1 1.0
C10 A:2UX701 3.7 39.8 1.0
CZ A:ARG525 4.0 56.0 1.0
O A:HOH801 4.2 36.9 1.0
NH2 A:ARG525 4.2 51.8 1.0
CD2 A:HIS504 4.3 44.8 1.0
ND1 A:HIS504 4.3 39.5 1.0
C9 A:2UX701 4.3 40.3 1.0
C11 A:2UX701 4.7 37.4 1.0
CG A:HIS504 4.8 43.1 1.0
O A:ALA521 4.8 32.9 1.0
CA A:ARG525 4.8 46.4 1.0

Fluorine binding site 4 out of 6 in 4op2

Go back to Fluorine Binding Sites List in 4op2
Fluorine binding site 4 out of 6 in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:60.2
occ:1.00
F2 B:2UX701 0.0 60.2 1.0
C20 B:2UX701 1.3 44.4 1.0
F1 B:2UX701 2.1 50.4 1.0
C13 B:2UX701 2.3 36.9 1.0
F3 B:2UX701 2.3 59.9 1.0
C14 B:2UX701 2.6 32.1 1.0
C9 B:2UX701 2.8 30.4 1.0
C10 B:2UX701 2.9 30.7 1.0
CE1 B:HIS504 2.9 35.6 1.0
O B:HOH843 3.1 33.9 1.0
ND1 B:HIS504 3.2 36.3 1.0
O1 B:2UX701 3.4 34.1 1.0
NE2 B:HIS504 3.6 40.2 1.0
CG B:MET522 4.0 31.3 1.0
CG B:HIS504 4.0 36.4 1.0
C8 B:2UX701 4.1 33.0 1.0
O B:HOH900 4.1 28.5 1.0
CD2 B:HIS504 4.2 36.3 1.0
C11 B:2UX701 4.3 31.8 1.0
O B:GLU32 4.6 35.4 1.0
CB B:SER255 4.9 34.6 1.0
CA B:MET522 4.9 32.6 1.0
SD B:MET522 5.0 28.1 1.0

Fluorine binding site 5 out of 6 in 4op2

Go back to Fluorine Binding Sites List in 4op2
Fluorine binding site 5 out of 6 in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:59.9
occ:1.00
F3 B:2UX701 0.0 59.9 1.0
C20 B:2UX701 1.3 44.4 1.0
F1 B:2UX701 2.1 50.4 1.0
F2 B:2UX701 2.3 60.2 1.0
C13 B:2UX701 2.3 36.9 1.0
O1 B:2UX701 2.6 34.1 1.0
C10 B:2UX701 2.8 30.7 1.0
O B:ALA521 3.0 34.8 1.0
O B:HOH801 3.1 28.0 1.0
C9 B:2UX701 3.2 30.4 1.0
C B:ALA521 3.2 36.0 1.0
N B:MET522 3.4 34.1 1.0
CA B:MET522 3.5 32.6 1.0
C14 B:2UX701 3.7 32.1 1.0
CB B:ARG525 3.7 38.5 1.0
C11 B:2UX701 3.7 31.8 1.0
CG B:MET522 3.8 31.3 1.0
CB B:ALA521 3.9 33.5 1.0
CA B:ALA521 4.2 32.5 1.0
CB B:MET522 4.2 32.8 1.0
C8 B:2UX701 4.3 33.0 1.0
CG B:ARG525 4.4 37.9 1.0
NE B:ARG525 4.6 47.7 1.0
C B:MET522 4.6 31.6 1.0
C12 B:2UX701 4.7 33.1 1.0
N B:ARG525 4.9 40.1 1.0
CE1 B:HIS504 4.9 35.6 1.0
O B:HOH843 4.9 33.9 1.0
CA B:ARG525 4.9 40.3 1.0
O B:MET522 4.9 36.3 1.0

Fluorine binding site 6 out of 6 in 4op2

Go back to Fluorine Binding Sites List in 4op2
Fluorine binding site 6 out of 6 in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:50.4
occ:1.00
F1 B:2UX701 0.0 50.4 1.0
C20 B:2UX701 1.3 44.4 1.0
F3 B:2UX701 2.1 59.9 1.0
F2 B:2UX701 2.1 60.2 1.0
C13 B:2UX701 2.4 36.9 1.0
O1 B:2UX701 2.7 34.1 1.0
C14 B:2UX701 3.0 32.1 1.0
CG B:ARG525 3.2 37.9 1.0
NE2 B:HIS504 3.3 40.2 1.0
CB B:ARG525 3.3 38.5 1.0
CE1 B:HIS504 3.4 35.6 1.0
NE B:ARG525 3.5 47.7 1.0
C10 B:2UX701 3.7 30.7 1.0
O B:HOH803 3.8 42.5 1.0
CD B:ARG525 3.9 40.8 1.0
CD2 B:HIS504 4.0 36.3 1.0
ND1 B:HIS504 4.1 36.3 1.0
O B:HOH801 4.2 28.0 1.0
C9 B:2UX701 4.3 30.4 1.0
CG B:HIS504 4.5 36.4 1.0
CZ B:ARG525 4.5 52.0 1.0
O B:ALA521 4.7 34.8 1.0
NH2 B:ARG525 4.7 51.6 1.0
C11 B:2UX701 4.8 31.8 1.0
CA B:MET522 4.8 32.6 1.0
CG B:MET522 4.8 31.3 1.0
CA B:ARG525 4.9 40.3 1.0

Reference:

N.Tamayo, M.H.Norman, M.D.Bartberger, Y.Bo, J.Chen, S.Chmait, R.Cupples, C.Fotsch, C.Hale, F-T.Hong, S.R.Jordan, L.Liu, D.J.Lloyd, C.Moyer, N.Nishimura, G.Sivits, S.Tadesse, G.Van, K.C.Yang, D.J.St. Jean. Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 5. New Aryl Sulfones Series, Optimization Through Conformational Analysis J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
Page generated: Sun Dec 13 12:09:53 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy