Fluorine in PDB 5y2i: Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A

Enzymatic activity of Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A

All present enzymatic activity of Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A:
5.4.2.11; 5.4.2.4;

Protein crystallography data

The structure of Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A, PDB code: 5y2i was solved by L.Jiang, L.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.57 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.762, 85.036, 102.480, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.4

Other elements in 5y2i:

The structure of Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A (pdb code 5y2i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A, PDB code: 5y2i:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5y2i

Go back to Fluorine Binding Sites List in 5y2i
Fluorine binding site 1 out of 3 in the Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:52.9
occ:1.00
 F01 B:8KX301 0.0 52.9 1.0
C B:8KX301 1.3 38.8 1.0
F02 B:8KX301 2.1 37.2 1.0
F B:8KX301 2.3 54.4 1.0
C18 B:8KX301 2.3 46.6 1.0
O B:HOH467 2.5 32.5 1.0
C17 B:8KX301 2.6 50.6 1.0
CD2 B:PHE22 3.0 30.3 1.0
N B:PHE22 3.0 22.1 1.0
CE2 B:PHE22 3.1 32.2 1.0
CG B:PHE22 3.2 29.5 1.0
O B:ASN20 3.4 24.5 1.0
CZ B:PHE22 3.4 36.3 1.0
C B:ASN20 3.5 29.4 1.0
CD1 B:PHE22 3.5 31.2 1.0
N B:ARG21 3.6 24.0 1.0
CE1 B:PHE22 3.6 37.7 1.0
O B:HOH540 3.6 38.6 1.0
C19 B:8KX301 3.6 49.9 1.0
C B:ARG21 3.7 27.4 1.0
CA B:PHE22 3.8 25.5 1.0
CA B:ARG21 3.8 23.6 1.0
CB B:PHE22 4.0 23.6 1.0
C16 B:8KX301 4.0 56.9 1.0
CA B:ASN20 4.2 27.1 1.0
O B:LEU98 4.4 24.9 1.0
O B:HOH539 4.5 48.1 1.0
O B:GLU19 4.6 29.0 1.0
O B:HOH446 4.7 44.0 1.0
C20 B:8KX301 4.7 56.4 1.0
O B:ARG21 4.8 22.4 1.0
C15 B:8KX301 4.9 59.4 1.0

Fluorine binding site 2 out of 3 in 5y2i

Go back to Fluorine Binding Sites List in 5y2i
Fluorine binding site 2 out of 3 in the Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:37.2
occ:1.00
 F02 B:8KX301 0.0 37.2 1.0
C B:8KX301 1.3 38.8 1.0
F B:8KX301 2.1 54.4 1.0
F01 B:8KX301 2.1 52.9 1.0
C18 B:8KX301 2.4 46.6 1.0
O B:GLU19 2.5 29.0 1.0
C B:ASN20 3.0 29.4 1.0
CA B:ASN20 3.0 27.1 1.0
N B:ARG21 3.1 24.0 1.0
N B:PHE22 3.1 22.1 1.0
C19 B:8KX301 3.2 49.9 1.0
C B:GLU19 3.2 28.4 1.0
C17 B:8KX301 3.3 50.6 1.0
N B:ASN20 3.5 25.9 1.0
O B:ASN20 3.6 24.5 1.0
CA B:PHE22 3.9 25.5 1.0
O B:HOH446 3.9 44.0 1.0
CA B:ARG21 3.9 23.6 1.0
C B:ARG21 4.0 27.4 1.0
O B:HOH467 4.2 32.5 1.0
CB B:ASN20 4.4 28.4 1.0
C20 B:8KX301 4.4 56.4 1.0
CA B:GLU19 4.4 23.4 1.0
O B:LEU18 4.5 25.1 1.0
CG B:PHE22 4.5 29.5 1.0
C16 B:8KX301 4.5 56.9 1.0
OD1 B:ASN20 4.6 31.8 1.0
CD1 B:PHE22 4.7 31.2 1.0
CD2 B:PHE22 4.8 30.3 1.0
CB B:PHE22 4.8 23.6 1.0
CG B:ASN20 5.0 30.8 1.0
C15 B:8KX301 5.0 59.4 1.0

Fluorine binding site 3 out of 3 in 5y2i

Go back to Fluorine Binding Sites List in 5y2i
Fluorine binding site 3 out of 3 in the Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi- 004A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:54.4
occ:1.00
 F B:8KX301 0.0 54.4 1.0
C B:8KX301 1.3 38.8 1.0
F02 B:8KX301 2.1 37.2 1.0
F01 B:8KX301 2.3 52.9 1.0
C18 B:8KX301 2.3 46.6 1.0
C19 B:8KX301 2.7 49.9 1.0
CD1 B:PHE22 2.8 31.2 1.0
CA B:PHE22 2.9 25.5 1.0
N B:PHE22 2.9 22.1 1.0
CG B:PHE22 3.0 29.5 1.0
CE1 B:PHE22 3.3 37.7 1.0
C17 B:8KX301 3.5 50.6 1.0
CB B:PHE22 3.5 23.6 1.0
CD2 B:PHE22 3.8 30.3 1.0
CZ B:PHE22 4.0 36.3 1.0
C20 B:8KX301 4.1 56.4 1.0
O B:GLU19 4.2 29.0 1.0
CE2 B:PHE22 4.2 32.2 1.0
C B:ARG21 4.2 27.4 1.0
C B:PHE22 4.3 25.6 1.0
CE2 B:TYR92 4.4 28.1 1.0
CZ B:TYR92 4.5 34.8 1.0
N B:ARG21 4.5 24.0 1.0
C16 B:8KX301 4.6 56.9 1.0
O B:HOH461 4.6 34.3 1.0
N B:SER23 4.6 26.0 1.0
O B:HOH467 4.7 32.5 1.0
CD2 B:TYR92 4.7 25.8 1.0
C B:ASN20 4.8 29.4 1.0
OH B:TYR92 4.8 33.2 1.0
CA B:ARG21 4.8 23.6 1.0
C15 B:8KX301 4.9 59.4 1.0
CE1 B:TYR92 4.9 31.2 1.0
C B:GLU19 4.9 28.4 1.0

Reference:

L.Jiang, L.Zhou. Phosphoglycerate Mutase 1 (PGAM1) Complexed with Its Inhibitor Pgmi-004A To Be Published.
Page generated: Sun Dec 13 12:42:59 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