Fluorine in PDB 8vmf: Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide

Enzymatic activity of Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide

All present enzymatic activity of Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide:
2.7.11.1; 2.7.11.26;

Protein crystallography data

The structure of Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide, PDB code: 8vmf was solved by M.D.Enos, M.Gavagan, N.Jameson, J.G.Zalatan, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.07 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 82.251, 82.251, 280.354, 90, 90, 120
R / Rfree (%) 20.9 / 25.1

Other elements in 8vmf:

The structure of Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide (pdb code 8vmf). 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 Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide, PDB code: 8vmf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8vmf

Go back to Fluorine Binding Sites List in 8vmf
Fluorine binding site 1 out of 3 in the Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide


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 A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:64.8
occ:0.59
 F1 A:AF3503 0.0 64.8 0.6
AL A:AF3503 1.6 83.2 0.6
NZ A:LYS183 2.4 59.2 1.0
F2 A:AF3503 2.8 86.3 0.6
F3 A:AF3503 2.8 89.5 0.6
CE A:LYS183 3.0 51.9 1.0
OD2 A:ASP181 3.3 57.9 1.0
O A:HOH703 3.6 64.7 1.0
MG A:MG501 3.8 70.5 1.0
OG A:SER219 3.8 57.4 1.0
OD2 A:ASP200 4.1 71.0 1.0
OG A:SER66 4.1 86.2 0.4
OD1 A:ASP181 4.1 49.4 1.0
CG A:ASP181 4.1 52.7 1.0
CD A:LYS183 4.4 46.3 1.0
O1B A:ADP504 4.4 100.5 0.8
CB A:SER66 4.7 96.6 0.4
ND2 A:ASN186 4.8 51.2 1.0
O A:HOH647 4.9 61.2 1.0
CB A:SER219 4.9 56.9 1.0
OD1 A:ASN186 5.0 51.6 1.0

Fluorine binding site 2 out of 3 in 8vmf

Go back to Fluorine Binding Sites List in 8vmf
Fluorine binding site 2 out of 3 in the Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide


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 A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:86.3
occ:0.59
 F2 A:AF3503 0.0 86.3 0.6
AL A:AF3503 1.6 83.2 0.6
O3B A:ADP504 2.8 102.3 0.8
F1 A:AF3503 2.8 64.8 0.6
F3 A:AF3503 2.8 89.5 0.6
MG A:MG502 2.8 82.7 1.0
O A:HOH647 3.1 61.2 1.0
OD2 A:ASP200 3.2 71.0 1.0
CZ A:PHE67 3.3 124.4 0.6
OD2 A:ASP181 3.5 57.9 1.0
O1B A:ADP504 3.6 100.5 0.8
CE2 A:PHE67 3.6 122.8 0.6
PB A:ADP504 3.7 100.2 0.8
OD1 A:ASP200 3.9 62.9 1.0
CG A:ASP200 4.0 67.1 1.0
CE1 A:PHE67 4.0 126.1 0.6
CB A:SER66 4.1 96.6 0.4
OG A:SER66 4.3 86.2 0.4
MG A:MG501 4.3 70.5 1.0
N A:SER66 4.4 101.0 0.4
O3A A:ADP504 4.6 97.5 0.8
CD2 A:PHE67 4.6 123.8 0.6
CG A:ASP181 4.7 52.7 1.0
CD1 A:PHE67 4.7 123.4 0.4
CA A:SER66 4.8 104.3 0.4
N A:PHE67 4.8 122.8 0.4
CD1 A:PHE67 4.9 124.7 0.6
O2B A:ADP504 5.0 100.2 0.8

Fluorine binding site 3 out of 3 in 8vmf

Go back to Fluorine Binding Sites List in 8vmf
Fluorine binding site 3 out of 3 in the Crystal Structure of A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide


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 A Transition-State Mimic of the Gsk-3/Axin Complex Bound to A Beta-Catenin S45D Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:89.5
occ:0.59
 F3 A:AF3503 0.0 89.5 0.6
AL A:AF3503 1.6 83.2 0.6
N A:SER66 2.5 101.0 0.4
O1B A:ADP504 2.6 100.5 0.8
F1 A:AF3503 2.8 64.8 0.6
F2 A:AF3503 2.8 86.3 0.6
OG A:SER66 2.8 86.2 0.4
CB A:SER66 3.1 96.6 0.4
C A:GLY65 3.2 87.1 0.4
CA A:GLY65 3.3 82.9 0.4
CA A:SER66 3.4 104.3 0.4
O A:HOH703 3.4 64.7 1.0
CE2 A:PHE67 3.5 122.8 0.6
MG A:MG501 3.6 70.5 1.0
PB A:ADP504 3.6 100.2 0.8
O3B A:ADP504 3.7 102.3 0.8
CZ A:PHE67 4.1 124.4 0.6
O A:GLY65 4.3 87.0 0.4
OD2 A:ASP200 4.5 71.0 1.0
CD2 A:PHE67 4.5 123.8 0.6
O2B A:ADP504 4.5 100.2 0.8
C A:SER66 4.5 114.3 0.4
NZ A:LYS183 4.5 59.2 1.0
N A:PHE67 4.5 122.8 0.4
N A:GLY65 4.8 77.2 0.4
O3A A:ADP504 4.9 97.5 0.8

Reference:

M.D.Enos, M.Gavagan, N.Jameson, J.G.Zalatan, W.I.Weis. Structural and Functional Effects of Phosphopriming and Scaffolding in the Kinase GSK3BETA Sci.Signal. 2024.
ISSN: ESSN 1937-9145
DOI: 10.1126/SCISIGNAL.ADO0881
Page generated: Sat Sep 28 20:37:45 2024

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