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Fluorine in PDB 3qhw: Structure of A PCDK2/Cyclina Transition-State Mimic

Enzymatic activity of Structure of A PCDK2/Cyclina Transition-State Mimic

All present enzymatic activity of Structure of A PCDK2/Cyclina Transition-State Mimic:
2.7.11.22;

Protein crystallography data

The structure of Structure of A PCDK2/Cyclina Transition-State Mimic, PDB code: 3qhw was solved by M.A.Young, D.M.Jacobsen, Z.Q.Bao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.73 / 1.91
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.025, 163.450, 73.390, 90.00, 107.08, 90.00
R / Rfree (%) 18.8 / 21.9

Other elements in 3qhw:

The structure of Structure of A PCDK2/Cyclina Transition-State Mimic also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of A PCDK2/Cyclina Transition-State Mimic (pdb code 3qhw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of A PCDK2/Cyclina Transition-State Mimic, PDB code: 3qhw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3qhw

Go back to Fluorine Binding Sites List in 3qhw
Fluorine binding site 1 out of 6 in the Structure of A PCDK2/Cyclina Transition-State Mimic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of A PCDK2/Cyclina Transition-State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:47.9
occ:1.00
 F1 A:MGF300 0.0 47.9 1.0
MG A:MGF300 1.8 80.3 1.0
MG A:MG298 1.9 34.3 1.0
OD2 A:ASP145 2.6 34.5 1.0
OD1 A:ASN132 2.8 28.2 1.0
ND2 A:ASN132 3.0 27.9 1.0
F3 A:MGF300 3.0 60.6 1.0
O1B A:ADP297 3.0 63.4 1.0
O A:HOH445 3.1 36.7 1.0
F2 A:MGF300 3.2 89.7 1.0
OG1 J:THR0 3.2 49.9 1.0
CG A:ASN132 3.3 35.2 1.0
CE A:LYS129 3.3 30.7 1.0
OD2 A:ASP127 3.3 38.0 1.0
NZ A:LYS129 3.6 39.1 1.0
CG A:ASP145 3.9 37.1 1.0
O1A A:ADP297 4.0 56.1 1.0
MG A:MG299 4.1 65.4 1.0
O A:HOH302 4.1 44.5 1.0
OE1 A:GLN131 4.1 67.5 1.0
PB A:ADP297 4.3 67.6 1.0
CB J:THR0 4.3 50.0 1.0
CG A:ASP127 4.3 36.1 1.0
O2B A:ADP297 4.4 66.4 1.0
CG A:GLN131 4.5 42.1 1.0
CB A:ASP145 4.6 27.8 1.0
CD A:GLN131 4.7 65.8 1.0
CD A:LYS129 4.7 30.1 1.0
CB A:ASN132 4.7 25.3 1.0
OD1 A:ASP145 4.8 34.4 1.0
OD1 A:ASP127 4.8 40.5 1.0

Fluorine binding site 2 out of 6 in 3qhw

Go back to Fluorine Binding Sites List in 3qhw
Fluorine binding site 2 out of 6 in the Structure of A PCDK2/Cyclina Transition-State Mimic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of A PCDK2/Cyclina Transition-State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:89.7
occ:1.00
 F2 A:MGF300 0.0 89.7 1.0
MG A:MGF300 1.8 80.3 1.0
N A:THR14 3.0 0.3 1.0
F3 A:MGF300 3.1 60.6 1.0
F1 A:MGF300 3.2 47.9 1.0
OG1 J:THR0 3.2 49.9 1.0
O1B A:ADP297 3.3 63.4 1.0
CB J:THR0 3.3 50.0 1.0
OG1 A:THR14 3.3 0.3 1.0
CA A:GLY13 3.5 96.6 1.0
N J:THR0 3.7 63.2 1.0
C A:GLY13 3.7 97.2 1.0
CB A:THR14 3.8 0.7 1.0
NZ A:LYS129 4.0 39.1 1.0
CA A:THR14 4.0 0.3 1.0
CA J:THR0 4.1 56.6 1.0
MG A:MG298 4.2 34.3 1.0
PB A:ADP297 4.3 67.6 1.0
OE1 A:GLN131 4.4 67.5 1.0
O A:HOH445 4.4 36.7 1.0
CG2 J:THR0 4.5 51.2 1.0
O3B A:ADP297 4.6 81.3 1.0
C J:LYS-1 4.7 68.0 1.0
CE A:LYS129 4.8 30.7 1.0
O2B A:ADP297 4.8 66.4 1.0
CA J:LYS-1 4.8 84.7 1.0
N A:TYR15 4.9 93.0 1.0
O A:GLY13 4.9 95.3 1.0
N A:GLY13 4.9 97.5 1.0
MG A:MG299 5.0 65.4 1.0
OD2 A:ASP145 5.0 34.5 1.0

Fluorine binding site 3 out of 6 in 3qhw

Go back to Fluorine Binding Sites List in 3qhw
Fluorine binding site 3 out of 6 in the Structure of A PCDK2/Cyclina Transition-State Mimic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of A PCDK2/Cyclina Transition-State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:60.6
occ:1.00
 F3 A:MGF300 0.0 60.6 1.0
MG A:MGF300 1.8 80.3 1.0
MG A:MG299 2.0 65.4 1.0
O A:HOH302 3.0 44.5 1.0
O2B A:ADP297 3.0 66.4 1.0
F1 A:MGF300 3.0 47.9 1.0
OG1 J:THR0 3.0 49.9 1.0
OD2 A:ASP145 3.1 34.5 1.0
F2 A:MGF300 3.1 89.7 1.0
CB J:THR0 3.4 50.0 1.0
O1B A:ADP297 3.4 63.4 1.0
O A:HOH730 3.4 77.1 1.0
OD2 A:ASP127 3.5 38.0 1.0
CG2 J:THR0 3.5 51.2 1.0
CD2 A:TYR15 3.5 82.0 1.0
PB A:ADP297 3.7 67.6 1.0
MG A:MG298 3.9 34.3 1.0
CG A:ASP145 4.0 37.1 1.0
OD1 A:ASP145 4.1 34.4 1.0
CE2 A:TYR15 4.1 88.9 1.0
O3B A:ADP297 4.5 81.3 1.0
N A:TYR15 4.5 93.0 1.0
N A:THR14 4.5 0.3 1.0
CG A:TYR15 4.6 79.4 1.0
CB A:THR14 4.6 0.7 1.0
CG A:ASP127 4.7 36.1 1.0
CB A:TYR15 4.7 80.6 1.0
OG1 A:THR14 4.8 0.3 1.0
CA J:THR0 4.9 56.6 1.0
ND2 A:ASN132 5.0 27.9 1.0

Fluorine binding site 4 out of 6 in 3qhw

Go back to Fluorine Binding Sites List in 3qhw
Fluorine binding site 4 out of 6 in the Structure of A PCDK2/Cyclina Transition-State Mimic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of A PCDK2/Cyclina Transition-State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F300

b:47.7
occ:1.00
 F1 C:MGF300 0.0 47.7 1.0
MG C:MGF300 1.8 64.3 1.0
MG C:MG298 2.0 44.1 1.0
OD2 C:ASP145 2.9 46.5 1.0
OG1 K:THR0 2.9 48.5 1.0
O3B C:ADP297 3.0 75.8 1.0
CE C:LYS129 3.0 28.0 1.0
O C:HOH464 3.0 45.4 1.0
F3 C:MGF300 3.1 64.0 1.0
ND2 C:ASN132 3.1 23.1 1.0
F2 C:MGF300 3.1 96.7 1.0
OD1 C:ASN132 3.1 28.3 1.0
OD2 C:ASP127 3.3 40.6 1.0
NZ C:LYS129 3.3 34.9 1.0
CG C:ASN132 3.5 27.7 1.0
O C:HOH678 3.8 71.6 1.0
MG C:MG299 4.0 62.3 0.6
CG C:ASP145 4.1 38.5 1.0
OE1 C:GLN131 4.1 68.5 1.0
CB K:THR0 4.2 55.2 1.0
O2A C:ADP297 4.2 66.2 1.0
CG C:ASP127 4.2 36.3 1.0
PB C:ADP297 4.3 78.5 1.0
O C:HOH302 4.4 35.7 1.0
CD C:LYS129 4.5 31.5 1.0
CG C:GLN131 4.6 42.9 1.0
OD1 C:ASP127 4.6 36.0 1.0
O1B C:ADP297 4.6 83.4 1.0
CD C:GLN131 4.7 65.8 1.0
OD1 C:ASP145 4.9 36.7 1.0
CA C:GLY13 4.9 41.8 0.5
CB C:ASP145 4.9 23.2 1.0
CG C:LYS129 5.0 26.3 1.0
CB C:ASN132 5.0 28.6 1.0
CG2 K:THR0 5.0 51.3 1.0

Fluorine binding site 5 out of 6 in 3qhw

Go back to Fluorine Binding Sites List in 3qhw
Fluorine binding site 5 out of 6 in the Structure of A PCDK2/Cyclina Transition-State Mimic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of A PCDK2/Cyclina Transition-State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F300

b:96.7
occ:1.00
 F2 C:MGF300 0.0 96.7 1.0
MG C:MGF300 1.8 64.3 1.0
N C:THR14 2.3 55.1 0.5
O C:HOH678 2.4 71.6 1.0
CA C:GLY13 2.8 41.8 0.5
C C:GLY13 2.9 44.5 0.5
F1 C:MGF300 3.1 47.7 1.0
F3 C:MGF300 3.1 64.0 1.0
O3B C:ADP297 3.2 75.8 1.0
OG1 K:THR0 3.3 48.5 1.0
OG1 C:THR14 3.3 55.1 0.5
CA C:THR14 3.4 59.7 0.5
CB C:THR14 3.6 56.5 0.5
CB K:THR0 3.6 55.2 1.0
PB C:ADP297 4.0 78.5 1.0
O2B C:ADP297 4.1 89.7 1.0
N K:THR0 4.1 55.1 1.0
O C:GLY13 4.1 52.1 0.5
N C:GLY13 4.2 49.5 0.5
N C:TYR15 4.2 75.9 0.5
NZ C:LYS129 4.3 34.9 1.0
C C:THR14 4.4 65.9 0.5
MG C:MG298 4.4 44.1 1.0
CA K:THR0 4.5 59.2 1.0
O C:HOH464 4.5 45.4 1.0
CE2 C:TYR15 4.5 81.3 0.5
O1B C:ADP297 4.5 83.4 1.0
OE1 C:GLN131 4.7 68.5 1.0
CG2 K:THR0 4.7 51.3 1.0
O C:HOH603 4.8 63.5 1.0
OH C:TYR15 4.9 86.1 0.5
MG C:MG299 4.9 62.3 0.6
O C:GLU12 5.0 62.6 0.5
CD2 C:TYR15 5.0 85.2 0.5

Fluorine binding site 6 out of 6 in 3qhw

Go back to Fluorine Binding Sites List in 3qhw
Fluorine binding site 6 out of 6 in the Structure of A PCDK2/Cyclina Transition-State Mimic


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of A PCDK2/Cyclina Transition-State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F300

b:64.0
occ:1.00
 F3 C:MGF300 0.0 64.0 1.0
MG C:MGF300 1.8 64.3 1.0
MG C:MG299 2.0 62.3 0.6
O C:HOH731 3.0 80.5 1.0
F1 C:MGF300 3.1 47.7 1.0
OG1 K:THR0 3.1 48.5 1.0
O1B C:ADP297 3.1 83.4 1.0
O C:HOH302 3.1 35.7 1.0
F2 C:MGF300 3.1 96.7 1.0
CD2 C:TYR15 3.2 85.2 0.5
OD2 C:ASP145 3.2 46.5 1.0
O3B C:ADP297 3.3 75.8 1.0
OD2 C:ASP127 3.4 40.6 1.0
OH C:TYR15 3.4 86.1 0.5
CB K:THR0 3.5 55.2 1.0
CG2 K:THR0 3.6 51.3 1.0
PB C:ADP297 3.7 78.5 1.0
CE2 C:TYR15 3.7 81.3 0.5
CE2 C:TYR15 3.9 86.6 0.5
CZ C:TYR15 4.0 85.5 0.5
MG C:MG298 4.0 44.1 1.0
OD1 C:ASP145 4.0 36.7 1.0
CG C:ASP145 4.0 38.5 1.0
N C:TYR15 4.3 75.9 0.5
CG C:TYR15 4.3 85.8 0.5
N C:THR14 4.4 55.1 0.5
CB C:TYR15 4.4 83.2 0.5
O2B C:ADP297 4.5 89.7 1.0
CB C:THR14 4.6 56.5 0.5
CG C:ASP127 4.6 36.3 1.0
CD2 C:TYR15 4.9 81.7 0.5
CA C:THR14 5.0 59.7 0.5
CA C:TYR15 5.0 81.4 0.5
OG1 C:THR14 5.0 55.1 0.5
ND2 C:ASN132 5.0 23.1 1.0
CA K:THR0 5.0 59.2 1.0

Reference:

Z.Q.Bao, D.M.Jacobsen, M.A.Young. Briefly Bound to Activate: Transient Binding of A Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase For Catalysis. Structure V. 19 675 2011.
ISSN: ISSN 0969-2126
PubMed: 21565702
DOI: 10.1016/J.STR.2011.02.016
Page generated: Sun Dec 13 11:53:52 2020

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