Atomistry » Fluorine » PDB 3ptm-3qri » 3qhr
Atomistry »
  Fluorine »
    PDB 3ptm-3qri »
      3qhr »

Fluorine in PDB 3qhr: 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: 3qhr 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) 37.80 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.690, 163.910, 73.280, 90.00, 107.38, 90.00
R / Rfree (%) 17.9 / 21

Other elements in 3qhr:

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 3qhr). 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: 3qhr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3qhr

Go back to Fluorine Binding Sites List in 3qhr
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:56.5
occ:1.00
 F1 A:MGF300 0.0 56.5 1.0
MG A:MGF300 1.8 97.3 1.0
MG A:MG299 2.2 36.9 1.0
OG1 K:THR0 2.6 71.4 1.0
OD2 A:ASP127 3.0 37.8 1.0
ND2 A:ASN132 3.0 27.3 1.0
OD2 A:ASP145 3.0 58.2 1.0
F3 A:MGF300 3.1 67.2 1.0
CE A:LYS129 3.1 33.8 1.0
F2 A:MGF300 3.1 80.9 1.0
OD1 A:ASN132 3.2 30.2 1.0
NZ A:LYS129 3.2 32.3 1.0
O3B A:ADP297 3.3 62.9 1.0
O A:HOH341 3.5 46.1 1.0
CG A:ASN132 3.5 35.2 1.0
CB K:THR0 3.9 70.3 1.0
MG A:MG298 4.0 59.0 1.0
O A:HOH306 4.1 40.2 1.0
CG A:ASP127 4.1 42.5 1.0
CG A:ASP145 4.2 47.5 1.0
OE1 A:GLN131 4.4 94.1 1.0
O A:HOH654 4.4 76.7 1.0
O1A A:ADP297 4.4 57.9 1.0
CD A:LYS129 4.6 32.0 1.0
PB A:ADP297 4.6 72.3 1.0
O A:HOH473 4.6 0.6 1.0
OD1 A:ASP127 4.6 44.8 1.0
CG2 K:THR0 4.7 67.5 1.0
CG A:GLN131 4.7 52.1 1.0
O2B A:ADP297 4.8 73.7 1.0
CD A:GLN131 4.9 86.1 1.0
N K:THR0 4.9 75.3 1.0
CB A:ASP145 4.9 39.0 1.0
CA K:THR0 4.9 71.9 1.0
CB A:ASN132 5.0 28.6 1.0

Fluorine binding site 2 out of 6 in 3qhr

Go back to Fluorine Binding Sites List in 3qhr
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:80.9
occ:1.00
 F2 A:MGF300 0.0 80.9 1.0
MG A:MGF300 1.8 97.3 1.0
N A:THR14 2.7 0.6 1.0
O A:HOH654 2.8 76.7 1.0
O3B A:ADP297 3.1 62.9 1.0
F3 A:MGF300 3.1 67.2 1.0
F1 A:MGF300 3.1 56.5 1.0
CA A:GLY13 3.4 0.6 1.0
CB A:THR14 3.5 0.8 1.0
OG1 K:THR0 3.5 71.4 1.0
C A:GLY13 3.5 0.1 1.0
OG1 A:THR14 3.6 0.5 1.0
CA A:THR14 3.6 0.1 1.0
O A:HOH473 3.7 0.6 1.0
CB K:THR0 3.7 70.3 1.0
PB A:ADP297 4.0 72.3 1.0
MG A:MG299 4.1 36.9 1.0
N K:THR0 4.1 75.3 1.0
O1B A:ADP297 4.2 0.9 1.0
NZ A:LYS129 4.3 32.3 1.0
CA K:THR0 4.5 71.9 1.0
OE1 A:GLN131 4.6 94.1 1.0
N A:TYR15 4.6 0.8 1.0
O2B A:ADP297 4.6 73.7 1.0
O A:HOH341 4.6 46.1 1.0
C A:THR14 4.7 0.5 1.0
O A:GLY13 4.7 0.0 1.0
MG A:MG298 4.7 59.0 1.0
N A:GLY13 4.8 0.5 1.0
CG2 A:THR14 4.9 0.7 1.0
CE K:LYS-1 4.9 1.0 1.0
CG2 K:THR0 4.9 67.5 1.0

Fluorine binding site 3 out of 6 in 3qhr

Go back to Fluorine Binding Sites List in 3qhr
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:67.2
occ:1.00
 F3 A:MGF300 0.0 67.2 1.0
MG A:MGF300 1.8 97.3 1.0
MG A:MG298 2.1 59.0 1.0
O A:HOH306 2.8 40.2 1.0
OG1 K:THR0 3.0 71.4 1.0
O A:HOH333 3.1 59.8 1.0
F1 A:MGF300 3.1 56.5 1.0
F2 A:MGF300 3.1 80.9 1.0
CD2 A:TYR15 3.2 91.7 1.0
OD2 A:ASP145 3.2 58.2 1.0
CB K:THR0 3.3 70.3 1.0
O2B A:ADP297 3.4 73.7 1.0
CG2 K:THR0 3.4 67.5 1.0
O3B A:ADP297 3.5 62.9 1.0
OD2 A:ASP127 3.6 37.8 1.0
CE2 A:TYR15 3.8 0.7 1.0
PB A:ADP297 3.9 72.3 1.0
CB A:THR14 4.1 0.8 1.0
MG A:MG299 4.1 36.9 1.0
CG A:ASP145 4.1 47.5 1.0
OD1 A:ASP145 4.3 51.3 1.0
CG A:TYR15 4.3 96.3 1.0
N A:THR14 4.4 0.6 1.0
N A:TYR15 4.5 0.8 1.0
CB A:TYR15 4.6 96.2 1.0
O1B A:ADP297 4.6 0.9 1.0
CA A:THR14 4.7 0.1 1.0
CG2 A:THR14 4.8 0.7 1.0
CA K:THR0 4.8 71.9 1.0
CG A:ASP127 4.8 42.5 1.0
OG1 A:THR14 4.9 0.5 1.0
CD1 A:LEU148 4.9 54.1 1.0

Fluorine binding site 4 out of 6 in 3qhr

Go back to Fluorine Binding Sites List in 3qhr
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:61.5
occ:1.00
 F1 C:MGF300 0.0 61.5 1.0
MG C:MGF300 1.8 65.0 1.0
MG C:MG299 2.0 41.7 1.0
OD2 C:ASP145 2.8 54.7 1.0
ND2 C:ASN132 2.9 23.4 1.0
OD1 C:ASN132 3.0 29.8 1.0
OG1 J:THR0 3.0 84.5 1.0
F3 C:MGF300 3.1 70.8 1.0
F2 C:MGF300 3.1 0.9 1.0
OD2 C:ASP127 3.2 40.8 1.0
O C:HOH352 3.2 38.5 1.0
O3B C:ADP297 3.2 75.8 1.0
CE C:LYS129 3.2 31.9 1.0
CG C:ASN132 3.3 34.0 1.0
NZ C:LYS129 3.4 34.9 1.0
MG C:MG298 3.8 71.6 1.0
CG C:ASP145 3.9 45.9 1.0
O1A C:ADP297 4.1 66.6 1.0
CG C:ASP127 4.2 42.7 1.0
CB J:THR0 4.3 82.2 1.0
O C:HOH304 4.3 45.6 1.0
OE1 C:GLN131 4.4 93.8 1.0
PB C:ADP297 4.5 78.0 1.0
CB C:ASP145 4.6 39.9 1.0
CD C:LYS129 4.6 30.2 1.0
CG C:GLN131 4.6 51.9 1.0
O2B C:ADP297 4.7 81.3 1.0
OD1 C:ASP127 4.7 39.8 1.0
O J:HOH655 4.8 96.1 1.0
CB C:ASN132 4.8 26.0 1.0
CD C:GLN131 4.9 85.2 1.0
OD1 C:ASP145 4.9 54.6 1.0

Fluorine binding site 5 out of 6 in 3qhr

Go back to Fluorine Binding Sites List in 3qhr
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:0.9
occ:1.00
 F2 C:MGF300 0.0 0.9 1.0
MG C:MGF300 1.8 65.0 1.0
O J:HOH655 2.3 96.1 1.0
N C:THR14 2.8 0.5 1.0
O3B C:ADP297 2.9 75.8 1.0
F3 C:MGF300 3.1 70.8 1.0
F1 C:MGF300 3.1 61.5 1.0
CA C:GLY13 3.3 0.2 1.0
C C:GLY13 3.5 0.0 1.0
OG1 J:THR0 3.5 84.5 1.0
CB C:THR14 3.7 0.8 1.0
MG C:MG299 3.8 41.7 1.0
CA C:THR14 3.8 0.4 1.0
OG1 C:THR14 3.9 0.9 1.0
PB C:ADP297 3.9 78.0 1.0
CB J:THR0 4.0 82.2 1.0
O C:HOH352 4.0 38.5 1.0
O1B C:ADP297 4.1 0.8 1.0
NZ C:LYS129 4.3 34.9 1.0
N J:THR0 4.3 96.2 1.0
OE1 C:GLN131 4.3 93.8 1.0
NZ J:LYS-1 4.5 0.7 1.0
CD J:LYS-1 4.5 0.9 1.0
MG C:MG298 4.6 71.6 1.0
O2B C:ADP297 4.6 81.3 1.0
O C:HOH560 4.6 0.7 1.0
N C:GLY13 4.7 0.8 1.0
N C:TYR15 4.7 0.6 1.0
O C:GLY13 4.7 0.4 1.0
OD2 C:ASP145 4.8 54.7 1.0
CA J:THR0 4.8 97.9 1.0
CG J:LYS-1 4.8 0.0 1.0
C C:THR14 4.8 0.5 1.0
CB J:LYS-1 4.9 0.9 1.0
O C:GLU12 5.0 0.4 1.0
CE J:LYS-1 5.0 0.8 1.0

Fluorine binding site 6 out of 6 in 3qhr

Go back to Fluorine Binding Sites List in 3qhr
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:70.8
occ:1.00
 F3 C:MGF300 0.0 70.8 1.0
MG C:MGF300 1.8 65.0 1.0
MG C:MG298 2.1 71.6 1.0
OG1 J:THR0 3.0 84.5 1.0
F2 C:MGF300 3.1 0.9 1.0
F1 C:MGF300 3.1 61.5 1.0
OD2 C:ASP145 3.2 54.7 1.0
CD2 C:TYR15 3.2 93.0 1.0
O2B C:ADP297 3.3 81.3 1.0
O C:HOH304 3.3 45.6 1.0
CB J:THR0 3.3 82.2 1.0
O3B C:ADP297 3.4 75.8 1.0
O C:HOH551 3.5 88.3 1.0
CG2 J:THR0 3.6 78.4 1.0
OD2 C:ASP127 3.7 40.8 1.0
PB C:ADP297 3.8 78.0 1.0
CE2 C:TYR15 3.8 0.3 1.0
MG C:MG299 3.9 41.7 1.0
CB C:THR14 4.0 0.8 1.0
CG C:ASP145 4.1 45.9 1.0
OD1 C:ASP145 4.3 54.6 1.0
N C:THR14 4.3 0.5 1.0
CG C:TYR15 4.3 97.1 1.0
N C:TYR15 4.4 0.6 1.0
O1B C:ADP297 4.5 0.8 1.0
CB C:TYR15 4.6 97.1 1.0
CA C:THR14 4.7 0.4 1.0
CG2 C:THR14 4.7 0.8 1.0
OG1 C:THR14 4.8 0.9 1.0
CA J:THR0 4.8 97.9 1.0
CG C:ASP127 4.9 42.7 1.0
C C:THR14 5.0 0.5 1.0
O J:HOH655 5.0 96.1 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: Wed Jul 31 22:02:23 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy