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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

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