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Magnesium 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:

Fluorine (F) 6 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of A PCDK2/Cyclina Transition-State Mimic, PDB code: 3qhr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3qhr

Go back to Magnesium Binding Sites List in 3qhr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg298

b:59.0
occ:1.00
 O A:HOH333 2.1 59.8 1.0
F3 A:MGF300 2.1 67.2 1.0
OD2 A:ASP145 2.1 58.2 1.0
O2B A:ADP297 2.3 73.7 1.0
OD1 A:ASP145 2.3 51.3 1.0
O A:HOH306 2.4 40.2 1.0
CG A:ASP145 2.5 47.5 1.0
MG A:MGF300 3.3 97.3 1.0
PB A:ADP297 3.4 72.3 1.0
O3B A:ADP297 3.6 62.9 1.0
CD2 A:TYR15 3.7 91.7 1.0
CB A:ASP145 4.0 39.0 1.0
MG A:MG299 4.0 36.9 1.0
F1 A:MGF300 4.0 56.5 1.0
O A:HOH553 4.1 62.2 1.0
NZ A:LYS33 4.2 58.7 1.0
CB A:TYR15 4.3 96.2 1.0
CA A:GLY147 4.4 38.4 1.0
O3A A:ADP297 4.4 62.6 1.0
CG A:TYR15 4.4 96.3 1.0
OD2 A:ASP127 4.5 37.8 1.0
N A:GLY147 4.5 26.5 1.0
O1B A:ADP297 4.5 0.9 1.0
O1A A:ADP297 4.5 57.9 1.0
CE2 A:TYR15 4.6 0.7 1.0
F2 A:MGF300 4.7 80.9 1.0
OG1 K:THR0 4.8 71.4 1.0
O A:ASP145 4.8 31.4 1.0
PA A:ADP297 4.8 59.6 1.0
CA A:ASP145 4.8 43.9 1.0
C A:ASP145 4.9 36.5 1.0
C A:GLY147 5.0 35.8 1.0

Magnesium binding site 2 out of 6 in 3qhr

Go back to Magnesium Binding Sites List in 3qhr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg299

b:36.9
occ:1.00
 O A:HOH341 2.0 46.1 1.0
OD1 A:ASN132 2.1 30.2 1.0
F1 A:MGF300 2.2 56.5 1.0
O3B A:ADP297 2.2 62.9 1.0
O1A A:ADP297 2.3 57.9 1.0
OD2 A:ASP145 2.5 58.2 1.0
MG A:MGF300 3.1 97.3 1.0
CG A:ASN132 3.1 35.2 1.0
CG A:ASP145 3.4 47.5 1.0
PB A:ADP297 3.5 72.3 1.0
ND2 A:ASN132 3.5 27.3 1.0
PA A:ADP297 3.5 59.6 1.0
CB A:ASP145 3.7 39.0 1.0
O3A A:ADP297 3.8 62.6 1.0
O2B A:ADP297 4.0 73.7 1.0
MG A:MG298 4.0 59.0 1.0
O A:HOH473 4.0 0.6 1.0
F2 A:MGF300 4.1 80.9 1.0
F3 A:MGF300 4.1 67.2 1.0
O5' A:ADP297 4.4 59.8 1.0
OD1 A:ASP145 4.4 51.3 1.0
CB A:ASN132 4.4 28.6 1.0
C5' A:ADP297 4.4 65.0 1.0
OE1 A:GLN131 4.5 94.1 1.0
CG A:GLN131 4.5 52.1 1.0
O3' A:ADP297 4.6 60.6 1.0
CE A:LYS129 4.6 33.8 1.0
O A:GLN131 4.7 33.7 1.0
O2A A:ADP297 4.7 74.2 1.0
O1B A:ADP297 4.7 0.9 1.0
CA A:ASN132 4.7 29.9 1.0
OD2 A:ASP127 4.8 37.8 1.0
C3' A:ADP297 4.8 56.1 1.0
OG1 K:THR0 4.8 71.4 1.0
O A:HOH306 4.9 40.2 1.0
CD A:GLN131 5.0 86.1 1.0

Magnesium binding site 3 out of 6 in 3qhr

Go back to Magnesium Binding Sites List in 3qhr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg300

b:97.3
occ:1.00
 MG A:MGF300 0.0 97.3 1.0
F3 A:MGF300 1.8 67.2 1.0
F2 A:MGF300 1.8 80.9 1.0
F1 A:MGF300 1.8 56.5 1.0
OG1 K:THR0 2.5 71.4 1.0
O3B A:ADP297 2.8 62.9 1.0
MG A:MG299 3.1 36.9 1.0
CB K:THR0 3.2 70.3 1.0
MG A:MG298 3.3 59.0 1.0
OD2 A:ASP145 3.4 58.2 1.0
OD2 A:ASP127 3.7 37.8 1.0
PB A:ADP297 3.8 72.3 1.0
O2B A:ADP297 3.9 73.7 1.0
O A:HOH306 4.0 40.2 1.0
CG2 K:THR0 4.0 67.5 1.0
N A:THR14 4.0 0.6 1.0
NZ A:LYS129 4.0 32.3 1.0
O A:HOH654 4.1 76.7 1.0
CB A:THR14 4.3 0.8 1.0
O A:HOH341 4.3 46.1 1.0
CA K:THR0 4.4 71.9 1.0
N K:THR0 4.4 75.3 1.0
CE A:LYS129 4.5 33.8 1.0
O1B A:ADP297 4.5 0.9 1.0
O A:HOH473 4.6 0.6 1.0
CG A:ASP145 4.6 47.5 1.0
ND2 A:ASN132 4.7 27.3 1.0
OG1 A:THR14 4.7 0.5 1.0
OD1 A:ASN132 4.7 30.2 1.0
CA A:GLY13 4.7 0.6 1.0
CA A:THR14 4.8 0.1 1.0
O A:HOH333 4.8 59.8 1.0
CD2 A:TYR15 4.8 91.7 1.0
C A:GLY13 4.9 0.1 1.0
CG A:ASP127 4.9 42.5 1.0
O1A A:ADP297 5.0 57.9 1.0

Magnesium binding site 4 out of 6 in 3qhr

Go back to Magnesium Binding Sites List in 3qhr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg298

b:71.6
occ:1.00
 F3 C:MGF300 2.1 70.8 1.0
OD2 C:ASP145 2.1 54.7 1.0
O2B C:ADP297 2.1 81.3 1.0
O C:HOH551 2.2 88.3 1.0
OD1 C:ASP145 2.4 54.6 1.0
CG C:ASP145 2.6 45.9 1.0
O C:HOH304 2.7 45.6 1.0
MG C:MGF300 3.2 65.0 1.0
PB C:ADP297 3.2 78.0 1.0
O3B C:ADP297 3.4 75.8 1.0
CD2 C:TYR15 3.7 93.0 1.0
MG C:MG299 3.8 41.7 1.0
F1 C:MGF300 3.8 61.5 1.0
O C:HOH438 3.9 67.4 1.0
CB C:ASP145 4.1 39.9 1.0
O3A C:ADP297 4.2 72.5 1.0
CB C:TYR15 4.3 97.1 1.0
NZ C:LYS33 4.3 63.0 1.0
O1B C:ADP297 4.3 0.8 1.0
O1A C:ADP297 4.4 66.6 1.0
CG C:TYR15 4.4 97.1 1.0
OD2 C:ASP127 4.4 40.8 1.0
CE2 C:TYR15 4.6 0.3 1.0
F2 C:MGF300 4.6 0.9 1.0
CA C:GLY147 4.6 36.2 1.0
PA C:ADP297 4.7 67.5 1.0
N C:GLY147 4.7 28.7 1.0
OG1 J:THR0 4.7 84.5 1.0
O C:ASP145 4.8 32.0 1.0
CA C:ASP145 4.9 44.4 1.0
N C:TYR15 4.9 0.6 1.0
C C:ASP145 5.0 38.1 1.0

Magnesium binding site 5 out of 6 in 3qhr

Go back to Magnesium Binding Sites List in 3qhr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg299

b:41.7
occ:1.00
 F1 C:MGF300 2.0 61.5 1.0
O C:HOH352 2.0 38.5 1.0
O3B C:ADP297 2.2 75.8 1.0
O1A C:ADP297 2.2 66.6 1.0
OD1 C:ASN132 2.2 29.8 1.0
OD2 C:ASP145 2.3 54.7 1.0
MG C:MGF300 2.8 65.0 1.0
CG C:ASN132 3.2 34.0 1.0
CG C:ASP145 3.3 45.9 1.0
PB C:ADP297 3.4 78.0 1.0
PA C:ADP297 3.4 67.5 1.0
ND2 C:ASN132 3.5 23.4 1.0
CB C:ASP145 3.7 39.9 1.0
O3A C:ADP297 3.7 72.5 1.0
F2 C:MGF300 3.8 0.9 1.0
MG C:MG298 3.8 71.6 1.0
O2B C:ADP297 3.9 81.3 1.0
F3 C:MGF300 3.9 70.8 1.0
O5' C:ADP297 4.3 63.0 1.0
OD1 C:ASP145 4.3 54.6 1.0
C5' C:ADP297 4.4 63.5 1.0
O C:HOH560 4.5 0.7 1.0
OE1 C:GLN131 4.5 93.8 1.0
CB C:ASN132 4.5 26.0 1.0
CG C:GLN131 4.6 51.9 1.0
O3' C:ADP297 4.6 62.0 1.0
O2A C:ADP297 4.6 69.2 1.0
CE C:LYS129 4.6 31.9 1.0
O1B C:ADP297 4.7 0.8 1.0
C3' C:ADP297 4.8 56.0 1.0
O C:GLN131 4.8 29.6 1.0
OD2 C:ASP127 4.8 40.8 1.0
OG1 J:THR0 4.8 84.5 1.0
CA C:ASN132 4.9 28.4 1.0

Magnesium binding site 6 out of 6 in 3qhr

Go back to Magnesium Binding Sites List in 3qhr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg300

b:65.0
occ:1.00
 MG C:MGF300 0.0 65.0 1.0
F3 C:MGF300 1.8 70.8 1.0
F2 C:MGF300 1.8 0.9 1.0
F1 C:MGF300 1.8 61.5 1.0
OG1 J:THR0 2.6 84.5 1.0
O3B C:ADP297 2.6 75.8 1.0
MG C:MG299 2.8 41.7 1.0
MG C:MG298 3.2 71.6 1.0
OD2 C:ASP145 3.2 54.7 1.0
CB J:THR0 3.5 82.2 1.0
PB C:ADP297 3.6 78.0 1.0
OD2 C:ASP127 3.8 40.8 1.0
O J:HOH655 3.8 96.1 1.0
O2B C:ADP297 3.8 81.3 1.0
O C:HOH352 3.9 38.5 1.0
N C:THR14 4.1 0.5 1.0
NZ C:LYS129 4.1 34.9 1.0
CG2 J:THR0 4.3 78.4 1.0
O C:HOH304 4.4 45.6 1.0
CG C:ASP145 4.4 45.9 1.0
CB C:THR14 4.4 0.8 1.0
O1B C:ADP297 4.4 0.8 1.0
CE C:LYS129 4.5 31.9 1.0
ND2 C:ASN132 4.5 23.4 1.0
OD1 C:ASN132 4.6 29.8 1.0
N J:THR0 4.6 96.2 1.0
CA C:GLY13 4.6 0.2 1.0
CA J:THR0 4.7 97.9 1.0
O1A C:ADP297 4.7 66.6 1.0
OG1 C:THR14 4.8 0.9 1.0
CA C:THR14 4.8 0.4 1.0
C C:GLY13 4.9 0.0 1.0
CD2 C:TYR15 4.9 93.0 1.0
O3A C:ADP297 4.9 72.5 1.0
CG C:ASP127 4.9 42.7 1.0
OE1 C:GLN131 5.0 93.8 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: Thu Aug 15 10:03:06 2024

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