Atomistry » Magnesium » PDB 3q89-3qpo » 3qhw
Atomistry »
  Magnesium »
    PDB 3q89-3qpo »
      3qhw »

Magnesium 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:

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 3qhw). 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: 3qhw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3qhw

Go back to Magnesium Binding Sites List in 3qhw
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:34.3
occ:1.00
 F1 A:MGF300 1.9 47.9 1.0
OD1 A:ASN132 2.1 28.2 1.0
O1A A:ADP297 2.1 56.1 1.0
OD2 A:ASP145 2.2 34.5 1.0
O A:HOH445 2.2 36.7 1.0
O1B A:ADP297 2.4 63.4 1.0
MG A:MGF300 3.0 80.3 1.0
CG A:ASN132 3.1 35.2 1.0
CG A:ASP145 3.2 37.1 1.0
PA A:ADP297 3.4 56.5 1.0
ND2 A:ASN132 3.5 27.9 1.0
PB A:ADP297 3.5 67.6 1.0
CB A:ASP145 3.6 27.8 1.0
O3A A:ADP297 3.8 59.0 1.0
O2B A:ADP297 3.9 66.4 1.0
F3 A:MGF300 3.9 60.6 1.0
O3' A:ADP297 4.2 51.4 1.0
F2 A:MGF300 4.2 89.7 1.0
MG A:MG299 4.2 65.4 1.0
OD1 A:ASP145 4.3 34.4 1.0
O5' A:ADP297 4.3 54.1 1.0
C5' A:ADP297 4.3 58.9 1.0
CB A:ASN132 4.4 25.3 1.0
OE1 A:GLN131 4.4 67.5 1.0
CG A:GLN131 4.5 42.1 1.0
O2A A:ADP297 4.6 56.9 1.0
CA A:ASN132 4.6 29.5 1.0
C3' A:ADP297 4.7 52.6 1.0
CE A:LYS129 4.7 30.7 1.0
O A:GLN131 4.7 28.7 1.0
OD2 A:ASP127 4.8 38.0 1.0
O3B A:ADP297 4.8 81.3 1.0
O A:HOH302 4.8 44.5 1.0
CD A:GLN131 4.9 65.8 1.0
N A:ASN132 4.9 26.8 1.0
OG1 J:THR0 4.9 49.9 1.0
C A:GLN131 5.0 35.0 1.0

Magnesium binding site 2 out of 6 in 3qhw

Go back to Magnesium Binding Sites List in 3qhw
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:65.4
occ:1.00
 F3 A:MGF300 2.0 60.6 1.0
O A:HOH730 2.1 77.1 1.0
O2B A:ADP297 2.2 66.4 1.0
OD1 A:ASP145 2.4 34.4 1.0
O A:HOH302 2.5 44.5 1.0
OD2 A:ASP145 2.6 34.5 1.0
CG A:ASP145 2.8 37.1 1.0
MG A:MGF300 3.5 80.3 1.0
PB A:ADP297 3.5 67.6 1.0
CD2 A:TYR15 3.7 82.0 1.0
O1B A:ADP297 3.9 63.4 1.0
O A:HOH657 4.0 61.2 1.0
F1 A:MGF300 4.1 47.9 1.0
MG A:MG298 4.2 34.3 1.0
CB A:TYR15 4.3 80.6 1.0
CA A:GLY147 4.3 27.2 1.0
OD2 A:ASP127 4.3 38.0 1.0
CB A:ASP145 4.3 27.8 1.0
N A:GLY147 4.3 27.4 1.0
NZ A:LYS33 4.4 61.1 1.0
CG A:TYR15 4.4 79.4 1.0
O3A A:ADP297 4.5 59.0 1.0
O3B A:ADP297 4.5 81.3 1.0
CE2 A:TYR15 4.6 88.9 1.0
C A:GLY147 4.8 34.2 1.0
OG1 J:THR0 4.8 49.9 1.0
O1A A:ADP297 4.8 56.1 1.0
N A:LEU148 4.8 26.6 1.0
O A:ASP145 4.8 24.1 1.0
C A:ASP145 4.9 25.6 1.0
N A:TYR15 5.0 93.0 1.0
F2 A:MGF300 5.0 89.7 1.0
CG2 J:THR0 5.0 51.2 1.0
PA A:ADP297 5.0 56.5 1.0
CA A:ASP145 5.0 28.4 1.0

Magnesium binding site 3 out of 6 in 3qhw

Go back to Magnesium Binding Sites List in 3qhw
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:80.3
occ:1.00
 MG A:MGF300 0.0 80.3 1.0
F1 A:MGF300 1.8 47.9 1.0
F3 A:MGF300 1.8 60.6 1.0
F2 A:MGF300 1.8 89.7 1.0
OG1 J:THR0 2.6 49.9 1.0
O1B A:ADP297 2.7 63.4 1.0
MG A:MG298 3.0 34.3 1.0
CB J:THR0 3.2 50.0 1.0
OD2 A:ASP145 3.3 34.5 1.0
MG A:MG299 3.5 65.4 1.0
OD2 A:ASP127 3.6 38.0 1.0
PB A:ADP297 3.7 67.6 1.0
O2B A:ADP297 3.7 66.4 1.0
NZ A:LYS129 4.0 39.1 1.0
O A:HOH445 4.0 36.7 1.0
O A:HOH302 4.1 44.5 1.0
CG2 J:THR0 4.1 51.2 1.0
N A:THR14 4.1 0.3 1.0
CE A:LYS129 4.3 30.7 1.0
CA A:GLY13 4.5 96.6 1.0
CA J:THR0 4.5 56.6 1.0
CG A:ASP145 4.5 37.1 1.0
N J:THR0 4.5 63.2 1.0
O3B A:ADP297 4.5 81.3 1.0
ND2 A:ASN132 4.5 27.9 1.0
OD1 A:ASN132 4.5 28.2 1.0
OG1 A:THR14 4.6 0.3 1.0
C A:GLY13 4.7 97.2 1.0
CB A:THR14 4.8 0.7 1.0
O1A A:ADP297 4.8 56.1 1.0
CG A:ASP127 4.8 36.1 1.0
OE1 A:GLN131 4.8 67.5 1.0
CG A:ASN132 5.0 35.2 1.0
O3A A:ADP297 5.0 59.0 1.0

Magnesium binding site 4 out of 6 in 3qhw

Go back to Magnesium Binding Sites List in 3qhw
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:44.1
occ:1.00
 OD1 C:ASN132 1.9 28.3 1.0
F1 C:MGF300 2.0 47.7 1.0
O C:HOH464 2.1 45.4 1.0
OD2 C:ASP145 2.2 46.5 1.0
O2A C:ADP297 2.3 66.2 1.0
O3B C:ADP297 2.3 75.8 1.0
CG C:ASN132 2.8 27.7 1.0
CG C:ASP145 3.1 38.5 1.0
MG C:MGF300 3.1 64.3 1.0
ND2 C:ASN132 3.2 23.1 1.0
PA C:ADP297 3.5 66.2 1.0
CB C:ASP145 3.6 23.2 1.0
PB C:ADP297 3.6 78.5 1.0
O3A C:ADP297 4.0 69.9 1.0
F3 C:MGF300 4.0 64.0 1.0
MG C:MG299 4.0 62.3 0.6
OD1 C:ASP145 4.0 36.7 1.0
O1B C:ADP297 4.2 83.4 1.0
CB C:ASN132 4.2 28.6 1.0
O3' C:ADP297 4.3 61.6 1.0
F2 C:MGF300 4.4 96.7 1.0
CE C:LYS129 4.4 28.0 1.0
CG C:GLN131 4.5 42.9 1.0
OE1 C:GLN131 4.5 68.5 1.0
O5' C:ADP297 4.5 63.5 1.0
CA C:ASN132 4.5 26.8 1.0
O1A C:ADP297 4.6 65.5 1.0
OD2 C:ASP127 4.6 40.6 1.0
C5' C:ADP297 4.6 63.9 1.0
O C:GLN131 4.6 26.0 1.0
OG1 K:THR0 4.8 48.5 1.0
N C:ASN132 4.8 23.7 1.0
C3' C:ADP297 4.8 60.1 1.0
O C:HOH302 4.9 35.7 1.0
O2B C:ADP297 4.9 89.7 1.0
C C:GLN131 4.9 34.1 1.0
CD C:GLN131 5.0 65.8 1.0

Magnesium binding site 5 out of 6 in 3qhw

Go back to Magnesium Binding Sites List in 3qhw
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:62.3
occ:0.61
 F3 C:MGF300 2.0 64.0 1.0
O C:HOH731 2.1 80.5 1.0
OD1 C:ASP145 2.2 36.7 1.0
O C:HOH302 2.2 35.7 1.0
OD2 C:ASP145 2.4 46.5 1.0
CG C:ASP145 2.6 38.5 1.0
O1B C:ADP297 2.6 83.4 1.0
MG C:MGF300 3.4 64.3 1.0
PB C:ADP297 3.7 78.5 1.0
O3B C:ADP297 3.7 75.8 1.0
OD2 C:ASP127 3.9 40.6 1.0
F1 C:MGF300 4.0 47.7 1.0
MG C:MG298 4.0 44.1 1.0
CD2 C:TYR15 4.0 85.2 0.5
CB C:ASP145 4.0 23.2 1.0
CA C:GLY147 4.2 26.8 1.0
N C:GLY147 4.2 28.2 1.0
O C:ASP145 4.3 26.4 1.0
OH C:TYR15 4.4 86.1 0.5
CE2 C:TYR15 4.4 81.3 0.5
NZ C:LYS33 4.5 60.7 1.0
CB C:TYR15 4.5 83.2 0.5
O3A C:ADP297 4.5 69.9 1.0
C C:ASP145 4.5 28.1 1.0
N C:LEU148 4.6 25.0 1.0
CZ C:TYR15 4.6 85.5 0.5
CA C:ASP145 4.7 29.8 1.0
C C:GLY147 4.7 34.6 1.0
CG C:TYR15 4.7 85.8 0.5
OG1 K:THR0 4.7 48.5 1.0
O2A C:ADP297 4.7 66.2 1.0
ND2 C:ASN132 4.8 23.1 1.0
CE2 C:TYR15 4.9 86.6 0.5
O2B C:ADP297 4.9 89.7 1.0
F2 C:MGF300 4.9 96.7 1.0
PA C:ADP297 5.0 66.2 1.0

Magnesium binding site 6 out of 6 in 3qhw

Go back to Magnesium Binding Sites List in 3qhw
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:64.3
occ:1.00
 MG C:MGF300 0.0 64.3 1.0
F3 C:MGF300 1.8 64.0 1.0
F1 C:MGF300 1.8 47.7 1.0
F2 C:MGF300 1.8 96.7 1.0
OG1 K:THR0 2.5 48.5 1.0
O3B C:ADP297 2.6 75.8 1.0
MG C:MG298 3.1 44.1 1.0
CB K:THR0 3.3 55.2 1.0
MG C:MG299 3.4 62.3 0.6
OD2 C:ASP145 3.5 46.5 1.0
O C:HOH678 3.5 71.6 1.0
PB C:ADP297 3.6 78.5 1.0
OD2 C:ASP127 3.7 40.6 1.0
O1B C:ADP297 3.7 83.4 1.0
N C:THR14 3.7 55.1 0.5
CA C:GLY13 4.0 41.8 0.5
O C:HOH464 4.1 45.4 1.0
CG2 K:THR0 4.1 51.3 1.0
NZ C:LYS129 4.1 34.9 1.0
O2B C:ADP297 4.3 89.7 1.0
C C:GLY13 4.3 44.5 0.5
O C:HOH302 4.3 35.7 1.0
CE C:LYS129 4.4 28.0 1.0
CG C:ASP145 4.5 38.5 1.0
OG1 C:THR14 4.5 55.1 0.5
CA K:THR0 4.6 59.2 1.0
CB C:THR14 4.6 56.5 0.5
N K:THR0 4.6 55.1 1.0
CE2 C:TYR15 4.6 81.3 0.5
ND2 C:ASN132 4.6 23.1 1.0
CD2 C:TYR15 4.6 85.2 0.5
OH C:TYR15 4.7 86.1 0.5
O C:HOH731 4.7 80.5 1.0
CA C:THR14 4.7 59.7 0.5
OD1 C:ASN132 4.7 28.3 1.0
N C:TYR15 4.7 75.9 0.5
CG C:ASP127 4.8 36.3 1.0
O2A C:ADP297 4.8 66.2 1.0
O3A C:ADP297 4.9 69.9 1.0
OD1 C:ASP145 4.9 36.7 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 10:03:14 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy