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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

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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

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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

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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

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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

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