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Sodium in PDB 3tnw: Structure of CDK2/Cyclin A in Complex with CAN508

Enzymatic activity of Structure of CDK2/Cyclin A in Complex with CAN508

All present enzymatic activity of Structure of CDK2/Cyclin A in Complex with CAN508:
2.7.11.22;

Protein crystallography data

The structure of Structure of CDK2/Cyclin A in Complex with CAN508, PDB code: 3tnw was solved by S.Baumli, A.J.Hole, J.A.Endicott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.94 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.050, 134.570, 148.280, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of CDK2/Cyclin A in Complex with CAN508 (pdb code 3tnw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of CDK2/Cyclin A in Complex with CAN508, PDB code: 3tnw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3tnw

Go back to Sodium Binding Sites List in 3tnw
Sodium binding site 1 out of 2 in the Structure of CDK2/Cyclin A in Complex with CAN508


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of CDK2/Cyclin A in Complex with CAN508 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4

b:35.6
occ:1.00
O D:GLN203 2.6 34.2 1.0
O D:HOH440 2.7 38.0 1.0
O D:ILE206 2.8 27.7 1.0
O D:MET200 2.8 30.6 1.0
O D:HOH878 2.9 44.4 1.0
O D:HOH472 2.9 39.0 1.0
C D:GLN203 3.8 28.6 1.0
C D:ILE206 3.9 33.8 1.0
C D:MET200 3.9 33.8 1.0
CB D:GLN203 4.3 23.9 1.0
CA D:GLN203 4.4 26.4 1.0
N D:GLN203 4.5 26.6 1.0
CA D:LYS201 4.5 33.4 1.0
CG2 D:THR207 4.5 29.3 1.0
CG D:MET200 4.5 32.8 1.0
N D:ILE206 4.5 26.2 1.0
CA D:THR207 4.5 31.0 1.0
O D:LYS201 4.6 33.5 1.0
C D:LYS201 4.6 32.7 1.0
O D:HOH441 4.6 31.7 1.0
N D:LYS201 4.6 29.8 1.0
N D:THR207 4.7 27.2 1.0
C D:PRO204 4.7 43.1 1.0
N D:PRO204 4.8 30.2 1.0
CA D:ILE206 4.8 31.7 1.0
O D:PRO204 4.8 43.2 1.0
CA D:PRO204 4.9 37.9 1.0
N D:ASP205 4.9 25.9 1.0
CA D:MET200 4.9 31.2 1.0

Sodium binding site 2 out of 2 in 3tnw

Go back to Sodium Binding Sites List in 3tnw
Sodium binding site 2 out of 2 in the Structure of CDK2/Cyclin A in Complex with CAN508


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of CDK2/Cyclin A in Complex with CAN508 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1

b:40.1
occ:1.00
O D:HOH452 3.3 48.2 1.0
O D:HOH540 3.4 39.2 1.0
CG D:GLN254 3.8 27.5 1.0
CD D:GLN254 3.9 30.1 1.0
CD1 D:LEU214 3.9 22.0 1.0
CE3 D:TRP217 3.9 37.4 1.0
NE2 D:GLN254 4.0 31.4 1.0
CD2 D:TRP217 4.0 30.3 1.0
CB D:GLN254 4.0 24.5 1.0
CB D:TRP217 4.1 25.9 1.0
CG D:TRP217 4.1 31.0 1.0
CA D:LEU214 4.2 30.1 1.0
OE1 D:GLN254 4.4 31.8 1.0
O D:ILE213 4.5 29.8 1.0
CZ3 D:TRP217 4.7 34.1 1.0
CA D:GLN254 4.7 23.6 1.0
N D:LEU214 4.7 27.1 1.0
CG2 D:ILE213 4.7 30.9 1.0
CB D:LEU214 4.7 22.9 1.0
C D:ILE213 4.8 31.3 1.0
CE2 D:TRP217 4.9 33.5 1.0
O D:LEU214 4.9 26.6 1.0
CG D:LEU214 4.9 28.2 1.0
CD1 D:TRP217 5.0 43.4 1.0

Reference:

S.Baumli, A.J.Hole, M.E.Noble, J.A.Endicott. The CDK9 C-Helix Exhibits Conformational Plasticity That May Explain the Selectivity of CAN508. Acs Chem.Biol. V. 7 811 2012.
ISSN: ISSN 1554-8929
PubMed: 22292676
DOI: 10.1021/CB2004516
Page generated: Tue Dec 15 06:26:27 2020

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