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Sodium in PDB 4ek4: Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor

Enzymatic activity of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor

All present enzymatic activity of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor:
2.7.11.22;

Protein crystallography data

The structure of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor, PDB code: 4ek4 was solved by Y.N.Kang, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.05 / 1.26
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.420, 71.626, 72.607, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.4

Other elements in 4ek4:

The structure of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor also contains other interesting chemical elements:

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor (pdb code 4ek4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor, PDB code: 4ek4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4ek4

Go back to Sodium Binding Sites List in 4ek4
Sodium binding site 1 out of 5 in the Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:43.2
occ:1.00
 O A:HOH485 2.5 21.7 1.0
OE2 A:GLU195 2.6 15.4 1.0
O A:HOH418 3.1 26.4 0.8
CD A:LYS88 3.2 25.1 1.0
CE A:LYS88 3.4 23.3 0.3
OH A:TYR168 3.6 9.8 1.0
CD A:GLU195 3.7 11.3 1.0
O A:HOH569 4.0 24.9 1.0
OE1 A:GLU195 4.1 11.0 1.0
CZ3 A:TRP167 4.3 13.2 1.0
CE A:MET91 4.3 12.4 0.5
CG A:PRO130 4.3 13.4 1.0
CG A:LYS88 4.5 22.1 1.0
CB A:PRO130 4.6 13.1 1.0
CE3 A:TRP167 4.8 11.3 1.0
NZ A:LYS88 4.9 23.6 0.3
CZ A:TYR168 4.9 8.8 1.0
CD A:PRO130 4.9 12.3 1.0
CG A:GLU195 4.9 11.1 1.0
SD A:MET91 5.0 23.3 0.5

Sodium binding site 2 out of 5 in 4ek4

Go back to Sodium Binding Sites List in 4ek4
Sodium binding site 2 out of 5 in the Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:58.4
occ:1.00
 OE2 A:GLU208 2.7 27.4 1.0
O A:HOH555 3.3 28.6 1.0
CD A:GLU208 3.6 18.9 1.0
O A:HOH439 3.7 31.1 1.0
OE1 A:GLU208 3.7 20.9 1.0
O A:HOH599 3.9 38.3 1.0
O A:HOH482 3.9 17.9 1.0
NH1 A:ARG169 4.7 16.5 1.0
O A:HOH548 4.7 32.2 1.0
CG A:GLU208 4.9 17.1 1.0
O A:HOH618 5.0 52.2 1.0

Sodium binding site 3 out of 5 in 4ek4

Go back to Sodium Binding Sites List in 4ek4
Sodium binding site 3 out of 5 in the Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:45.2
occ:0.50
 OD2 A:ASP256 2.2 14.8 0.5
OD2 A:ASP256 2.4 17.7 0.5
O A:HOH503 2.9 29.8 1.0
NZ A:LYS105 2.9 17.4 1.0
CG A:ASP256 3.3 14.8 0.5
CG A:ASP256 3.3 14.3 0.5
OD1 A:ASP256 3.5 13.4 0.5
CE1 A:PHE285 3.6 12.3 1.0
CE A:LYS105 3.7 12.5 1.0
OD1 A:ASP256 3.8 12.6 0.5
CD1 A:PHE285 3.9 12.5 1.0
O A:HOH528 3.9 26.6 1.0
CD2 A:LEU101 4.1 22.7 0.5
CB A:ASP256 4.4 15.2 0.5
O A:HOH508 4.5 26.4 1.0
CB A:ASP256 4.6 15.1 0.5
O A:HOH543 4.6 36.1 1.0
OD2 A:ASP288 4.7 23.1 1.0
CZ A:PHE285 4.7 12.5 1.0
OD1 A:ASP288 4.8 25.8 1.0
O A:PHE285 4.8 13.4 1.0

Sodium binding site 4 out of 5 in 4ek4

Go back to Sodium Binding Sites List in 4ek4
Sodium binding site 4 out of 5 in the Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:45.0
occ:1.00
 OD2 A:ASP68 2.7 22.8 0.5
CG A:ASP68 3.6 21.6 0.5
CB A:ASP68 3.6 20.5 1.0
CB A:LEU67 3.7 16.9 1.0
CG1 A:VAL79 3.9 15.2 1.0
C A:LEU67 4.1 16.6 1.0
ND2 A:ASN23 4.1 31.9 0.8
O A:LEU67 4.2 19.1 1.0
CB A:VAL79 4.2 14.3 1.0
N A:ASP68 4.3 17.5 1.0
OE1 A:GLU28 4.4 34.3 1.0
CA A:LEU67 4.5 16.0 1.0
CA A:ASP68 4.6 19.4 1.0
CG2 A:VAL79 4.6 16.4 1.0
CZ A:PHE4 4.7 31.0 1.0
OD1 A:ASP68 4.8 24.4 0.5
CD1 A:LEU67 4.8 19.1 1.0
CG A:LEU67 4.8 17.0 1.0

Sodium binding site 5 out of 5 in 4ek4

Go back to Sodium Binding Sites List in 4ek4
Sodium binding site 5 out of 5 in the Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:57.0
occ:1.00
 OD1 A:ASP68 2.7 24.4 0.5
NZ A:LYS56 3.0 24.0 0.5
N A:VAL69 3.1 21.2 1.0
O A:VAL69 3.1 27.0 1.0
CD A:LYS56 3.6 19.4 0.5
CG A:ASP68 3.6 21.6 0.5
CE A:LYS56 3.7 21.2 0.5
CA A:ASP68 3.7 19.4 1.0
C A:VAL69 3.8 24.9 1.0
CD A:LYS56 3.8 25.9 0.5
CB A:ASP68 3.9 20.5 1.0
NZ A:LYS56 3.9 29.7 0.5
CA A:VAL69 3.9 24.0 1.0
C A:ASP68 3.9 19.4 1.0
CB A:VAL69 4.0 24.8 1.0
CE A:LYS56 4.4 27.2 0.5
CG2 A:VAL69 4.7 25.3 1.0
OD2 A:ASP68 4.8 22.8 0.5

Reference:

Y.N.Kang, J.A.Stuckey. Crystal Structure of the CDK2 in Complex with Aminopyrazole Inhibitor To Be Published.
Page generated: Mon Oct 7 15:09:48 2024

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