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Sodium in PDB 5ack: Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket

Enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket

All present enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket:
2.7.11.1;

Protein crystallography data

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket, PDB code: 5ack was solved by J.O.Schulze, E.Kroon, A.Doemling, R.M.Biondi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.568 / 1.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.980, 44.540, 47.810, 90.00, 101.25, 90.00
R / Rfree (%) 14.16 / 16.55

Other elements in 5ack:

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket (pdb code 5ack). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket, PDB code: 5ack:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ack

Go back to Sodium Binding Sites List in 5ack
Sodium binding site 1 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na900

b:42.9
occ:1.00
 O2B A:ATP500 2.2 35.4 0.6
OD2 A:ASP223 2.2 26.0 0.6
O1A A:ATP500 2.4 41.6 1.0
O3G A:ATP500 2.5 44.1 0.9
O A:HOH2022 2.5 35.9 1.0
CG A:ASP223 3.1 24.2 0.6
PB A:ATP500 3.1 37.3 0.6
O3A A:ATP500 3.2 37.1 0.6
OD1 A:ASP223 3.3 26.0 0.6
PA A:ATP500 3.4 39.6 1.0
NA A:NA902 3.4 29.8 0.6
O A:HOH2190 3.5 42.8 1.0
HH A:TYR126 3.6 32.8 0.5
HZ3 A:LYS111 3.6 18.6 0.4
PG A:ATP500 3.6 43.0 0.6
HZ1 A:LYS111 3.6 31.5 0.6
OD1 A:ASP223 3.7 22.6 0.5
OH A:TYR126 3.8 27.3 0.5
HZ2 A:LYS111 3.8 31.5 0.6
O3B A:ATP500 3.8 40.1 0.8
HZ2 A:LYS111 3.9 18.6 0.4
CG A:ASP223 3.9 20.7 0.5
OD2 A:ASP223 4.1 22.2 0.5
O1G A:ATP500 4.1 44.0 0.8
NZ A:LYS111 4.1 26.2 0.6
NZ A:LYS111 4.2 15.5 0.4
HB3 A:ASP223 4.3 23.4 0.6
HB2 A:ASP223 4.3 20.2 0.5
NA A:NA902 4.3 30.1 0.4
CB A:ASP223 4.3 19.5 0.6
O A:HOH2020 4.4 34.9 1.0
O A:HOH2058 4.4 24.4 1.0
O2A A:ATP500 4.5 38.2 1.0
O1B A:ATP500 4.5 39.1 1.0
O5' A:ATP500 4.5 38.1 1.0
HE2 A:LYS111 4.5 29.0 0.6
HA A:ASP223 4.5 18.1 0.5
HE3 A:LYS111 4.6 19.0 0.4
CB A:ASP223 4.6 16.8 0.5
HA A:ASP223 4.7 19.0 0.6
HZ1 A:LYS111 4.8 18.6 0.4
HZ3 A:LYS111 4.8 31.5 0.6
CE A:LYS111 4.9 24.1 0.6
O2G A:ATP500 4.9 44.7 1.0
HB2 A:ASP223 5.0 23.4 0.6
OG A:SER94 5.0 35.1 1.0

Sodium binding site 2 out of 4 in 5ack

Go back to Sodium Binding Sites List in 5ack
Sodium binding site 2 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:34.9
occ:1.00
 O A:HOH2221 2.2 35.1 1.0
O A:HOH2220 2.4 40.0 1.0
O A:GLY244 2.6 15.6 1.0
HG1 A:THR245 2.7 17.8 1.0
OG1 A:THR245 2.7 14.8 1.0
HA A:THR245 3.2 17.2 1.0
HZ1 A:LYS207 3.3 22.3 1.0
O A:HOH2330 3.4 44.8 1.0
C A:GLY244 3.5 14.7 1.0
OD2 A:ASP205 3.7 17.9 1.0
CA A:THR245 3.8 14.4 1.0
CB A:THR245 3.8 14.5 1.0
HZ2 A:LYS207 3.8 22.3 1.0
O A:HOH2219 3.9 25.0 1.0
N A:THR245 3.9 14.1 1.0
NZ A:LYS207 4.0 18.6 1.0
HG21 A:THR245 4.0 18.4 1.0
OD1 A:ASP205 4.2 15.4 1.0
H A:GLY244 4.3 17.7 1.0
CG A:ASP205 4.4 15.4 1.0
CG2 A:THR245 4.4 15.3 1.0
HZ3 A:LYS207 4.4 22.3 1.0
HB A:THR245 4.5 17.4 1.0
CA A:GLY244 4.6 14.6 1.0
H A:THR245 4.7 16.9 1.0
HA2 A:GLY244 4.7 17.6 1.0
O2 A:DTD700 4.8 44.9 1.0
O A:HOH2222 4.8 19.3 1.0
HG22 A:THR245 4.8 18.4 1.0
HE2 A:LYS207 4.9 20.8 1.0
N A:GLY244 4.9 14.7 1.0
O A:HOH2230 5.0 40.8 1.0
C2 A:DTD700 5.0 43.4 1.0

Sodium binding site 3 out of 4 in 5ack

Go back to Sodium Binding Sites List in 5ack
Sodium binding site 3 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:29.8
occ:0.62
 NA A:NA902 0.0 29.8 0.6
NA A:NA902 1.5 30.1 0.4
O2B A:ATP500 2.2 35.4 0.6
OD2 A:ASP223 2.3 26.0 0.6
OD1 A:ASN210 2.3 16.8 1.0
O A:HOH2181 3.1 33.3 1.0
CG A:ASP223 3.1 24.2 0.6
OD2 A:ASP223 3.3 22.2 0.5
HB2 A:ASP223 3.4 20.2 0.5
NA A:NA900 3.4 42.9 1.0
CG A:ASN210 3.5 15.8 1.0
PB A:ATP500 3.5 37.3 0.6
O A:HOH2190 3.6 42.8 1.0
HD22 A:ASN210 3.6 18.3 1.0
OD1 A:ASP223 3.7 26.0 0.6
CG A:ASP223 3.8 20.7 0.5
ND2 A:ASN210 3.9 15.2 1.0
HB2 A:ASP223 4.0 23.4 0.6
O1B A:ATP500 4.0 39.1 1.0
CB A:ASP223 4.0 19.5 0.6
CB A:ASP223 4.1 16.8 0.5
HB3 A:ASP223 4.1 23.4 0.6
HE3 A:LYS207 4.2 20.8 1.0
O1G A:ATP500 4.2 44.0 0.8
O3B A:ATP500 4.3 40.1 0.8
HA A:ASN210 4.3 16.8 1.0
HG21 A:THR222 4.4 21.2 1.0
HB3 A:GLU209 4.5 23.8 1.0
HB3 A:ASP223 4.5 20.2 0.5
O A:GLU209 4.5 16.3 1.0
OD1 A:ASP223 4.6 22.6 0.5
O3G A:ATP500 4.6 44.1 0.9
PG A:ATP500 4.6 43.0 0.6
CB A:ASN210 4.7 15.1 1.0
HZ2 A:LYS207 4.7 22.3 1.0
HE2 A:LYS207 4.7 20.8 1.0
HB2 A:GLU209 4.8 23.8 1.0
O1A A:ATP500 4.8 41.6 1.0
O3A A:ATP500 4.8 37.1 0.6
HD21 A:ASN210 4.8 18.3 1.0
CE A:LYS207 4.8 17.3 1.0
CA A:ASN210 4.9 14.0 1.0
C A:GLU209 4.9 14.7 1.0

Sodium binding site 4 out of 4 in 5ack

Go back to Sodium Binding Sites List in 5ack
Sodium binding site 4 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:30.1
occ:0.38
 NA A:NA902 0.0 30.1 0.4
NA A:NA902 1.5 29.8 0.6
OD1 A:ASN210 2.9 16.8 1.0
O2B A:ATP500 3.0 35.4 0.6
HE3 A:LYS207 3.0 20.8 1.0
HZ2 A:LYS207 3.2 22.3 1.0
HD22 A:ASN210 3.3 18.3 1.0
OD2 A:ASP223 3.4 26.0 0.6
OD2 A:ASP223 3.4 22.2 0.5
O1G A:ATP500 3.5 44.0 0.8
CE A:LYS207 3.6 17.3 1.0
HE2 A:LYS207 3.7 20.8 1.0
CG A:ASN210 3.7 15.8 1.0
NZ A:LYS207 3.8 18.6 1.0
ND2 A:ASN210 3.8 15.2 1.0
PB A:ATP500 3.9 37.3 0.6
HB3 A:GLU209 4.0 23.8 1.0
HB2 A:GLU209 4.1 23.8 1.0
O A:HOH2181 4.1 33.3 1.0
HZ3 A:LYS207 4.1 22.3 1.0
O3B A:ATP500 4.1 40.1 0.8
O1B A:ATP500 4.3 39.1 1.0
NA A:NA900 4.3 42.9 1.0
CG A:ASP223 4.3 24.2 0.6
CG A:ASP223 4.3 20.7 0.5
PG A:ATP500 4.3 43.0 0.6
HB2 A:ASP223 4.5 20.2 0.5
CB A:GLU209 4.6 19.8 1.0
HZ1 A:LYS207 4.6 22.3 1.0
HD21 A:ASN210 4.7 18.3 1.0
O3G A:ATP500 4.8 44.1 0.9
HB3 A:ASP223 4.8 23.4 0.6
O A:HOH2330 4.8 44.8 1.0
HB2 A:ASP223 4.8 23.4 0.6
CB A:ASP223 4.9 16.8 0.5
CB A:ASP223 5.0 19.5 0.6
HA A:ASN210 5.0 16.8 1.0

Reference:

E.Kroon, J.O.Schulze, E.Suss, C.J.Camacho, R.M.Biondi, A.Domling. Discovery of A Potent Allosteric Kinase Modulator By Combining Computational and Synthetic Methods. Angew.Chem.Int.Ed.Engl. V. 54 13933 2015.
ISSN: ISSN 1433-7851
PubMed: 26385475
DOI: 10.1002/ANIE.201506310
Page generated: Mon Oct 7 19:53:13 2024

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