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Sodium in PDB 4aw1: Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the Pif-Pocket

Enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the Pif-Pocket

All present enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the Pif-Pocket:
2.7.11.1;

Protein crystallography data

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the Pif-Pocket, PDB code: 4aw1 was solved by J.O.Schulze, K.Busschots, L.A.Lopez-Garcia, C.Lammi, A.Stroba, S.Zeuzem, A.Piiper, P.M.Alzari, S.Neimanis, J.M.Arencibia, M.Engel, R.M.Biondi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.301 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.650, 42.670, 46.330, 90.00, 98.52, 90.00
R / Rfree (%) 16.41 / 18.58

Other elements in 4aw1:

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the Pif-Pocket also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Manganese (Mn) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the Pif-Pocket (pdb code 4aw1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the Pif-Pocket, PDB code: 4aw1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4aw1

Go back to Sodium Binding Sites List in 4aw1
Sodium binding site 1 out of 2 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 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 PS210 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1365

b:23.8
occ:1.00
OD2 A:ASP223 2.5 31.1 1.0
O1A A:ATP1360 2.5 26.0 1.0
OD1 A:ASN210 2.6 17.9 1.0
O A:HOH2091 2.7 25.8 1.0
O A:HOH2088 3.0 52.6 1.0
O3B A:ATP1360 3.0 38.9 1.0
HD22 A:ASN210 3.1 22.8 1.0
O A:HOH2090 3.2 12.7 1.0
O1G A:ATP1360 3.2 49.9 1.0
CG A:ASP223 3.3 25.3 1.0
HB2 A:ASP223 3.4 26.2 1.0
CG A:ASN210 3.4 18.7 1.0
PG A:ATP1360 3.6 49.6 1.0
PA A:ATP1360 3.6 23.8 1.0
ND2 A:ASN210 3.6 19.0 1.0
O1B A:ATP1360 3.6 36.3 1.0
PB A:ATP1360 3.8 32.7 1.0
CB A:ASP223 3.8 21.8 1.0
MN A:MN1364 3.8 48.3 1.0
HB3 A:ASP223 3.9 26.2 1.0
O2G A:ATP1360 3.9 50.0 1.0
O3A A:ATP1360 3.9 28.9 1.0
HE3 A:LYS207 4.1 28.5 1.0
HZ2 A:LYS207 4.3 33.9 1.0
OD1 A:ASP223 4.3 21.6 1.0
HD21 A:ASN210 4.4 22.8 1.0
O2A A:ATP1360 4.4 25.2 1.0
HE2 A:LYS207 4.5 28.5 1.0
OD2 A:ASP205 4.6 27.5 1.0
HG2 A:GLU209 4.7 37.5 0.6
CE A:LYS207 4.7 23.8 1.0
HB3 A:GLU209 4.7 28.6 0.5
OE1 A:GLU209 4.7 29.9 0.6
O5' A:ATP1360 4.8 23.1 1.0
HA A:ASN210 4.8 20.5 1.0
CB A:ASN210 4.8 16.7 1.0
C5' A:ATP1360 5.0 19.0 1.0
NZ A:LYS207 5.0 28.3 1.0
O3G A:ATP1360 5.0 50.0 1.0

Sodium binding site 2 out of 2 in 4aw1

Go back to Sodium Binding Sites List in 4aw1
Sodium binding site 2 out of 2 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 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 PS210 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1366

b:28.3
occ:1.00
O A:HOH2044 2.7 27.5 1.0
HB3 A:GLU194 2.7 21.7 1.0
O A:SER191 2.7 15.2 1.0
OE1 A:GLU194 2.9 27.1 1.0
HA A:SER191 3.2 17.8 0.3
HA A:SER191 3.2 17.5 0.7
OG A:SER191 3.3 22.1 0.7
HG2 A:GLU194 3.5 21.8 1.0
HE2 A:HIS139 3.5 21.5 1.0
CD A:GLU194 3.5 25.4 1.0
HB2 A:TYR195 3.5 19.4 1.0
H A:TYR195 3.6 19.2 1.0
CB A:GLU194 3.6 18.1 1.0
C A:SER191 3.6 15.1 1.0
HB3 A:SER191 3.7 20.1 0.3
CG A:GLU194 3.7 18.1 1.0
CA A:SER191 3.8 14.6 0.7
CA A:SER191 3.8 14.8 0.3
N A:TYR195 3.9 16.0 1.0
HG A:SER191 3.9 26.6 0.7
O A:HOH2077 4.1 37.2 1.0
CB A:SER191 4.2 16.3 0.7
HB2 A:GLU194 4.2 21.7 1.0
CB A:SER191 4.2 16.8 0.3
HZ3 A:LYS337 4.2 53.8 1.0
NE2 A:HIS139 4.2 17.9 1.0
CB A:TYR195 4.3 16.2 1.0
O A:HOH2138 4.4 55.1 1.0
C A:GLU194 4.5 15.7 1.0
HA A:TYR195 4.5 19.5 1.0
HB3 A:TYR195 4.5 19.4 1.0
CA A:TYR195 4.5 16.2 1.0
CA A:GLU194 4.5 15.5 1.0
HZ2 A:LYS337 4.5 53.8 1.0
OE2 A:GLU194 4.6 25.9 1.0
HB2 A:SER191 4.6 19.6 0.7
H A:GLU194 4.6 18.2 1.0
HG3 A:GLU194 4.7 21.8 1.0
OG A:SER191 4.7 19.9 0.3
NZ A:LYS337 4.8 44.8 1.0
N A:ALA192 4.8 14.2 1.0
HE3 A:LYS337 4.8 46.5 1.0
HB3 A:SER191 4.9 19.6 0.7
HD2 A:HIS139 4.9 23.1 1.0
N A:GLU194 4.9 15.2 1.0
CD2 A:HIS139 4.9 19.3 1.0

Reference:

K.Busschots, L.A.Lopez-Garcia, C.Lammi, A.Stroba, S.Zeuzem, A.Piiper, P.M.Alzari, S.Neimanis, J.M.Arencibia, M.Engel, J.O.Schulze, R.M.Biondi. Substrate-Selective Inhibition of Protein Kinase PDK1 By Small Compounds That Bind to the Pif-Pocket Allosteric Docking Site. Chem.Biol. V. 19 1152 2012.
ISSN: ISSN 1074-5521
PubMed: 22999883
DOI: 10.1016/J.CHEMBIOL.2012.07.017
Page generated: Tue Dec 15 06:33:10 2020

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