Sodium in PDB 4yhf: Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor

All present enzymatic activity of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor:
2.7.10.2;

The structure of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor, PDB code: 4yhf was solved by V.O.Paavilainen, J.M.Mcfarland, J.Taunton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.55 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.770, 77.090, 88.030, 90.00, 96.43, 90.00
R / Rfree (%)	17.4 / 20.8

The structure of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Sodium atom in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor (pdb code 4yhf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor, PDB code: 4yhf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:30.1 occ:1.00 H A:GLU624 2.3 21.7 1.0 CL A:CL714 2.8 58.6 1.0 HB2 A:SER623 2.8 23.5 1.0 N A:GLU624 3.1 18.1 1.0 HA A:SER623 3.2 25.3 1.0 CB A:SER623 3.7 19.6 1.0 CA A:SER623 3.7 21.1 1.0 CB A:GLU624 3.8 17.9 1.0 C A:SER623 3.9 20.6 1.0 HH22 A:ARG618 4.0 54.1 1.0 CA A:GLU624 4.1 23.7 1.0 HB3 A:SER623 4.2 23.5 1.0 NH2 A:ARG618 4.3 45.1 1.0 H A:LYS625 4.4 19.8 1.0 HH21 A:ARG618 4.4 54.1 1.0 O A:HOH830 4.5 24.9 1.0 OG A:SER623 4.6 20.2 1.0 HA A:GLU624 4.7 28.4 1.0 CZ A:ARG618 4.9 37.1 1.0 HH12 A:ARG618 4.9 36.1 1.0 HG A:SER623 4.9 24.3 1.0

Sodium binding site 2 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:21.2 occ:1.00 HB3 A:GLU500 2.7 13.2 1.0 O A:GLN497 2.8 15.2 1.0 O A:HOH861 2.9 16.9 1.0 O A:HOH813 2.9 12.6 1.0 HG3 A:MET501 3.1 18.9 1.0 HB3 A:GLN497 3.1 17.9 1.0 HA A:GLN497 3.1 19.0 1.0 HG2 A:GLU500 3.3 28.8 1.0 C A:GLN497 3.6 16.6 1.0 CB A:GLU500 3.6 11.0 1.0 CA A:GLN497 3.6 15.8 1.0 HG3 A:GLU500 3.7 28.8 1.0 HG2 A:MET501 3.7 18.9 1.0 CG A:GLU500 3.7 24.0 1.0 H A:MET501 3.7 13.6 1.0 CB A:GLN497 3.7 14.9 1.0 CG A:MET501 3.8 15.8 1.0 HE3 A:MET501 3.9 18.1 1.0 HG2 A:GLN497 4.0 22.5 1.0 N A:MET501 4.0 11.3 1.0 HB2 A:GLU500 4.2 13.2 1.0 O A:GLY533 4.2 12.8 1.0 HE2 A:MET501 4.4 18.1 1.0 C A:GLU500 4.4 11.1 1.0 CG A:GLN497 4.4 18.7 1.0 CE A:MET501 4.5 15.1 1.0 HA A:MET501 4.5 11.6 1.0 O A:HOH841 4.5 23.8 1.0 HB2 A:GLN497 4.5 17.9 1.0 CA A:GLU500 4.5 10.5 1.0 H A:GLU500 4.6 13.7 1.0 CA A:MET501 4.7 9.7 1.0 N A:LEU498 4.8 11.8 1.0 CB A:MET501 4.8 11.1 1.0 N A:GLU500 5.0 11.4 1.0 HG23 A:VAL535 5.0 12.6 1.0 SD A:MET501 5.0 15.3 1.0

Sodium binding site 3 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:31.9 occ:1.00 H A:ARG618 2.4 13.9 1.0 HB2 A:TYR617 3.0 19.9 1.0 N A:ARG618 3.2 11.6 1.0 HA A:TYR617 3.3 14.3 1.0 HB3 A:ARG618 3.3 19.9 1.0 HB2 A:ARG618 3.4 19.9 1.0 CB A:ARG618 3.7 16.6 1.0 CB A:TYR617 3.8 16.6 1.0 CA A:TYR617 3.8 11.9 1.0 C A:TYR617 4.0 11.5 1.0 HB3 A:TYR617 4.0 19.9 1.0 CA A:ARG618 4.1 11.1 1.0 OH A:TYR627 4.3 13.8 1.0 HE2 A:TYR627 4.4 20.2 1.0 CZ A:TYR627 4.6 19.2 1.0 O A:HOH816 4.6 28.6 1.0 CE2 A:TYR627 4.6 16.8 1.0 HH A:TYR627 4.7 16.5 1.0 HD3 A:ARG618 4.7 24.1 1.0 HA A:ARG618 4.8 13.3 1.0 HD1 A:TYR617 4.8 19.7 1.0 O A:ARG618 4.9 13.2 1.0

Sodium binding site 4 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:62.5 occ:1.00 O A:HOH814 2.8 41.7 1.0 CL A:CL715 2.9 54.0 1.0 HE22 A:GLN497 3.4 39.9 1.0 O A:HOH809 3.8 36.5 1.0 O A:HIS491 4.1 31.9 1.0 NE2 A:GLN497 4.2 33.3 1.0 OE1 A:GLN497 4.6 26.2 1.0 HE21 A:GLN497 4.7 39.9 1.0 O A:ARG492 4.7 18.7 1.0 CD A:GLN497 4.8 28.8 1.0 HB2 A:ARG492 5.0 25.6 1.0

Sodium binding site 5 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:31.4 occ:1.00 H A:GLU455 2.0 20.8 1.0 O A:HOH926 2.7 38.3 1.0 N A:GLU455 2.8 17.4 1.0 HB2 A:GLU455 2.9 26.1 1.0 HB3 A:GLU455 2.9 26.1 1.0 HA A:HIS454 3.0 14.4 1.0 CB A:GLU455 3.2 21.8 1.0 CD2 A:HIS454 3.6 13.8 1.0 CA A:GLU455 3.6 15.7 1.0 CG A:HIS454 3.7 19.6 1.0 C A:HIS454 3.7 12.2 1.0 CA A:HIS454 3.7 12.0 1.0 NE2 A:HIS454 3.8 13.5 1.0 HD2 A:HIS454 3.8 16.6 1.0 ND1 A:HIS454 3.9 13.0 1.0 CE1 A:HIS454 3.9 11.8 1.0 HA A:GLU455 4.1 18.9 1.0 HE2 A:HIS454 4.1 16.2 1.0 CB A:HIS454 4.3 17.4 1.0 HD1 A:HIS454 4.3 15.6 1.0 HE1 A:HIS454 4.4 14.1 1.0 H A:LYS456 4.5 13.5 1.0 O A:HOH910 4.5 30.6 1.0 O A:HOH864 4.5 28.1 1.0 CG A:GLU455 4.7 31.5 1.0 HG2 A:GLU455 4.8 37.8 1.0 C A:GLU455 4.8 15.4 1.0 HB2 A:HIS454 4.8 20.9 1.0 O A:HIS454 4.9 12.1 1.0 N A:HIS454 5.0 17.8 1.0 N A:LYS456 5.0 11.3 1.0 HB3 A:HIS454 5.0 20.9 1.0

Sodium binding site 6 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:45.7 occ:1.00 HH A:TYR476 3.8 39.7 1.0 OH A:TYR476 4.0 33.1 1.0 CE2 A:TYR418 4.2 18.7 1.0 CZ A:TYR418 4.3 29.7 1.0 HE2 A:TYR476 4.3 20.5 1.0 HE2 A:TYR418 4.4 22.4 1.0 CD2 A:TYR418 4.4 30.5 1.0 CZ A:TYR476 4.5 26.0 1.0 CE2 A:TYR476 4.6 17.1 1.0 CE1 A:TYR418 4.6 25.0 1.0 HD2 A:TYR418 4.7 36.5 1.0 CG A:TYR418 4.7 24.9 1.0 OH A:TYR418 4.8 34.2 1.0 CD1 A:TYR418 4.8 23.9 1.0 HH A:TYR418 4.8 41.0 1.0

Sodium binding site 7 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na708 b:29.0 occ:1.00 OG A:SER575 2.6 13.2 1.0 O A:LYS573 2.7 23.1 1.0 OE2 A:GLU567 2.7 21.2 1.0 HG A:SER575 2.7 15.9 1.0 HG3 A:GLU567 2.9 24.0 1.0 HB3 A:SER578 2.9 15.5 1.0 O A:HOH892 2.9 25.2 1.0 HG2 A:GLU567 3.2 24.0 1.0 H A:SER575 3.3 23.3 1.0 CG A:GLU567 3.3 20.0 1.0 HB3 A:SER575 3.4 23.1 1.0 CD A:GLU567 3.4 16.8 1.0 CB A:SER575 3.5 19.2 1.0 N A:SER575 3.6 19.4 1.0 H A:SER578 3.6 18.3 1.0 HB2 A:LYS577 3.6 22.4 1.0 C A:LYS573 3.7 26.2 1.0 CB A:SER578 3.8 12.9 1.0 HA A:PHE574 3.8 26.4 1.0 N A:SER578 3.9 15.3 1.0 HG23 A:VAL568 4.0 28.9 1.0 C A:PHE574 4.0 22.7 1.0 CA A:SER575 4.1 21.1 1.0 OG A:SER578 4.1 18.6 1.0 HH12 A:ARG641 4.2 15.6 1.0 HG A:SER578 4.2 22.3 1.0 CA A:PHE574 4.3 22.0 1.0 CA A:SER578 4.3 14.0 1.0 HB2 A:ALA638 4.3 21.9 1.0 HB1 A:ALA638 4.3 21.9 1.0 HA A:SER578 4.3 16.8 1.0 HB2 A:SER575 4.4 23.1 1.0 CB A:LYS573 4.4 24.3 1.0 N A:PHE574 4.4 24.8 1.0 HG3 A:PRO565 4.4 20.0 1.0 H A:LYS577 4.5 17.7 1.0 HB2 A:SER578 4.5 15.5 1.0 C A:LYS577 4.5 13.9 1.0 CB A:LYS577 4.5 18.6 1.0 HG2 A:PRO565 4.6 20.0 1.0 HG22 A:VAL568 4.6 28.9 1.0 OE1 A:GLU567 4.7 13.8 1.0 CG2 A:VAL568 4.7 24.1 1.0 CB A:ALA638 4.7 18.2 1.0 C A:SER575 4.7 21.7 1.0 CA A:LYS573 4.7 21.0 1.0 O A:PHE574 4.8 29.2 1.0 CB A:GLU567 4.8 20.0 1.0 NH1 A:ARG641 4.8 13.0 1.0 O A:SER575 4.9 16.7 1.0 HB3 A:LYS577 4.9 22.4 1.0 CA A:LYS577 4.9 15.4 1.0 HH11 A:ARG641 4.9 15.6 1.0 N A:LYS577 4.9 14.8 1.0 HA A:SER575 5.0 25.3 1.0 HG21 A:VAL568 5.0 28.9 1.0 HB3 A:ALA638 5.0 21.9 1.0 HB2 A:GLU567 5.0 23.9 1.0 CG A:PRO565 5.0 16.7 1.0 O A:HOH848 5.0 37.8 1.0

Sodium binding site 8 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na709 b:35.0 occ:1.00 CL A:CL716 2.6 61.4 1.0 O A:ARG520 2.7 14.0 1.0 HB2 A:ASP521 3.1 17.4 1.0 HG3 A:PRO560 3.2 28.3 1.0 HB3 A:SER543 3.2 27.6 1.0 OG A:SER543 3.3 43.0 1.0 HB3 A:ARG520 3.6 20.9 0.4 HB3 A:ARG520 3.6 20.9 0.6 CB A:SER543 3.7 23.0 1.0 C A:ARG520 3.7 17.1 1.0 H22 A:EDO710 3.7 26.3 1.0 HG2 A:PRO560 3.8 28.3 1.0 CG A:PRO560 3.8 23.6 1.0 HE2 A:PHE574 3.8 36.3 1.0 HD2 A:PRO560 3.9 27.2 1.0 HB2 A:SER543 3.9 27.6 1.0 CB A:ASP521 3.9 14.5 1.0 HG A:SER543 4.0 51.6 1.0 HA A:ASP521 4.0 16.3 1.0 HD3 A:PRO560 4.0 27.2 1.0 CD A:PRO560 4.1 22.7 1.0 CB A:ARG520 4.3 17.5 0.4 CG A:ASP521 4.3 18.9 1.0 CA A:ASP521 4.4 13.6 1.0 HE A:ARG520 4.4 32.3 0.4 CB A:ARG520 4.4 17.4 0.6 HZ A:PHE574 4.4 35.7 1.0 HE1 A:PHE559 4.4 35.2 1.0 CE2 A:PHE574 4.4 30.2 1.0 N A:ASP521 4.4 12.1 1.0 HB2 A:ARG520 4.4 20.9 0.4 HB2 A:ARG520 4.5 20.9 0.6 HH21 A:ARG520 4.5 29.7 0.4 OD1 A:ASP521 4.6 14.9 1.0 CA A:ARG520 4.6 15.2 0.4 CA A:ARG520 4.6 13.9 0.6 CE1 A:PHE559 4.6 29.3 1.0 HB3 A:ASP521 4.7 17.4 1.0 CZ A:PHE574 4.7 29.8 1.0 C2 A:EDO710 4.8 21.9 1.0 HA A:ARG520 4.8 16.7 0.4 HO2 A:EDO710 4.9 33.3 1.0 O1 A:EDO710 4.9 37.1 1.0 OD2 A:ASP521 4.9 21.6 1.0 CZ A:PHE559 5.0 33.9 1.0 HZ A:PHE559 5.0 40.7 1.0

Sodium binding site 9 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na717 b:28.6 occ:1.00 H B:ARG600 2.1 15.6 1.0 HA B:TYR598 2.6 16.8 1.0 N B:ARG600 2.9 13.0 1.0 CL B:CL724 2.9 49.7 1.0 H11 B:EDO721 2.9 44.4 1.0 CB B:ARG600 3.1 24.4 1.0 C B:TYR598 3.2 14.3 1.0 H B:GLU599 3.2 15.7 1.0 N B:GLU599 3.2 13.1 1.0 CA B:TYR598 3.3 14.0 1.0 HD2 B:PHE601 3.4 26.0 1.0 H21 B:EDO721 3.6 38.6 1.0 CA B:ARG600 3.6 21.2 1.0 HE2 B:PHE601 3.6 29.0 1.0 O B:TYR598 3.8 11.3 1.0 C1 B:EDO721 3.8 37.0 1.0 CD2 B:PHE601 3.9 21.7 1.0 C B:GLU599 3.9 17.0 1.0 O2 B:EDO721 3.9 24.9 1.0 C2 B:EDO721 4.0 32.2 1.0 H B:PHE601 4.0 19.9 1.0 CE2 B:PHE601 4.0 24.2 1.0 CA B:GLU599 4.1 17.9 1.0 HB3 B:TYR598 4.1 12.8 1.0 HB3 B:GLU599 4.1 25.7 1.0 H B:TYR598 4.2 18.4 1.0 N B:TYR598 4.2 15.3 1.0 CB B:TYR598 4.3 10.7 1.0 O1 B:EDO721 4.3 30.3 1.0 HA B:ARG600 4.4 25.4 1.0 N B:PHE601 4.4 16.6 1.0 HO2 B:EDO721 4.4 29.9 1.0 CG B:ARG600 4.5 35.5 1.0 C B:ARG600 4.5 25.9 1.0 HO1 B:EDO721 4.6 36.3 1.0 CB B:GLU599 4.6 21.4 1.0 H12 B:EDO721 4.7 44.4 1.0 CD B:ARG600 4.7 37.3 1.0 HD1 B:TYR598 4.9 13.6 1.0 CG B:PHE601 4.9 18.9 1.0 HA B:GLU599 4.9 21.5 1.0 HB2 B:TYR598 4.9 12.8 1.0 HB2 B:GLU599 5.0 25.7 1.0

Sodium binding site 10 out of 24 in the Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Bruton'S Tyrosine Kinase in Complex with A T-Butyl Cyanoacrylamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:37.2 occ:1.00 HB3 A:HIS620 2.4 33.6 1.0 CB A:HIS620 3.3 28.0 1.0 HB2 A:HIS620 3.5 33.6 1.0 HD22 A:LEU621 4.0 20.9 1.0 CG A:HIS620 4.0 39.0 1.0 C A:HIS620 4.3 17.3 1.0 O A:HIS620 4.3 15.7 1.0 HD1 A:HIS620 4.3 60.2 1.0 CA A:HIS620 4.4 23.7 1.0 HD23 A:LEU621 4.4 20.9 1.0 ND1 A:HIS620 4.4 50.1 1.0 HG A:LEU621 4.4 13.6 1.0 CD2 A:LEU621 4.6 17.4 1.0 HA A:HIS620 4.7 28.4 1.0 HA A:LEU621 4.7 17.1 1.0 N A:LEU621 4.7 12.7 1.0 CD2 A:HIS620 4.9 35.8 1.0

J.M.Bradshaw, J.M.Mcfarland, V.O.Paavilainen, A.Bisconte, D.Tam, V.T.Phan, S.Romanov, D.Finkle, J.Shu, V.Patel, T.Ton, X.Li, D.G.Loughhead, P.A.Nunn, D.E.Karr, M.E.Gerritsen, J.O.Funk, T.O.Owens, E.Verner, K.A.Brameld, R.J.Hill, D.M.Goldstein, J.Taunton. Prolonged and Tunable Residence Time Using Reversible Covalent Kinase Inhibitors Nat.Struct.Mol.Biol. 2015.
ISSN: ESSN 1545-9985
DOI: 10.1038/NCHEMBIO.1817