Zinc in PDB 2z0p: Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase

All present enzymatic activity of Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase:
2.7.10.2;

The structure of Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase, PDB code: 2z0p was solved by K.Murayama, M.Kato-Murayama, C.Mishima, M.Shirouzu, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.67 / 2.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.417, 62.499, 117.064, 90.00, 94.33, 90.00
R / Rfree (%)	24.2 / 30

The binding sites of Zinc atom in the Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase (pdb code 2z0p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase, PDB code: 2z0p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:44.5 occ:1.00 SG A:CYS165 2.0 42.8 1.0 ND1 A:HIS143 2.1 54.2 1.0 SG A:CYS154 2.3 57.5 1.0 SG A:CYS155 2.5 61.5 1.0 CB A:CYS165 2.8 48.2 1.0 CE1 A:HIS143 3.0 54.2 1.0 CG A:HIS143 3.2 54.8 1.0 CB A:CYS155 3.2 60.8 1.0 CB A:HIS143 3.5 53.4 1.0 CB A:CYS154 3.7 61.3 1.0 N A:CYS155 3.8 59.6 1.0 N A:CYS165 3.8 49.4 1.0 CA A:HIS143 3.8 55.1 1.0 C A:CYS154 3.9 61.6 1.0 CA A:CYS165 3.9 51.0 1.0 CB A:TYR152 4.0 68.0 1.0 CA A:CYS155 4.1 59.8 1.0 NE2 A:HIS143 4.1 54.5 1.0 CD2 A:HIS143 4.2 55.1 1.0 CA A:CYS154 4.3 61.8 1.0 O A:CYS154 4.3 61.6 1.0 CG A:TYR152 4.3 67.0 1.0 CD1 A:TYR152 4.6 66.8 1.0 CD A:PRO144 4.6 60.7 1.0 N A:CYS154 4.7 63.4 1.0 C A:CYS165 4.8 54.3 1.0 C A:HIS143 4.8 57.9 1.0 N A:HIS143 4.9 54.4 1.0 N A:PRO144 5.0 59.7 1.0 CD2 A:TYR152 5.0 66.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:42.7 occ:1.00 SG B:CYS165 1.9 42.3 1.0 ND1 B:HIS143 2.0 47.4 1.0 SG B:CYS154 2.3 54.5 1.0 SG B:CYS155 2.5 52.0 1.0 CB B:CYS165 2.9 51.3 1.0 CE1 B:HIS143 2.9 46.9 1.0 CG B:HIS143 3.1 47.7 1.0 CB B:CYS155 3.2 54.1 1.0 CB B:CYS154 3.3 58.4 1.0 N B:CYS155 3.3 58.9 1.0 CB B:HIS143 3.5 45.5 1.0 N B:CYS165 3.7 54.3 1.0 CA B:HIS143 3.8 45.8 1.0 CA B:CYS155 3.8 57.0 1.0 CA B:CYS165 3.9 53.8 1.0 NE2 B:HIS143 4.0 47.0 1.0 C B:CYS154 4.0 59.6 1.0 CD2 B:HIS143 4.1 49.1 1.0 CB B:TYR152 4.2 66.5 1.0 CA B:CYS154 4.2 59.8 1.0 CG B:TYR152 4.3 65.8 1.0 CD B:PRO144 4.5 46.0 1.0 CD2 B:TYR152 4.5 65.2 1.0 C B:CYS155 4.6 57.5 1.0 O B:CYS155 4.6 58.5 1.0 N B:CYS154 4.7 62.0 1.0 C B:GLY164 4.7 55.1 1.0 N B:HIS143 4.8 46.0 1.0 C B:HIS143 4.8 46.2 1.0 O B:TYR142 4.9 48.9 1.0 C B:CYS165 4.9 57.1 1.0 CD1 B:TYR152 4.9 65.8 1.0 N B:PRO144 5.0 46.8 1.0 O B:CYS154 5.0 59.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:55.4 occ:1.00 ND1 C:HIS143 2.0 55.3 1.0 SG C:CYS165 2.1 47.8 1.0 SG C:CYS154 2.2 64.4 1.0 SG C:CYS155 2.3 65.0 1.0 CE1 C:HIS143 2.9 54.3 1.0 CB C:CYS165 2.9 59.1 1.0 CG C:HIS143 3.1 55.8 1.0 CB C:CYS154 3.3 67.1 1.0 CB C:CYS155 3.3 67.0 1.0 CB C:HIS143 3.6 54.5 1.0 N C:CYS155 3.6 67.8 1.0 CB C:TYR152 3.7 73.3 1.0 C C:CYS154 3.8 69.0 1.0 N C:CYS165 3.9 63.2 1.0 CA C:HIS143 3.9 55.9 1.0 CA C:CYS165 4.0 61.6 1.0 NE2 C:HIS143 4.0 54.0 1.0 CA C:CYS154 4.1 69.0 1.0 CG C:TYR152 4.1 72.8 1.0 CA C:CYS155 4.1 68.4 1.0 CD2 C:HIS143 4.2 54.6 1.0 CD2 C:TYR152 4.4 72.3 1.0 O C:CYS154 4.4 68.8 1.0 NE2 C:GLN157 4.5 59.1 1.0 CD C:PRO144 4.5 57.8 1.0 N C:CYS154 4.6 70.1 1.0 CD1 C:TYR152 4.8 73.0 1.0 C C:HIS143 4.8 57.8 1.0 N C:HIS143 4.9 56.1 1.0 O C:TYR152 5.0 74.2 1.0 N C:PRO144 5.0 58.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of pH Domain of Bruton'S Tyrosine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn304 b:36.5 occ:1.00 ND1 D:HIS143 2.1 40.0 1.0 SG D:CYS165 2.2 41.1 1.0 SG D:CYS154 2.3 38.1 1.0 SG D:CYS155 2.3 52.0 1.0 CE1 D:HIS143 3.0 39.2 1.0 CB D:CYS165 3.1 47.5 1.0 CG D:HIS143 3.1 41.2 1.0 CB D:CYS155 3.2 48.4 1.0 CB D:HIS143 3.5 39.3 1.0 CB D:CYS154 3.5 44.9 1.0 N D:CYS155 3.6 46.8 1.0 CA D:HIS143 3.8 40.3 1.0 N D:CYS165 3.9 47.8 1.0 C D:CYS154 4.0 46.9 1.0 CB D:TYR152 4.0 54.4 1.0 CA D:CYS155 4.0 47.5 1.0 CA D:CYS165 4.1 49.1 1.0 NE2 D:HIS143 4.2 39.2 1.0 CD2 D:HIS143 4.2 41.1 1.0 CA D:CYS154 4.2 46.6 1.0 CG D:TYR152 4.3 51.5 1.0 CD D:PRO144 4.4 42.3 1.0 O D:CYS154 4.6 47.7 1.0 CD1 D:TYR152 4.6 51.2 1.0 N D:CYS154 4.7 46.8 1.0 C D:HIS143 4.8 42.5 1.0 N D:HIS143 4.8 41.3 1.0 N D:PRO144 4.9 42.4 1.0 CD2 D:TYR152 4.9 49.8 1.0 O D:TYR142 4.9 43.8 1.0 NE2 D:GLN157 5.0 43.3 1.0

K.Murayama, M.Kato-Murayama, C.Mishima, R.Akasaka, M.Shirouzu, Y.Fukui, S.Yokoyama. Crystal Structure of the Bruton'S Tyrosine Kinase pH Domain with Phosphatidylinositol Biochem.Biophys.Res.Commun. V. 377 23 2008.
ISSN: ISSN 0006-291X
PubMed: 18809383
DOI: 10.1016/J.BBRC.2008.09.055