Nickel in PDB 4omo: Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E

All present enzymatic activity of Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E:
2.7.10.2;

The structure of Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E, PDB code: 4omo was solved by A.Camara-Artigas, J.Bacarizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.11 / 1.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.711, 45.464, 57.807, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 16.8

The binding sites of Nickel atom in the Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E (pdb code 4omo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E, PDB code: 4omo:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:15.3 occ:1.00 N A:HIS83 1.8 14.0 1.0 ND1 A:HIS83 1.8 14.4 1.0 N A:SER82 1.9 18.3 1.0 N A:GLY81 2.0 22.3 1.0 C A:SER82 2.7 14.9 1.0 C A:GLY81 2.7 20.4 1.0 CA A:SER82 2.8 18.6 1.0 O A:HOH363 2.8 22.6 1.0 CG A:HIS83 2.8 13.7 1.0 CE1 A:HIS83 2.9 17.5 1.0 CA A:GLY81 2.9 25.2 1.0 CA A:HIS83 2.9 12.7 1.0 H A:MET84 3.0 13.3 1.0 HE1 A:HIS83 3.1 24.6 1.0 CB A:HIS83 3.2 14.0 1.0 HB3 A:HIS83 3.2 10.4 1.0 HA A:SER82 3.5 19.8 1.0 HA2 A:GLY81 3.5 31.0 1.0 HA3 A:GLY81 3.5 32.7 1.0 N A:MET84 3.5 11.5 1.0 HA A:HIS83 3.7 14.3 1.0 C A:HIS83 3.7 13.4 1.0 HG A:SER82 3.7 14.6 1.0 OG A:SER82 3.8 20.2 1.0 CB A:SER82 3.9 21.2 1.0 O A:SER82 3.9 17.8 1.0 O A:GLY81 3.9 24.1 1.0 NE2 A:HIS83 3.9 17.3 1.0 CD2 A:HIS83 4.0 16.1 1.0 HB2 A:HIS83 4.1 22.8 1.0 HB3 A:SER82 4.3 19.3 1.0 HB3 A:MET84 4.6 11.4 1.0 O A:HOH370 4.6 23.6 1.0 HB2 A:SER82 4.6 27.4 1.0 HB2 A:MET84 4.6 13.1 1.0 O A:HOH364 4.7 35.1 1.0 O A:HOH367 4.7 36.0 1.0 CA A:MET84 4.8 10.6 1.0 HD2 A:HIS83 4.8 20.8 1.0 O A:HIS83 4.9 16.0 1.0 CB A:MET84 4.9 12.4 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the C-Src Tyrosine Kinase SH3 Domain Mutant Q128E within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:18.9 occ:1.00 N B:SER82 1.8 20.9 1.0 N B:HIS83 1.9 15.2 1.0 N B:GLY81 1.9 23.0 1.0 ND1 B:HIS83 2.0 20.6 1.0 C B:GLY81 2.7 25.5 1.0 C B:SER82 2.7 17.4 1.0 CA B:GLY81 2.8 27.8 1.0 CA B:SER82 2.8 18.4 1.0 CG B:HIS83 2.9 15.8 1.0 CA B:HIS83 3.0 14.5 1.0 CE1 B:HIS83 3.0 22.7 1.0 HE1 B:HIS83 3.2 31.5 1.0 CB B:HIS83 3.2 16.1 1.0 HB3 B:HIS83 3.2 27.9 1.0 H B:MET84 3.3 6.9 1.0 HA3 B:GLY81 3.3 31.6 1.0 HA B:SER82 3.5 8.8 1.0 HA2 B:GLY81 3.5 38.3 1.0 HB2 B:SER82 3.6 32.3 1.0 HA B:HIS83 3.7 26.4 1.0 O B:HOH304 3.7 19.3 1.0 N B:MET84 3.8 11.6 1.0 C B:HIS83 3.8 12.6 1.0 CB B:SER82 3.8 24.2 1.0 O B:GLY81 3.9 27.8 1.0 O B:SER82 3.9 18.0 1.0 NE2 B:HIS83 4.1 21.5 1.0 CD2 B:HIS83 4.1 17.9 1.0 HB2 B:HIS83 4.2 14.9 1.0 HG2 B:MET84 4.4 24.6 1.0 HB3 B:SER82 4.5 17.9 1.0 OG B:SER82 4.6 30.8 1.0 O B:HIS83 4.9 14.4 1.0 HB2 B:MET84 4.9 5.9 1.0 HD2 B:HIS83 4.9 10.8 1.0 HG B:SER82 4.9 42.0 1.0

J.Bacarizo, S.Martinez-Rodriguez, J.M.Martin-Garcia, M.Andujar-Sanchez, E.Ortiz-Salmeron, J.L.Neira, A.Camara-Artigas. Electrostatic Effects in the Folding of the SH3 Domain of the C-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation. Plos One V. 9 13224 2014.
ISSN: ESSN 1932-6203
PubMed: 25490095
DOI: 10.1371/JOURNAL.PONE.0113224