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Nickel in PDB 6xx4: Crystal Structure of the C-Src SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin

Enzymatic activity of Crystal Structure of the C-Src SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin

All present enzymatic activity of Crystal Structure of the C-Src SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of the C-Src SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin, PDB code: 6xx4 was solved by A.Camara-Artigas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.80 / 1.05
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 35.571, 35.571, 81.128, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 18.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the C-Src SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin (pdb code 6xx4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of the C-Src SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin, PDB code: 6xx4:

Nickel binding site 1 out of 1 in 6xx4

Go back to Nickel Binding Sites List in 6xx4
Nickel binding site 1 out of 1 in the Crystal Structure of the C-Src SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin


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 SH3 Domain H122R-Q128E Mutant in Complex with Ni(II) at pH 7.5 Co-Crystallized with Methyl Beta- Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:27.6
occ:1.00
 N A:GLY81 1.9 28.3 1.0
ND1 A:HIS83 1.9 27.4 1.0
N A:HIS83 2.0 28.6 1.0
N A:SER82 2.0 27.3 1.0
CG A:HIS83 2.8 29.3 1.0
C A:SER82 2.9 31.6 1.0
C A:GLY81 2.9 30.5 1.0
CA A:GLY81 2.9 30.6 1.0
CA A:HIS83 3.0 31.0 1.0
CA A:SER82 3.0 29.4 1.0
CE1 A:HIS83 3.0 29.6 1.0
HB3 A:HIS83 3.0 37.8 1.0
CB A:HIS83 3.1 31.5 1.0
HE1 A:HIS83 3.3 35.5 1.0
HA3 A:GLY81 3.4 36.7 1.0
H A:MET84 3.5 27.7 1.0
HA A:SER82 3.6 35.3 1.0
HA2 A:GLY81 3.6 36.7 1.0
HG A:SER82 3.6 34.3 1.0
C A:HIS83 3.7 29.5 1.0
HA A:HIS83 3.7 37.2 1.0
N A:MET84 3.8 23.1 1.0
CD2 A:HIS83 4.0 32.3 1.0
O A:SER82 4.0 31.2 1.0
HB2 A:HIS83 4.0 37.8 1.0
HG2 A:MET84 4.1 29.6 1.0
O A:GLY81 4.1 33.5 1.0
NE2 A:HIS83 4.1 32.8 1.0
OG A:SER82 4.1 28.6 1.0
CB A:SER82 4.1 29.5 1.0
HB3 A:SER82 4.5 35.4 1.0
O A:HIS83 4.7 31.6 1.0
HD2 A:HIS83 4.8 38.8 1.0
HB2 A:SER82 4.8 35.4 1.0
HE2 A:HIS83 4.9 39.4 1.0
CG A:MET84 5.0 24.6 1.0
HB2 A:MET84 5.0 25.2 1.0

Reference:

M.Plaza-Garrido, M.C.Salinas-Garcia, J.C.Martinez, A.Camara-Artigas. The Effect of An Engineered Atcun Motif on the Structure and Biophysical Properties of the SH3 Domain of C-Src Tyrosine Kinase. J.Biol.Inorg.Chem. 2020.
ISSN: ESSN 1432-1327
PubMed: 32279137
DOI: 10.1007/S00775-020-01785-0
Page generated: Thu Oct 10 08:59:25 2024

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