Nickel in PDB 3g50: Crystal Structure of Nisod D3A Mutant at 1.9 A

All present enzymatic activity of Crystal Structure of Nisod D3A Mutant at 1.9 A:
1.15.1.1;

The structure of Crystal Structure of Nisod D3A Mutant at 1.9 A, PDB code: 3g50 was solved by S.C.Garman, A.I.Guce, R.W.Herbst, P.A.Bryngelson, D.E.Cabelli, K.A.Higgins, K.C.Ryan, M.J.Maroney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.57 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	59.988, 112.274, 111.695, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24

The binding sites of Nickel atom in the Crystal Structure of Nisod D3A Mutant at 1.9 A (pdb code 3g50). 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 Nisod D3A Mutant at 1.9 A, PDB code: 3g50:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Nisod D3A Mutant at 1.9 A


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 Nisod D3A Mutant at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:49.2 occ:0.50 N A:HIS1 2.3 70.5 1.0 SG A:CYS2 2.4 67.1 1.0 N A:CYS2 2.5 69.0 1.0 SG A:CYS6 2.5 56.9 1.0 CB A:CYS2 3.0 67.9 1.0 C A:HIS1 3.2 69.8 1.0 CA A:CYS2 3.2 68.1 1.0 CA A:HIS1 3.3 70.5 1.0 CB A:CYS6 3.6 58.0 1.0 O A:HOH128 3.8 45.5 1.0 ND1 A:HIS1 3.8 73.3 1.0 N A:ALA3 3.9 66.1 1.0 C A:CYS2 4.0 67.3 1.0 N A:CYS6 4.1 59.2 1.0 CG A:HIS1 4.1 71.8 1.0 OH A:TYR9 4.2 53.8 1.0 O A:HIS1 4.3 70.1 1.0 CB A:HIS1 4.3 70.8 1.0 CA A:CYS6 4.3 57.8 1.0 CE1 A:HIS1 4.4 72.3 1.0 CZ A:TYR9 4.5 52.2 1.0 O A:VAL8 4.6 47.5 1.0 N A:GLY7 4.7 55.7 1.0 N A:VAL8 4.8 50.3 1.0 C A:CYS6 4.8 57.0 1.0 CE2 A:TYR9 4.9 51.1 1.0 CD2 A:HIS1 4.9 71.6 1.0 CE1 A:TYR9 4.9 50.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Nisod D3A Mutant at 1.9 A


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 Nisod D3A Mutant at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni203 b:71.8 occ:0.50 N C:HIS1 2.1 87.1 1.0 SG C:CYS6 2.8 70.6 1.0 N C:CYS2 3.0 86.7 1.0 SG C:CYS2 3.1 89.6 1.0 CA C:HIS1 3.2 87.0 1.0 C C:HIS1 3.4 86.9 1.0 CB C:CYS6 3.5 70.0 1.0 CA C:CYS2 3.9 86.5 1.0 OH C:TYR9 4.0 57.4 1.0 CB C:CYS2 4.1 86.8 1.0 C C:CYS2 4.2 85.5 1.0 N C:ALA3 4.2 84.2 1.0 CZ C:TYR9 4.3 54.5 1.0 N C:CYS6 4.4 71.7 1.0 CA C:CYS6 4.4 69.7 1.0 O C:HIS1 4.4 87.0 1.0 O C:VAL8 4.5 55.0 1.0 CB C:HIS1 4.5 87.2 1.0 CD2 C:HIS1 4.5 88.2 1.0 CG C:HIS1 4.6 87.6 1.0 N C:GLY7 4.7 65.7 1.0 CE2 C:TYR9 4.7 52.2 1.0 CE1 C:TYR9 4.8 50.9 1.0 N C:VAL8 4.8 58.8 1.0 O C:CYS2 4.9 85.5 1.0 C C:CYS6 4.9 67.9 1.0

R.W.Herbst, A.Guce, P.A.Bryngelson, K.A.Higgins, K.C.Ryan, D.E.Cabelli, S.C.Garman, M.J.Maroney. Role of Conserved Tyrosine Residues in Nisod Catalysis: A Case of Convergent Evolution Biochemistry V. 48 3354 2009.
ISSN: ISSN 0006-2960
PubMed: 19183068
DOI: 10.1021/BI802029T