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

Enzymatic activity of 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;

Protein crystallography data

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

Nickel Binding Sites:

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 3g50

Go back to Nickel Binding Sites List in 3g50
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 3g50

Go back to Nickel Binding Sites List in 3g50
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

Reference:

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
Page generated: Fri Sep 25 08:22:25 2020
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