Nickel in PDB 3g4x: Crystal Structure of Nisod Y9F Mutant

All present enzymatic activity of Crystal Structure of Nisod Y9F Mutant:
1.15.1.1;

The structure of Crystal Structure of Nisod Y9F Mutant, PDB code: 3g4x 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)	20.61 / 2.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.089, 112.568, 111.866, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 23.7

The structure of Crystal Structure of Nisod Y9F Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Nickel atom in the Crystal Structure of Nisod Y9F Mutant (pdb code 3g4x). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Nisod Y9F Mutant, PDB code: 3g4x:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Nisod Y9F Mutant


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 Y9F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:24.9 occ:0.50 N A:CYS2 2.0 29.2 1.0 N A:HIS1 2.0 29.0 0.4 N A:HIS1 2.1 29.4 0.6 SG A:CYS2 2.2 34.4 1.0 ND1 A:HIS1 2.2 31.3 0.6 SG A:CYS6 2.3 32.6 1.0 C A:HIS1 2.9 28.8 0.5 CA A:HIS1 2.9 29.2 0.6 CA A:HIS1 2.9 28.9 0.4 CA A:CYS2 3.0 30.4 1.0 CB A:CYS2 3.0 30.6 1.0 CE1 A:HIS1 3.2 31.8 0.6 CG A:HIS1 3.2 30.9 0.6 CB A:CYS6 3.5 31.8 1.0 CB A:HIS1 3.6 29.4 0.6 CL A:CL301C 3.6 30.1 0.5 N A:ASP3 3.7 31.1 1.0 C A:CYS2 3.8 30.6 1.0 O A:HIS1 4.0 27.0 0.5 CB A:HIS1 4.1 29.1 0.4 N A:CYS6 4.1 32.3 1.0 CG A:HIS1 4.1 30.0 0.4 O A:VAL8 4.3 26.6 1.0 NE2 A:HIS1 4.3 33.0 0.6 CD2 A:HIS1 4.4 32.3 0.6 CA A:CYS6 4.4 31.4 1.0 CD2 A:HIS1 4.4 30.2 0.4 ND1 A:HIS1 4.7 31.5 0.4 N A:VAL8 4.9 28.5 1.0 O A:CYS2 4.9 29.5 1.0 N A:GLY7 4.9 30.3 1.0 N A:LEU4 4.9 31.7 1.0 C A:CYS6 4.9 31.1 1.0 CZ A:PHE9 5.0 31.2 1.0 NE2 A:HIS1 5.0 30.5 0.4

Nickel binding site 2 out of 3 in the Crystal Structure of Nisod Y9F Mutant


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 Y9F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:31.3 occ:0.50 N B:HIS1 2.0 35.9 0.5 N B:HIS1 2.0 35.7 0.6 N B:CYS2 2.1 36.9 1.0 SG B:CYS2 2.2 39.9 1.0 SG B:CYS6 2.3 33.0 1.0 ND1 B:HIS1 2.6 36.9 0.6 C B:HIS1 2.9 35.9 0.5 CA B:HIS1 2.9 36.0 0.6 CA B:HIS1 2.9 35.9 0.5 CA B:CYS2 3.0 37.4 1.0 CB B:CYS2 3.1 38.3 1.0 CL B:CL302C 3.4 51.2 1.0 N B:ASP3 3.5 36.6 1.0 CB B:CYS6 3.5 32.8 1.0 CG B:HIS1 3.6 36.8 0.6 CE1 B:HIS1 3.6 36.6 0.6 CB B:HIS1 3.7 36.0 0.6 C B:CYS2 3.8 37.3 1.0 N B:CYS6 3.9 33.2 1.0 ND1 B:HIS1 4.0 36.3 0.5 O B:HIS1 4.1 35.1 0.5 CB B:HIS1 4.1 35.8 0.5 O B:VAL8 4.2 32.1 1.0 CG B:HIS1 4.2 35.9 0.5 CA B:CYS6 4.2 32.9 1.0 CG1 B:VAL8 4.4 33.1 1.0 N B:GLY7 4.6 32.6 1.0 N B:VAL8 4.7 32.1 1.0 CD2 B:HIS1 4.7 36.9 0.6 NE2 B:HIS1 4.7 35.7 0.6 CE1 B:HIS1 4.8 36.0 0.5 CA B:ASP3 4.8 35.0 1.0 C B:CYS6 4.8 33.1 1.0 N B:LEU4 4.8 34.0 1.0 CZ B:PHE9 4.9 24.6 1.0 O B:CYS2 4.9 37.1 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Nisod Y9F Mutant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Nisod Y9F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni203 b:27.5 occ:0.50 N C:HIS1 1.9 33.3 0.5 N C:HIS1 2.0 33.3 0.5 N C:CYS2 2.1 34.0 1.0 SG C:CYS2 2.1 38.7 1.0 SG C:CYS6 2.3 36.4 1.0 ND1 C:HIS1 2.6 36.0 0.5 C C:HIS1 2.9 33.4 0.5 CA C:HIS1 2.9 33.5 0.5 CA C:HIS1 2.9 33.6 0.5 CB C:CYS2 3.1 34.5 1.0 CA C:CYS2 3.1 34.6 1.0 CB C:CYS6 3.4 35.2 1.0 CG C:HIS1 3.5 34.7 0.5 CE1 C:HIS1 3.5 35.2 0.5 CL C:CL303C 3.6 51.1 1.0 CB C:HIS1 3.7 33.8 0.5 CG C:HIS1 3.8 34.7 0.5 N C:ASP3 3.8 33.3 1.0 C C:CYS2 3.9 34.4 1.0 CB C:HIS1 3.9 33.7 0.5 O C:HOH393 3.9 50.0 1.0 CD2 C:HIS1 3.9 34.7 0.5 N C:CYS6 4.0 34.8 1.0 O C:HIS1 4.1 32.4 0.5 ND1 C:HIS1 4.2 36.0 0.5 CA C:CYS6 4.2 34.8 1.0 O C:VAL8 4.3 32.3 1.0 NE2 C:HIS1 4.5 35.8 0.5 CE1 C:HIS1 4.6 35.0 0.5 NE2 C:HIS1 4.6 33.8 0.5 CD2 C:HIS1 4.6 34.2 0.5 N C:GLY7 4.7 33.9 1.0 C C:CYS6 4.8 34.2 1.0 N C:VAL8 4.8 32.6 1.0 O C:CYS2 5.0 34.0 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