Nickel in PDB 3g4z: Crystal Structure of Nisod Y9F Mutant at 1.9 A

All present enzymatic activity of Crystal Structure of Nisod Y9F Mutant at 1.9 A:
1.15.1.1;

The structure of Crystal Structure of Nisod Y9F Mutant at 1.9 A, PDB code: 3g4z 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)	20.91 / 1.87
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	59.876, 111.577, 111.553, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 25.4

The structure of Crystal Structure of Nisod Y9F Mutant at 1.9 A also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Nickel atom in the Crystal Structure of Nisod Y9F Mutant at 1.9 A (pdb code 3g4z). 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 at 1.9 A, PDB code: 3g4z:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Nisod Y9F 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 Y9F Mutant at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:34.0 occ:0.50 N A:CYS2 2.0 49.1 1.0 N A:HIS1 2.2 47.6 0.5 SG A:CYS2 2.2 52.0 1.0 SG A:CYS6 2.6 51.1 1.0 CB A:CYS2 2.9 50.0 1.0 CA A:CYS2 2.9 49.6 1.0 C A:HIS1 3.0 48.2 0.5 CA A:HIS1 3.1 47.8 0.5 N A:ASP3 3.5 49.2 1.0 CB A:CYS6 3.6 48.6 1.0 C A:CYS2 3.7 49.2 1.0 CD2 A:HIS1 3.7 48.4 0.5 BR A:BR301 3.9 0.1 1.0 CG A:HIS1 4.0 47.7 0.5 CB A:HIS1 4.1 47.7 0.5 O A:HIS1 4.1 47.7 0.5 O A:HOH170 4.2 45.4 1.0 N A:CYS6 4.2 49.2 1.0 O A:VAL8 4.3 34.1 1.0 CA A:CYS6 4.5 48.2 1.0 NE2 A:HIS1 4.5 47.9 0.5 N A:GLY7 4.8 45.0 1.0 CA A:ASP3 4.8 49.2 1.0 O A:CYS2 4.8 48.8 1.0 CZ A:PHE9 4.8 34.3 1.0 N A:LEU4 4.9 49.6 1.0 N A:VAL8 4.9 38.8 1.0 ND1 A:HIS1 4.9 47.1 0.5 C A:CYS6 5.0 46.9 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Nisod Y9F 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 Y9F Mutant at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:46.6 occ:0.50 N B:HIS1 2.1 63.3 1.0 N B:CYS2 2.1 62.9 1.0 SG B:CYS2 2.3 63.6 1.0 SG B:CYS6 2.6 57.2 1.0 C B:HIS1 2.9 63.1 1.0 CA B:HIS1 3.0 63.5 1.0 CA B:CYS2 3.1 62.5 1.0 CB B:CYS2 3.1 62.9 1.0 ND1 B:HIS1 3.4 64.5 1.0 N B:ASP3 3.6 61.5 1.0 CB B:CYS6 3.7 54.8 1.0 C B:CYS2 3.8 62.1 1.0 CG B:HIS1 4.0 64.5 1.0 CB B:HIS1 4.0 63.8 1.0 O B:HIS1 4.1 63.2 1.0 O B:VAL8 4.2 38.1 1.0 N B:CYS6 4.2 55.8 1.0 CE1 B:HIS1 4.2 62.5 1.0 CG1 B:VAL8 4.3 42.0 1.0 CA B:CYS6 4.5 54.8 1.0 N B:VAL8 4.6 44.1 1.0 N B:GLY7 4.7 51.6 1.0 CZ B:PHE9 4.7 30.3 1.0 CA B:ASP3 4.8 60.6 1.0 CE2 B:PHE9 4.9 30.4 1.0 C B:CYS6 4.9 53.5 1.0 CD2 B:HIS1 4.9 64.4 1.0 N B:LEU4 5.0 59.5 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Nisod Y9F 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 3 of Crystal Structure of Nisod Y9F Mutant at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni203 b:40.7 occ:0.50 N C:HIS1 2.0 52.1 1.0 N C:CYS2 2.1 52.0 1.0 SG C:CYS2 2.2 53.6 1.0 SG C:CYS6 2.4 50.6 1.0 C C:HIS1 2.9 52.2 1.0 CA C:HIS1 2.9 52.8 1.0 CB C:CYS2 3.0 51.5 1.0 CA C:CYS2 3.0 51.5 1.0 ND1 C:HIS1 3.4 58.0 1.0 CB C:CYS6 3.5 47.9 1.0 CG C:HIS1 3.7 55.1 1.0 N C:ASP3 3.9 50.3 1.0 CB C:HIS1 3.9 52.9 1.0 C C:CYS2 3.9 50.9 1.0 BR C:BR303 4.0 0.7 1.0 O C:HIS1 4.1 52.5 1.0 N C:CYS6 4.1 48.8 1.0 CE1 C:HIS1 4.1 56.2 1.0 O C:VAL8 4.1 36.0 1.0 CA C:CYS6 4.3 47.7 1.0 CD2 C:HIS1 4.6 55.8 1.0 N C:GLY7 4.6 45.1 1.0 N C:VAL8 4.7 39.5 1.0 NE2 C:HIS1 4.7 56.3 1.0 C C:CYS6 4.8 46.7 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