Nickel in PDB 4df0: Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus

The structure of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus, PDB code: 4df0 was solved by A.A.Fedorov, E.V.Fedorov, B.Desai, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.37 / 1.50
Space group	I 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	171.610, 171.610, 171.610, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.8

The structure of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus (pdb code 4df0). 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 Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus, PDB code: 4df0:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus


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 Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:30.1 occ:0.51 SG A:CYS83 2.2 21.3 1.0 SG A:CYS82 2.5 21.5 0.6 SG A:CYS82 2.9 28.2 0.4 CB A:CYS83 3.2 20.0 1.0 OXT A:PRO202 3.3 22.4 1.0 NE A:ARG127 3.4 23.3 1.0 CB A:CYS82 3.5 20.8 0.6 CB A:CYS82 3.5 20.6 0.4 O A:PRO202 3.6 25.5 1.0 C A:PRO202 3.6 28.1 1.0 CZ A:ARG127 3.8 30.7 1.0 C A:CYS82 3.8 19.4 0.4 N A:CYS83 3.9 17.8 1.0 NH2 A:ARG127 3.9 27.9 1.0 O A:CYS82 4.0 20.1 0.4 C A:CYS82 4.0 19.4 0.6 CE2 A:TYR101 4.1 18.2 1.0 CD A:ARG127 4.1 20.4 1.0 CG1 A:ILE57 4.1 19.9 1.0 CA A:CYS83 4.1 18.9 1.0 CB A:PRO202 4.3 24.8 1.0 CA A:CYS82 4.3 17.4 0.4 CA A:CYS82 4.4 17.4 0.6 O A:CYS82 4.5 18.1 0.6 CD1 A:ILE57 4.6 20.3 1.0 CA A:PRO202 4.6 21.1 1.0 NH1 A:ARG127 4.7 31.1 1.0 CG A:PRO202 4.7 28.4 1.0 CD2 A:TYR101 4.7 16.7 1.0 O A:VAL56 4.9 16.3 1.0 C A:CYS83 5.0 16.8 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus


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 Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:31.7 occ:0.50 SG B:CYS83 2.2 24.6 1.0 SG B:CYS82 2.5 33.8 0.7 SG B:CYS82 3.1 33.8 0.3 CB B:CYS83 3.2 27.4 1.0 OXT B:PRO202 3.5 22.7 1.0 NE B:ARG127 3.5 22.1 1.0 CB B:CYS82 3.6 26.6 0.7 O B:PRO202 3.6 25.0 1.0 C B:PRO202 3.7 24.3 1.0 CB B:CYS82 3.7 26.3 0.3 C B:CYS82 3.8 25.3 0.3 O B:CYS82 3.8 24.5 0.3 N B:CYS83 3.9 21.7 1.0 CZ B:ARG127 4.0 27.4 1.0 C B:CYS82 4.0 25.5 0.7 CG1 B:ILE57 4.1 21.8 1.0 CD B:ARG127 4.1 20.5 1.0 NH2 B:ARG127 4.1 29.8 1.0 CE2 B:TYR101 4.1 17.5 1.0 CA B:CYS83 4.2 19.6 1.0 CB B:PRO202 4.3 23.3 1.0 CA B:CYS82 4.4 24.2 0.3 O B:CYS82 4.4 22.0 0.7 CA B:CYS82 4.5 24.1 0.7 O B:HOH482 4.5 35.2 1.0 CD1 B:ILE57 4.5 21.7 1.0 CA B:PRO202 4.6 24.1 1.0 CG B:PRO202 4.7 30.3 1.0 CD2 B:TYR101 4.8 17.9 1.0 NH1 B:ARG127 5.0 28.8 1.0

A.A.Fedorov, E.V.Fedorov, B.Desai, J.A.Gerlt, S.C.Almo. Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus To Be Published.