Nickel in PDB 4df1: Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus Complexed with Inhibitor Bmp

The structure of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus Complexed with Inhibitor Bmp, PDB code: 4df1 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)	37.35 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.158, 62.071, 72.712, 90.00, 97.46, 90.00
R / Rfree (%)	15 / 17.9

The binding sites of Nickel atom in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Thermoproteus Neutrophilus Complexed with Inhibitor Bmp (pdb code 4df1). 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 Complexed with Inhibitor Bmp, PDB code: 4df1:
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 Complexed with Inhibitor Bmp


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 Complexed with Inhibitor Bmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:30.0 occ:0.59 SG A:CYS83 2.3 23.1 1.0 SG A:CYS82 2.6 35.9 1.0 CB A:CYS83 3.1 17.4 1.0 NE A:ARG127 3.5 15.7 1.0 OXT A:PRO202 3.6 16.4 1.0 CB A:CYS82 3.6 19.8 1.0 N A:CYS83 3.8 10.4 1.0 C A:CYS82 3.8 16.5 1.0 O A:PRO202 3.9 14.5 1.0 C A:PRO202 3.9 18.6 1.0 CD A:ARG127 4.1 14.4 1.0 CA A:CYS83 4.1 11.6 1.0 O A:CYS82 4.1 10.5 1.0 CZ A:ARG127 4.2 26.3 1.0 CE2 A:TYR101 4.3 10.7 1.0 CG1 A:ILE57 4.3 11.4 1.0 NH2 A:ARG127 4.3 23.3 1.0 CA A:CYS82 4.4 14.3 1.0 CB A:PRO202 4.7 14.5 1.0 CD1 A:ILE57 4.7 12.6 1.0 O A:HOH480 4.8 28.4 1.0 CG A:PRO202 4.9 20.5 1.0 CD2 A:TYR101 4.9 10.2 1.0 CA A:PRO202 5.0 14.2 1.0

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


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 Complexed with Inhibitor Bmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:31.0 occ:0.58 SG B:CYS83 2.3 19.8 1.0 SG B:CYS82 2.5 33.3 1.0 CB B:CYS83 3.2 11.4 1.0 NE B:ARG127 3.3 15.2 1.0 CB B:CYS82 3.6 20.7 1.0 N B:CYS83 3.7 13.6 1.0 O B:PRO202 3.8 15.1 1.0 OXT B:PRO202 3.8 17.8 1.0 C B:CYS82 3.8 14.2 1.0 CZ B:ARG127 3.8 28.9 1.0 CD B:ARG127 3.9 17.4 1.0 C B:PRO202 3.9 18.8 1.0 NH2 B:ARG127 4.1 21.5 1.0 CA B:CYS83 4.1 10.7 1.0 O B:CYS82 4.1 15.4 1.0 CG1 B:ILE57 4.3 15.8 1.0 CA B:CYS82 4.3 15.2 1.0 CE2 B:TYR101 4.3 11.8 1.0 O B:HOH470 4.6 29.9 1.0 NH1 B:ARG127 4.7 23.5 1.0 CB B:PRO202 4.7 16.6 1.0 CD1 B:ILE57 4.8 12.1 1.0 CG B:PRO202 4.9 21.1 1.0 CD2 B:TYR101 5.0 9.7 1.0 CA B:PRO202 5.0 15.5 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 Complexed with Inhibitor Bmp To Be Published.