Nickel in PDB 7u6h: Hald with Ornithine and Alpha-Ketoglutarate

The structure of Hald with Ornithine and Alpha-Ketoglutarate, PDB code: 7u6h was solved by C.V.Swenson, M.E.Neugebauer, E.N.Kissman, M.C.Y.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.84 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	72.05, 73.226, 73.176, 66.24, 75.8, 85.28
R / Rfree (%)	17.7 / 21.3

The structure of Hald with Ornithine and Alpha-Ketoglutarate also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Nickel atom in the Hald with Ornithine and Alpha-Ketoglutarate (pdb code 7u6h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Hald with Ornithine and Alpha-Ketoglutarate, PDB code: 7u6h:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Hald with Ornithine and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Hald with Ornithine and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:31.9 occ:1.00 NE2 A:HIS149 2.1 28.3 1.0 NE2 A:HIS217 2.1 27.0 1.0 O5 A:AKG307 2.2 38.1 1.0 O2 A:AKG307 2.2 46.1 1.0 CL A:CL302 2.4 37.2 1.0 C2 A:AKG307 2.8 42.1 1.0 C1 A:AKG307 2.9 46.4 1.0 CE1 A:HIS149 3.0 31.6 1.0 CE1 A:HIS217 3.0 30.1 1.0 CD2 A:HIS149 3.1 34.0 1.0 CD2 A:HIS217 3.1 28.9 1.0 ND1 A:HIS149 4.1 26.9 1.0 O1 A:AKG307 4.1 41.7 1.0 ND1 A:HIS217 4.2 28.8 1.0 CG A:HIS149 4.2 28.3 1.0 CG A:HIS217 4.2 29.3 1.0 C3 A:AKG307 4.3 32.8 1.0 O A:HOH422 4.4 25.5 1.0 CD2 A:LEU210 4.4 33.1 1.0 CG A:ORN303 4.6 29.8 1.0 NE2 A:HIS146 4.7 29.3 1.0 ND2 A:ASN232 4.7 28.4 1.0 C4 A:AKG307 4.8 25.9 1.0 CE1 A:HIS146 4.8 30.6 1.0

Nickel binding site 2 out of 4 in the Hald with Ornithine and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Hald with Ornithine and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:25.5 occ:1.00 NE2 B:HIS149 2.1 27.3 1.0 NE2 B:HIS217 2.1 28.8 1.0 O5 B:AKG308 2.3 44.4 1.0 O1 B:AKG308 2.3 44.6 1.0 CL B:CL302 2.3 38.7 1.0 C1 B:AKG308 2.9 45.7 1.0 C2 B:AKG308 2.9 41.4 1.0 CD2 B:HIS149 3.0 29.2 1.0 CE1 B:HIS217 3.0 28.8 1.0 CE1 B:HIS149 3.1 28.8 1.0 CD2 B:HIS217 3.1 27.1 1.0 ND1 B:HIS217 4.1 23.0 1.0 O2 B:AKG308 4.1 41.3 1.0 ND1 B:HIS149 4.1 25.9 1.0 CG B:HIS149 4.1 24.2 1.0 CG B:HIS217 4.2 30.3 1.0 C3 B:AKG308 4.4 36.6 1.0 CD2 B:LEU210 4.5 34.5 1.0 O B:HOH440 4.5 32.1 1.0 NE2 B:HIS146 4.7 27.9 1.0 CG B:ORN303 4.8 33.1 1.0 CA B:ORN303 4.9 31.3 1.0 CE1 B:HIS146 4.9 30.6 1.0 ND2 B:ASN232 4.9 28.3 1.0 CB B:ORN303 4.9 26.8 1.0 C4 B:AKG308 4.9 30.6 1.0

Nickel binding site 3 out of 4 in the Hald with Ornithine and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Hald with Ornithine and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:42.4 occ:1.00 O2 C:AKG307 2.0 53.8 1.0 NE2 C:HIS217 2.1 48.2 1.0 O5 C:AKG307 2.3 55.6 1.0 NE2 C:HIS149 2.3 48.0 1.0 CL C:CL302 2.4 49.6 1.0 C1 C:AKG307 2.7 57.4 1.0 C2 C:AKG307 2.8 56.3 1.0 CD2 C:HIS217 3.1 43.8 1.0 CE1 C:HIS217 3.1 41.0 1.0 CD2 C:HIS149 3.3 48.9 1.0 CE1 C:HIS149 3.3 49.3 1.0 O1 C:AKG307 3.9 53.5 1.0 ND1 C:HIS217 4.2 41.2 1.0 CG C:HIS217 4.2 46.2 1.0 C3 C:AKG307 4.4 56.2 1.0 CD2 C:LEU210 4.4 42.0 1.0 ND1 C:HIS149 4.4 40.0 1.0 CG C:HIS149 4.4 45.4 1.0 O C:HOH402 4.5 34.6 1.0 ND2 C:ASN232 4.7 49.0 1.0 CG C:ORN303 4.8 46.2 1.0 NE2 C:HIS146 4.8 52.5 1.0 CE1 C:HIS146 4.9 53.6 1.0 C4 C:AKG307 4.9 58.3 1.0

Nickel binding site 4 out of 4 in the Hald with Ornithine and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Hald with Ornithine and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:37.3 occ:1.00 NE2 D:HIS217 2.0 44.0 1.0 CE1 D:HIS149 2.1 46.0 1.0 O1 D:AKG306 2.2 56.4 1.0 O5 D:AKG306 2.3 50.2 1.0 CL D:CL302 2.4 50.6 1.0 NE2 D:HIS149 2.6 48.0 1.0 CE1 D:HIS217 2.9 39.1 1.0 C1 D:AKG306 3.0 61.3 1.0 C2 D:AKG306 3.0 55.0 1.0 CD2 D:HIS217 3.1 37.6 1.0 ND1 D:HIS149 3.3 50.1 1.0 CD2 D:HIS149 3.9 37.9 1.0 ND1 D:HIS217 4.0 37.0 1.0 O2 D:AKG306 4.2 58.6 1.0 CG D:HIS217 4.2 38.0 1.0 CG D:HIS149 4.3 47.5 1.0 CD2 D:LEU210 4.3 37.8 1.0 O D:HOH412 4.5 36.2 1.0 C3 D:AKG306 4.5 49.5 1.0 NE2 D:HIS146 4.7 46.5 1.0 CG D:ORN303 4.8 47.4 1.0 CE1 D:HIS146 4.8 49.7 1.0 ND2 D:ASN232 4.8 38.4 1.0 C4 D:AKG306 5.0 49.8 1.0

E.N.Kissman, M.E.Neugebauer, K.H.Sumida, C.V.Swenson, N.Sambold, M.C.Y.Chang. Structural Basis For Regio- and Substrate Selectivity in Radical Amino Acid Halogenases To Be Published.