Nickel in PDB 6c1w: A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase

All present enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase:
5.1.2.1;

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase, PDB code: 6c1w was solved by M.Fellner, B.Desguin, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.55 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.365, 157.897, 158.988, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 26.3

The binding sites of Nickel atom in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase (pdb code 6c1w). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase, PDB code: 6c1w:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:74.1 occ:1.00 S7 A:ENJ501 2.4 48.1 1.0 S2 A:ENJ501 2.4 51.4 1.0 C4 A:ENJ501 2.4 51.8 1.0 NE2 A:HIS200 2.5 50.3 1.0 C3 A:ENJ501 2.9 47.8 1.0 C5 A:ENJ501 2.9 49.0 1.0 C7 A:ENJ501 3.0 47.1 1.0 C1 A:ENJ501 3.1 51.1 1.0 CG A:PRO188 3.3 48.0 1.0 CD2 A:HIS200 3.4 51.0 1.0 CE1 A:HIS200 3.6 47.1 1.0 S A:ENJ501 3.8 66.7 1.0 C2 A:ENJ501 4.0 48.1 1.0 C6 A:ENJ501 4.0 43.5 1.0 CB A:PRO188 4.0 45.9 1.0 CZ A:PHE176 4.0 46.9 1.0 O A:ENJ501 4.1 57.0 1.0 NZ A:LYS184 4.3 47.3 1.0 O2 A:ENJ501 4.3 50.2 1.0 CD A:PRO188 4.3 45.0 1.0 O21 A:ENJ501 4.4 55.9 1.0 N1 A:ENJ501 4.6 48.8 1.0 CG A:HIS200 4.6 50.8 1.0 CE2 A:PHE176 4.6 44.9 1.0 ND1 A:HIS200 4.6 49.4 1.0 NE1 A:TRP358 4.7 53.6 1.0 OH A:TYR294 5.0 58.9 1.0

Nickel binding site 2 out of 3 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:51.5 occ:1.00 C4 B:4EY501 2.0 50.2 1.0 NE2 B:HIS200 2.2 45.4 1.0 S7 B:4EY501 2.3 39.6 1.0 S2 B:4EY501 2.4 47.4 1.0 C3 B:4EY501 2.8 50.2 1.0 C5 B:4EY501 3.0 49.7 1.0 C7 B:4EY501 3.0 47.7 1.0 CD2 B:HIS200 3.0 42.9 1.0 O4 B:SO4503 3.2 48.7 0.7 C1 B:4EY501 3.2 44.3 1.0 CE1 B:HIS200 3.2 41.0 1.0 CG B:PRO188 3.5 45.3 1.0 CZ B:PHE176 4.0 46.6 1.0 C2 B:4EY501 4.1 46.0 1.0 CB B:PRO188 4.2 42.5 1.0 C6 B:4EY501 4.2 44.5 1.0 CG B:HIS200 4.2 43.7 1.0 S B:SO4503 4.3 60.9 0.7 ND1 B:HIS200 4.3 40.4 1.0 NZ B:LYS184 4.4 47.0 1.0 O2 B:4EY501 4.4 51.4 1.0 O3 B:SO4503 4.4 55.9 0.7 CD B:PRO188 4.5 43.4 1.0 NE1 B:TRP358 4.5 48.2 1.0 CE2 B:PHE176 4.6 46.6 1.0 N1 B:4EY501 4.6 44.5 1.0 O2 B:SO4503 4.7 52.7 0.7 CD1 B:TRP358 4.9 47.4 1.0 CE B:LYS184 5.0 41.1 1.0 OH B:TYR294 5.0 51.5 1.0

Nickel binding site 3 out of 3 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni502 b:60.1 occ:1.00 NE2 C:HIS200 2.0 52.3 1.0 C4 C:4EY501 2.1 52.8 1.0 S7 C:4EY501 2.3 50.8 1.0 S2 C:4EY501 2.4 57.4 1.0 C3 C:4EY501 2.9 53.6 1.0 CE1 C:HIS200 3.0 50.8 1.0 C5 C:4EY501 3.0 51.4 1.0 CD2 C:HIS200 3.0 52.0 1.0 C7 C:4EY501 3.1 51.0 1.0 C1 C:4EY501 3.2 50.2 1.0 CG C:PRO188 3.5 46.7 1.0 CZ C:PHE176 3.8 53.0 1.0 O2 C:SO3503 3.9 56.3 0.8 S C:SO3503 4.1 65.6 0.8 ND1 C:HIS200 4.1 55.1 1.0 CG C:HIS200 4.2 54.0 1.0 C2 C:4EY501 4.2 51.0 1.0 O1 C:SO3503 4.3 57.2 0.8 CB C:PRO188 4.3 44.8 1.0 C6 C:4EY501 4.3 48.6 1.0 CD C:PRO188 4.4 50.4 1.0 CE2 C:PHE176 4.4 53.4 1.0 O2 C:4EY501 4.4 50.6 1.0 NZ C:LYS184 4.5 53.3 1.0 NE1 C:TRP358 4.6 53.9 1.0 N1 C:4EY501 4.8 54.0 1.0 OH C:TYR294 4.9 55.4 1.0 CE1 C:PHE176 4.9 49.3 1.0 CD1 C:TRP358 4.9 52.0 1.0

J.A.Rankin, R.C.Mauban, M.Fellner, B.Desguin, J.Mccracken, J.Hu, S.A.Varganov, R.P.Hausinger. Lactate Racemase Nickel-Pincer Cofactor Operates By A Proton-Coupled Hydride Transfer Mechanism. Biochemistry V. 57 3244 2018.
ISSN: ISSN 1520-4995
PubMed: 29489337
DOI: 10.1021/ACS.BIOCHEM.8B00100