Nickel in PDB 6n95: Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa, PDB code: 6n95 was solved by L.M.Stunkard, A.D.Dixon, T.J.Huth, J.R.Lohman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.927, 114.421, 193.430, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.2

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Nickel atom in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa (pdb code 6n95). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa, PDB code: 6n95:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:41.8 occ:1.00 NE2 B:HIS220 2.0 41.9 1.0 NE2 A:HIS220 2.0 35.7 1.0 NE2 C:HIS220 2.2 34.4 1.0 O C:HOH557 2.4 44.8 1.0 O B:HOH571 2.5 48.7 1.0 CE1 B:HIS220 2.9 45.3 1.0 CE1 C:HIS220 3.0 38.6 1.0 CE1 A:HIS220 3.0 41.9 1.0 CD2 A:HIS220 3.1 34.1 1.0 CD2 B:HIS220 3.1 36.1 1.0 CD2 C:HIS220 3.2 37.4 1.0 ND1 B:HIS220 4.0 40.1 1.0 ND1 C:HIS220 4.1 40.3 1.0 ND1 A:HIS220 4.1 38.3 1.0 CG B:HIS220 4.1 31.0 1.0 CG A:HIS220 4.2 28.0 1.0 CG C:HIS220 4.2 30.0 1.0 O A:HOH634 4.5 58.7 1.0 O B:HOH543 4.7 33.2 1.0 O B:HOH558 4.7 36.6 1.0 O A:HOH553 4.8 37.0 1.0 O C:HOH670 4.9 45.3 1.0 O C:HOH464 4.9 36.7 1.0 O C:HOH440 5.0 33.8 1.0 O A:HOH570 5.0 36.8 1.0

Nickel binding site 2 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:39.5 occ:1.00 NE2 D:HIS220 2.1 34.6 1.0 NE2 E:HIS220 2.1 35.1 1.0 NE2 F:HIS220 2.1 37.8 1.0 O F:HOH608 2.4 43.7 1.0 CE1 D:HIS220 2.9 39.5 1.0 CE1 E:HIS220 3.0 40.6 1.0 CE1 F:HIS220 3.0 45.4 1.0 CD2 E:HIS220 3.2 32.1 1.0 CD2 F:HIS220 3.2 34.2 1.0 CD2 D:HIS220 3.2 38.1 1.0 ND1 D:HIS220 4.0 43.0 1.0 ND1 E:HIS220 4.1 39.4 1.0 ND1 F:HIS220 4.2 42.2 1.0 CG E:HIS220 4.2 29.8 1.0 CG D:HIS220 4.2 31.3 1.0 CG F:HIS220 4.3 28.9 1.0 O E:HOH658 4.8 42.9 1.0 O E:HOH499 4.8 37.5 1.0 O D:HOH504 4.8 39.5 1.0 O F:HOH615 4.9 53.6 1.0 O F:HOH552 4.9 31.4 1.0 O E:HOH653 4.9 42.9 1.0

L.M.Stunkard, A.D.Dixon, T.J.Huth, J.R.Lohman. Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-Coa Decarboxylase Structure-Function Studies. J. Am. Chem. Soc. V. 141 5121 2019.
ISSN: ESSN 1520-5126
PubMed: 30869886
DOI: 10.1021/JACS.9B00650