Nickel in PDB 6n94: Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Amino(Dethia)-Coa

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Amino(Dethia)-Coa, PDB code: 6n94 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)	29.29 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.046, 114.816, 193.732, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.8

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Amino(Dethia)-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-Nitronate-Propionyl- Amino(Dethia)-Coa (pdb code 6n94). 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-Nitronate-Propionyl- Amino(Dethia)-Coa, PDB code: 6n94:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Amino(Dethia)-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-Nitronate-Propionyl- Amino(Dethia)-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:32.0 occ:1.00 NE2 A:HIS220 2.0 29.0 1.0 NE2 B:HIS220 2.0 34.8 1.0 NE2 C:HIS220 2.1 29.0 1.0 O C:HOH613 2.3 34.6 1.0 O A:HOH608 2.3 39.8 1.0 O A:HOH621 2.5 39.4 1.0 CE1 B:HIS220 2.9 39.5 1.0 CE1 A:HIS220 3.0 39.0 1.0 CD2 A:HIS220 3.0 28.4 1.0 CE1 C:HIS220 3.0 36.4 1.0 CD2 C:HIS220 3.1 26.4 1.0 CD2 B:HIS220 3.2 28.6 1.0 O B:HOH668 3.6 27.8 0.5 ND1 B:HIS220 4.1 37.4 1.0 ND1 A:HIS220 4.1 33.0 1.0 CG A:HIS220 4.1 23.8 1.0 ND1 C:HIS220 4.1 32.7 1.0 CG B:HIS220 4.2 28.5 1.0 CG C:HIS220 4.2 25.2 1.0 O A:HOH717 4.8 42.7 1.0 O B:HOH544 4.8 32.9 1.0 O B:HOH668 4.8 25.5 0.5 O B:HOH536 4.9 31.3 1.0 O A:HOH535 4.9 33.1 1.0 O A:HOH528 4.9 35.5 1.0 O C:HOH502 5.0 32.3 1.0

Nickel binding site 2 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Amino(Dethia)-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-Nitronate-Propionyl- Amino(Dethia)-Coa within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:30.8 occ:1.00 NE2 D:HIS220 2.0 26.0 1.0 NE2 F:HIS220 2.0 27.0 1.0 NE2 E:HIS220 2.1 25.4 1.0 O E:HOH577 2.2 36.8 1.0 O D:HOH586 2.3 42.8 1.0 O D:HOH601 2.4 43.8 1.0 CE1 F:HIS220 2.9 36.9 1.0 CE1 D:HIS220 3.0 33.4 1.0 CE1 E:HIS220 3.0 33.7 1.0 CD2 D:HIS220 3.1 24.5 1.0 CD2 E:HIS220 3.1 22.6 1.0 CD2 F:HIS220 3.1 27.4 1.0 ND1 D:HIS220 4.1 32.2 1.0 ND1 F:HIS220 4.1 34.8 1.0 ND1 E:HIS220 4.2 31.9 1.0 CG D:HIS220 4.2 24.2 1.0 CG F:HIS220 4.2 22.8 1.0 CG E:HIS220 4.2 24.2 1.0 O D:HOH692 4.6 39.1 1.0 O D:HOH519 4.8 36.1 1.0 O E:HOH553 4.8 34.3 1.0 O F:HOH609 4.8 48.6 1.0 O D:HOH489 4.8 36.8 1.0 O E:HOH697 4.8 36.1 1.0 O F:HOH684 4.9 42.2 1.0 O E:HOH461 5.0 28.6 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