Nickel in PDB 6n92: Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Coa

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Coa, PDB code: 6n92 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)	29.36 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.009, 114.319, 194.355, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.4

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

Potassium

(K)

1 atom

The binding sites of Nickel atom in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Coa (pdb code 6n92). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Coa, PDB code: 6n92:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-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-Nitronate-Propionyl- Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:23.2 occ:1.00 NE2 A:HIS220 2.0 22.0 1.0 NE2 C:HIS220 2.0 23.9 1.0 NE2 B:HIS220 2.0 23.6 1.0 O C:HOH606 2.3 28.4 1.0 O A:HOH591 2.3 32.7 1.0 O C:HOH626 2.3 38.8 1.0 CE1 B:HIS220 2.9 29.6 1.0 CE1 C:HIS220 2.9 28.9 1.0 CD2 A:HIS220 3.0 21.5 1.0 CE1 A:HIS220 3.0 29.5 1.0 CD2 C:HIS220 3.0 22.5 1.0 CD2 B:HIS220 3.1 20.0 1.0 O B:HOH714 3.9 24.7 0.5 O A:HOH740 4.0 15.3 0.2 ND1 C:HIS220 4.0 28.3 1.0 ND1 B:HIS220 4.1 25.6 1.0 ND1 A:HIS220 4.1 26.8 1.0 CG A:HIS220 4.1 18.4 1.0 CG C:HIS220 4.1 19.1 1.0 CG B:HIS220 4.2 19.7 1.0 O A:HOH673 4.3 23.4 0.5 O B:HOH570 4.8 28.5 1.0 O B:HOH714 4.8 19.2 0.5 O A:HOH740 4.8 33.5 0.8 O B:HOH487 5.0 30.6 1.0 O A:HOH532 5.0 29.3 1.0 O C:HOH430 5.0 21.2 1.0

Nickel binding site 2 out of 3 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-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-Nitronate-Propionyl- Coa within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:22.9 occ:1.00 NE2 F:HIS220 2.0 21.6 1.0 NE2 D:HIS220 2.0 23.6 1.0 NE2 E:HIS220 2.0 21.8 1.0 O F:HOH599 2.2 32.0 1.0 O D:HOH603 2.2 30.2 1.0 O F:HOH635 2.3 39.4 1.0 CE1 F:HIS220 2.9 31.0 1.0 CE1 D:HIS220 2.9 27.6 1.0 CE1 E:HIS220 3.0 27.4 1.0 CD2 F:HIS220 3.0 22.6 1.0 CD2 E:HIS220 3.0 20.2 1.0 CD2 D:HIS220 3.1 20.9 1.0 ND1 F:HIS220 4.1 29.5 1.0 ND1 D:HIS220 4.1 28.5 1.0 ND1 E:HIS220 4.1 27.8 1.0 CG F:HIS220 4.2 17.1 1.0 CG E:HIS220 4.2 18.3 1.0 CG D:HIS220 4.2 18.9 1.0 O F:HOH648 4.5 24.4 0.5 O D:HOH490 4.8 29.7 1.0 O D:HOH714 4.8 36.6 1.0 O D:HOH473 4.9 23.9 1.0 O E:HOH452 4.9 30.6 1.0 O F:HOH723 5.0 44.4 1.0

Nickel binding site 3 out of 3 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Coa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Coa within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni302 b:22.0 occ:1.00 OE1 F:GLU241 2.1 25.7 1.0 O F:HOH586 2.2 22.4 1.0 OS1 F:KG7304 2.2 21.2 1.0 N3 F:IMD305 2.2 39.4 1.0 NE2 F:HIS261 2.2 18.8 1.0 NS4 F:KG7304 2.2 22.7 1.0 CS1 F:KG7304 2.9 23.7 1.0 C2 F:IMD305 2.9 40.7 1.0 CS2 F:KG7304 2.9 24.7 1.0 CD F:GLU241 3.1 23.3 1.0 CD2 F:HIS261 3.1 20.6 1.0 OS4 F:KG7304 3.3 26.2 1.0 CE1 F:HIS261 3.3 21.1 1.0 C4 F:IMD305 3.3 43.2 1.0 OE2 F:GLU241 3.5 22.6 1.0 O F:HOH537 3.9 33.5 1.0 O F:HOH415 4.1 25.3 1.0 O F:KG7304 4.1 18.8 1.0 N1 F:IMD305 4.1 38.6 1.0 C5 F:IMD305 4.3 42.3 1.0 CG F:GLU241 4.3 20.7 1.0 CG F:HIS261 4.3 18.3 1.0 ND1 F:HIS261 4.3 19.1 1.0 CS3 F:KG7304 4.5 20.5 1.0 O F:HOH625 4.5 33.0 1.0 CB F:GLU241 4.6 17.6 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