Nickel in PDB 6n93: Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Oxa(Dethia)-Coa

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Oxa(Dethia)-Coa, PDB code: 6n93 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)	28.68 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.179, 114.653, 194.554, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.4

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Oxa(Dethia)-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- Oxa(Dethia)-Coa (pdb code 6n93). 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- Oxa(Dethia)-Coa, PDB code: 6n93:
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- Oxa(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- Oxa(Dethia)-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:23.6 occ:1.00 NE2 A:HIS220 2.0 21.9 1.0 NE2 B:HIS220 2.0 22.9 1.0 NE2 C:HIS220 2.0 20.7 1.0 O A:HOH612 2.4 11.7 0.5 O B:HOH608 2.4 14.2 0.5 N3 A:IMD303 2.4 41.6 1.0 CE1 A:HIS220 2.9 25.6 1.0 CE1 B:HIS220 2.9 26.6 1.0 CE1 C:HIS220 3.0 24.6 1.0 CD2 C:HIS220 3.0 19.4 1.0 CD2 B:HIS220 3.1 20.9 1.0 CD2 A:HIS220 3.1 20.4 1.0 C2 A:IMD303 3.3 43.9 1.0 C4 A:IMD303 3.4 42.0 1.0 O B:HOH608 3.7 22.3 0.5 O A:HOH612 3.8 22.0 0.5 ND1 A:HIS220 4.0 24.2 1.0 ND1 B:HIS220 4.1 24.1 1.0 ND1 C:HIS220 4.1 25.2 1.0 CG A:HIS220 4.2 17.9 1.0 CG C:HIS220 4.2 18.6 1.0 CG B:HIS220 4.2 19.9 1.0 N1 A:IMD303 4.5 38.8 1.0 C5 A:IMD303 4.5 43.1 1.0 O B:HOH566 4.9 26.7 1.0 O A:HOH728 4.9 40.5 1.0 O B:HOH508 5.0 26.4 1.0

Nickel binding site 2 out of 3 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Oxa(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- Oxa(Dethia)-Coa within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:21.3 occ:1.00 NE2 E:HIS220 1.9 19.2 1.0 NE2 D:HIS220 2.0 17.5 1.0 NE2 F:HIS220 2.0 19.3 1.0 O E:HOH592 2.2 34.8 1.0 O D:HOH507 2.4 30.8 1.0 O F:HOH634 2.4 35.0 1.0 CE1 E:HIS220 2.8 19.8 1.0 CE1 D:HIS220 2.9 22.6 1.0 CE1 F:HIS220 2.9 25.7 1.0 CD2 E:HIS220 3.0 17.2 1.0 CD2 F:HIS220 3.1 19.6 1.0 CD2 D:HIS220 3.1 18.2 1.0 ND1 E:HIS220 4.0 20.8 1.0 ND1 D:HIS220 4.1 23.0 1.0 ND1 F:HIS220 4.1 24.7 1.0 CG E:HIS220 4.1 15.7 1.0 CG D:HIS220 4.2 17.7 1.0 CG F:HIS220 4.2 16.4 1.0 O F:HOH646 4.5 19.2 0.5 O F:HOH718 4.7 42.3 1.0 O D:HOH708 4.8 30.1 1.0 O D:HOH501 4.8 35.1 1.0 O E:HOH529 4.9 30.3 1.0 O E:HOH710 5.0 30.2 1.0 O D:HOH476 5.0 27.8 1.0

Nickel binding site 3 out of 3 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Nitronate-Propionyl- Oxa(Dethia)-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- Oxa(Dethia)-Coa within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni302 b:21.0 occ:1.00 N3 F:IMD305 2.1 31.3 1.0 OE1 F:GLU241 2.2 26.5 1.0 O F:HOH556 2.2 24.6 1.0 OS1 F:KG7304 2.2 24.7 1.0 NE2 F:HIS261 2.2 18.1 1.0 NS4 F:KG7304 2.2 20.4 1.0 C2 F:IMD305 2.8 34.4 1.0 CS1 F:KG7304 2.9 22.2 1.0 CS2 F:KG7304 2.9 22.9 1.0 CD2 F:HIS261 3.1 19.7 1.0 CD F:GLU241 3.1 22.4 1.0 C4 F:IMD305 3.2 33.2 1.0 OS4 F:KG7304 3.2 25.2 1.0 CE1 F:HIS261 3.3 18.1 1.0 OE2 F:GLU241 3.5 22.7 1.0 O F:HOH602 4.0 37.0 1.0 N1 F:IMD305 4.0 33.4 1.0 O F:HOH405 4.1 25.2 1.0 O F:KG7304 4.1 21.2 1.0 C5 F:IMD305 4.2 33.4 1.0 CG F:HIS261 4.3 17.5 1.0 ND1 F:HIS261 4.3 18.0 1.0 CG F:GLU241 4.4 19.6 1.0 O F:HOH531 4.4 33.8 1.0 CS3 F:KG7304 4.5 19.8 1.0 CB F:GLU241 4.7 16.3 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