Nickel in PDB 6ec3: Crystal Structure of EVDMO1

The structure of Crystal Structure of EVDMO1, PDB code: 6ec3 was solved by K.M.Mcculloch, T.M.Iverson, C.A.Starbird, N.A.Perry, Q.Chen, S.Berndt, I.Yamakawa, L.V.Loukachevitch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 3.35
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	191.633, 191.633, 269.618, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.6

The binding sites of Nickel atom in the Crystal Structure of EVDMO1 (pdb code 6ec3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of EVDMO1, PDB code: 6ec3:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of EVDMO1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of EVDMO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni500 b:0.8 occ:1.00 NE2 A:HIS420 2.1 0.8 1.0 NE2 A:HIS349 2.2 0.5 1.0 OD1 A:ASP351 2.3 1.0 1.0 CE1 A:HIS349 2.7 0.4 1.0 C6 A:BTB501 3.0 0.8 1.0 CD2 A:HIS420 3.1 0.1 1.0 CE1 A:HIS420 3.1 0.2 1.0 CG A:ASP351 3.2 0.0 1.0 O6 A:BTB501 3.3 0.5 1.0 CD2 A:HIS349 3.4 0.2 1.0 OD2 A:ASP351 3.4 0.7 1.0 C5 A:BTB501 3.8 0.1 1.0 ND1 A:HIS349 3.9 0.1 1.0 ND1 A:HIS420 4.2 0.2 1.0 CG A:HIS420 4.2 0.8 1.0 CG A:HIS349 4.3 0.2 1.0 CB A:ASP351 4.6 0.5 1.0 CA A:ASP351 4.9 0.9 1.0 N A:ASP351 4.9 0.3 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of EVDMO1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of EVDMO1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni500 b:0.0 occ:1.00 NE2 B:HIS420 2.1 0.3 1.0 NE2 B:HIS349 2.2 0.0 1.0 OD1 B:ASP351 2.4 0.4 1.0 CE1 B:HIS349 2.8 0.5 1.0 CD2 B:HIS420 3.1 0.7 1.0 CE1 B:HIS420 3.1 0.0 1.0 O6 B:BTB501 3.4 0.0 1.0 CG B:ASP351 3.4 0.3 1.0 CD2 B:HIS349 3.4 0.2 1.0 OD2 B:ASP351 3.7 0.3 1.0 ND1 B:HIS349 4.0 0.2 1.0 ND1 B:HIS420 4.2 0.1 1.0 CG B:HIS420 4.2 0.9 1.0 CG B:HIS349 4.3 0.3 1.0 C6 B:BTB501 4.5 0.1 1.0 CB B:ASP351 4.8 0.5 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of EVDMO1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of EVDMO1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni500 b:0.9 occ:1.00 NE2 C:HIS420 2.0 0.8 1.0 NE2 C:HIS349 2.2 0.7 1.0 OD1 C:ASP351 2.3 1.0 1.0 CE1 C:HIS349 2.7 0.5 1.0 CD2 C:HIS420 3.0 0.7 1.0 CE1 C:HIS420 3.0 1.0 1.0 CG C:ASP351 3.3 0.1 1.0 CD2 C:HIS349 3.4 0.7 1.0 OD2 C:ASP351 3.5 0.7 1.0 ND1 C:HIS349 4.0 99.8 1.0 C1 C:BTB501 4.1 0.9 1.0 ND1 C:HIS420 4.1 0.3 1.0 CG C:HIS420 4.2 0.4 1.0 O1 C:BTB501 4.2 0.2 1.0 CG C:HIS349 4.3 0.9 1.0 CB C:ASP351 4.6 0.2 1.0 O6 C:BTB501 4.9 0.4 1.0

C.A.Starbird, N.A.Perry, Q.Chen, S.Berndt, I.Yamakawa, L.V.Loukachevitch, E.M.Limbrick, B.O.Bachmann, T.M.Iverson, K.M.Mcculloch. The Structure of the Bifunctional Everninomicin Biosynthetic Enzyme EVDMO1 Suggests Independent Activity of the Fused Methyltransferase-Oxidase Domains. Biochemistry V. 57 6827 2018.
ISSN: ISSN 1520-4995
PubMed: 30525509
DOI: 10.1021/ACS.BIOCHEM.8B00836