Nickel in PDB 8big: O-Methyltransferase PLU4895 in Complex with Sah

The structure of O-Methyltransferase PLU4895 in Complex with Sah, PDB code: 8big was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.06, 95.9, 522.99, 90, 90, 90
R / Rfree (%)	24.2 / 28.8

The structure of O-Methyltransferase PLU4895 in Complex with Sah also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Nickel atom in the O-Methyltransferase PLU4895 in Complex with Sah (pdb code 8big). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the O-Methyltransferase PLU4895 in Complex with Sah, PDB code: 8big:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the O-Methyltransferase PLU4895 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of O-Methyltransferase PLU4895 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:89.1 occ:1.00 O B:HOH1009 2.2 60.4 1.0 NE2 A:HIS301 2.4 64.2 1.0 NE2 B:HIS301 2.7 61.2 1.0 NZ B:LYS303 2.8 68.8 1.0 CE1 A:HIS301 3.0 64.0 1.0 CD2 B:HIS301 3.1 61.2 1.0 CE B:LYS303 3.2 68.2 1.0 CD A:LYS303 3.2 68.5 1.0 CG A:LYS303 3.5 66.7 1.0 CB A:LYS303 3.5 65.6 1.0 CD2 A:HIS301 3.6 63.9 1.0 CE1 B:HIS301 3.7 60.9 1.0 CE A:LYS303 3.8 69.7 1.0 CG2 A:ILE157 4.1 64.5 1.0 CG B:HIS301 4.2 60.6 1.0 ND1 A:HIS301 4.2 63.2 1.0 ND1 B:HIS301 4.5 60.6 1.0 NZ A:LYS303 4.5 70.9 1.0 CG A:HIS301 4.6 63.2 1.0 CD B:LYS303 4.6 67.3 1.0 CA A:LYS303 4.8 64.7 1.0 O A:TYR302 4.9 62.8 1.0

Nickel binding site 2 out of 4 in the O-Methyltransferase PLU4895 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of O-Methyltransferase PLU4895 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni402 b:96.6 occ:1.00 O D:HOH509 2.1 69.5 1.0 O D:HOH508 2.4 54.4 1.0 NE2 D:HIS301 2.4 72.4 1.0 CE1 D:HIS301 3.2 72.3 1.0 CD2 D:HIS301 3.4 72.0 1.0 ND1 D:HIS301 4.2 71.8 1.0 CG D:HIS301 4.3 71.4 1.0 CD D:LYS303 4.6 79.2 1.0

Nickel binding site 3 out of 4 in the O-Methyltransferase PLU4895 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of O-Methyltransferase PLU4895 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni403 b:108.5 occ:1.00 CE D:LYS162 3.5 82.7 1.0 N D:ASP159 3.6 78.8 1.0 NZ D:LYS162 3.6 82.8 1.0 CD1 D:TYR158 3.8 74.0 1.0 CE1 D:TYR158 4.0 73.7 1.0 CB D:ASP159 4.0 80.9 1.0 O D:ASP159 4.3 80.2 1.0 CA D:TYR158 4.3 76.4 1.0 CA D:ASP159 4.3 80.1 1.0 CG D:TYR158 4.4 74.3 1.0 C D:TYR158 4.5 77.6 1.0 CZ D:TYR158 4.6 73.8 1.0 O D:ILE157 4.6 76.8 1.0 OE1 D:GLU313 4.7 69.3 1.0 CD D:LYS162 4.8 82.7 1.0 C D:ASP159 4.8 80.0 1.0 OE2 D:GLU313 4.8 71.8 1.0 CB D:TYR158 5.0 75.1 1.0 CD2 D:TYR158 5.0 74.2 1.0

Nickel binding site 4 out of 4 in the O-Methyltransferase PLU4895 in Complex with Sah


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of O-Methyltransferase PLU4895 in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni402 b:93.0 occ:1.00 O G:HOH505 2.1 73.2 1.0 NE2 G:HIS301 2.4 85.9 1.0 NE2 E:HIS301 2.4 84.0 1.0 O E:HOH504 2.5 72.3 1.0 CE1 G:HIS301 3.1 85.8 1.0 CE1 E:HIS301 3.2 84.1 1.0 CD2 E:HIS301 3.3 83.9 1.0 CD2 G:HIS301 3.3 86.4 1.0 CD G:LYS303 3.8 94.7 1.0 ND1 G:HIS301 4.2 85.8 1.0 NZ G:LYS303 4.2 97.2 1.0 ND1 E:HIS301 4.3 83.7 1.0 CG G:HIS301 4.3 86.1 1.0 CG E:HIS301 4.4 83.6 1.0 CE G:LYS303 4.7 95.9 1.0 CD E:LYS303 4.8 89.6 1.0 CG2 E:ILE157 4.8 104.0 1.0 CB G:LYS303 4.8 92.4 1.0 CG G:LYS303 4.9 93.3 1.0

E.M.Huber, L.Kreling, A.K.Heinrich, M.Duennebacke, A.Poethig, H.B.Bode, M.Groll. A Set of Closely Related Methyltransferases For Site-Specific Tailoring of Anthraquinone Pigments Structure 2023.
ISSN: ISSN 0969-2126