Nickel in PDB 6q56: Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk

All present enzymatic activity of Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk:
2.1.1.217;

The structure of Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk, PDB code: 6q56 was solved by C.Degut, M.Roovers, P.Barraud, F.Brachet, A.Feller, V.Larue, A.Al Refaii, J.Caillet, L.Droogmans, C.Tisne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.24 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.560, 51.980, 108.130, 90.00, 110.60, 90.00
R / Rfree (%)	21.2 / 23.7

The binding sites of Nickel atom in the Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk (pdb code 6q56). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk, PDB code: 6q56:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk


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 the B. Subtilis M1A22 Trna Methyltransferase Trmk within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:57.2 occ:1.00 ND1 A:HIS125 1.7 64.3 1.0 O A:HOH420 1.9 69.1 1.0 NE2 A:HIS128 1.9 45.4 1.0 CE1 A:HIS125 2.5 71.4 1.0 CD2 A:HIS128 2.7 36.0 1.0 CG A:HIS125 2.9 47.6 1.0 CE1 A:HIS128 3.1 30.7 1.0 O A:HOH459 3.1 29.7 1.0 CB A:HIS125 3.3 37.7 1.0 NE2 A:HIS125 3.7 64.9 1.0 CD2 A:HIS125 3.9 72.1 1.0 CG A:HIS128 3.9 37.5 1.0 ND1 A:HIS128 4.1 37.6 1.0 CB A:ALA99 4.3 31.8 1.0 O A:HOH468 4.3 55.6 1.0 CA A:HIS125 4.7 40.3 1.0 N A:ALA99 4.8 27.2 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk


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 the B. Subtilis M1A22 Trna Methyltransferase Trmk within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:64.8 occ:1.00 ND1 B:HIS125 1.4 69.0 1.0 NE2 B:HIS128 1.8 40.4 1.0 O B:HOH404 1.9 45.0 1.0 CE1 B:HIS125 2.2 72.9 1.0 O B:HOH427 2.3 53.6 1.0 CG B:HIS125 2.7 50.6 1.0 CD2 B:HIS128 2.8 35.8 1.0 CE1 B:HIS128 2.8 38.0 1.0 CB B:HIS125 3.4 43.6 1.0 NE2 B:HIS125 3.4 55.0 1.0 CD2 B:HIS125 3.6 47.5 1.0 O B:HOH448 3.7 33.9 1.0 ND1 B:HIS128 3.9 28.9 1.0 CG B:HIS128 3.9 31.6 1.0 CB B:ALA99 4.6 36.8 1.0 CA B:HIS125 4.8 37.3 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk


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 the B. Subtilis M1A22 Trna Methyltransferase Trmk within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:56.5 occ:1.00 ND1 C:HIS125 1.7 49.3 1.0 O C:HOH406 1.8 40.4 1.0 NE2 C:HIS128 2.0 36.6 1.0 CE1 C:HIS125 2.6 48.1 1.0 CD2 C:HIS128 2.9 29.7 1.0 CG C:HIS125 2.9 30.8 1.0 CE1 C:HIS128 3.1 34.5 1.0 O C:HOH478 3.2 31.5 1.0 CB C:HIS125 3.4 28.6 1.0 NE2 C:HIS125 3.7 54.0 1.0 CD2 C:HIS125 3.9 32.5 1.0 CG C:HIS128 4.1 29.0 1.0 ND1 C:HIS128 4.1 38.0 1.0 CB C:ALA99 4.5 31.4 1.0 CA C:HIS125 4.8 36.7 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the B. Subtilis M1A22 Trna Methyltransferase Trmk within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:53.1 occ:1.00 ND1 D:HIS125 1.7 64.0 1.0 NE2 D:HIS128 1.9 39.9 1.0 O D:HOH479 2.1 52.6 1.0 CG D:HIS125 2.7 38.5 1.0 CE1 D:HIS125 2.7 49.5 1.0 CD2 D:HIS128 2.8 30.2 1.0 CE1 D:HIS128 2.9 36.1 1.0 O D:HOH476 3.0 30.2 1.0 CB D:HIS125 3.1 34.7 1.0 NE2 D:HIS125 3.8 34.2 1.0 CD2 D:HIS125 3.8 44.9 1.0 CG D:HIS128 4.0 30.4 1.0 ND1 D:HIS128 4.0 39.0 1.0 CB D:ALA99 4.2 30.2 1.0 CA D:HIS125 4.6 35.0 1.0 N D:ALA99 4.8 23.7 1.0

C.Degut, M.Roovers, P.Barraud, F.Brachet, A.Feller, V.Larue, A.Al Refaii, J.Caillet, L.Droogmans, C.Tisne. Structural Characterization of B. Subtilis M1A22 Trna Methyltransferase Trmk: Insights Into Trna Recognition. Nucleic Acids Res. V. 47 4736 2019.
ISSN: ESSN 1362-4962
PubMed: 30931478
DOI: 10.1093/NAR/GKZ230