Nickel in PDB 5zq8: Crystal Structure of Sprlmcd with U747 Stemloop Rna

The structure of Crystal Structure of Sprlmcd with U747 Stemloop Rna, PDB code: 5zq8 was solved by Y.Y.Jiang, H.L.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.37 / 2.18
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.230, 62.259, 79.818, 74.58, 85.47, 65.03
R / Rfree (%)	24.5 / 30.3

The binding sites of Nickel atom in the Crystal Structure of Sprlmcd with U747 Stemloop Rna (pdb code 5zq8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Sprlmcd with U747 Stemloop Rna, PDB code: 5zq8:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Sprlmcd with U747 Stemloop Rna


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 Sprlmcd with U747 Stemloop Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:50.4 occ:1.00 NE2 B:HIS440 2.3 34.3 1.0 NE2 B:HIS17 2.5 55.1 1.0 CD2 B:HIS440 3.2 32.0 1.0 CD2 B:HIS17 3.3 51.2 1.0 CE1 B:HIS440 3.3 32.0 1.0 CE1 B:HIS17 3.5 56.5 1.0 CE1 B:HIS441 4.2 26.9 1.0 CG B:HIS440 4.3 28.4 1.0 ND1 B:HIS440 4.4 29.2 1.0 CG B:HIS17 4.5 52.5 1.0 ND1 B:HIS17 4.5 51.5 1.0 NE2 B:HIS441 4.6 26.6 1.0 ND1 B:HIS441 4.7 26.1 1.0 CG B:GLU18 5.0 53.5 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Sprlmcd with U747 Stemloop Rna


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 Sprlmcd with U747 Stemloop Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:50.3 occ:1.00 NE2 A:HIS440 2.2 34.9 1.0 NE2 A:HIS17 2.6 39.8 1.0 CD2 A:HIS440 3.1 34.2 1.0 CE1 A:HIS440 3.2 35.3 1.0 CD2 A:HIS17 3.3 36.5 1.0 CE1 A:HIS17 3.7 39.5 1.0 CE1 A:HIS441 4.2 26.3 1.0 CG A:HIS440 4.3 31.5 1.0 ND1 A:HIS440 4.3 34.6 1.0 CG A:HIS17 4.5 36.0 1.0 NE2 A:HIS441 4.6 25.5 1.0 ND1 A:HIS17 4.7 38.6 1.0 ND1 A:HIS441 4.8 26.1 1.0

Y.Jiang, H.Yu, F.Li, L.Cheng, L.Zhu, Y.Shi, Q.Gong. Unveiling the Structural Features That Determine the Dual Methyltransferase Activities of Streptococcus Pneumoniae Rlmcd Plos Pathog. V. 14 07379 2018.
ISSN: ESSN 1553-7374
PubMed: 30388185
DOI: 10.1371/JOURNAL.PPAT.1007379