Nickel in PDB 6ya4: Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine

The structure of Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine, PDB code: 6ya4 was solved by M.T.Batuecas, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.07 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.612, 304.386, 128.383, 90, 90, 90
R / Rfree (%)	20 / 24

The binding sites of Nickel atom in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine (pdb code 6ya4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 7 binding sites of Nickel where determined in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine, PDB code: 6ya4:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7;

Nickel binding site 1 out of 7 in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine


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 Pnra From S. Pneumoniae in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni402 b:21.9 occ:1.00 CE1 C:HIS5 2.1 22.4 1.0 O C:GLY2 2.1 24.0 1.0 N C:GLY2 2.1 25.5 1.0 C C:GLY2 2.8 24.3 1.0 NE2 C:HIS5 2.9 23.7 1.0 CA C:GLY2 2.9 24.3 1.0 ND1 C:HIS5 3.1 23.4 1.0 N C:SER3 4.1 24.4 1.0 CD2 C:HIS5 4.2 20.3 1.0 CG C:HIS5 4.2 22.5 1.0 CA C:SER3 5.0 24.5 1.0

Nickel binding site 2 out of 7 in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine


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 Pnra From S. Pneumoniae in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni403 b:20.9 occ:1.00 CE1 C:HIS9 2.1 19.4 1.0 CE1 C:HIS7 2.1 27.3 1.0 NE2 C:HIS7 2.9 27.6 1.0 NE2 C:HIS9 3.0 19.6 1.0 ND1 C:HIS9 3.1 21.6 1.0 ND1 C:HIS7 3.3 28.9 1.0 CD2 C:HIS7 4.1 24.9 1.0 CD2 C:HIS9 4.2 17.7 1.0 CG C:HIS9 4.2 19.9 1.0 CG C:HIS7 4.3 26.3 1.0

Nickel binding site 3 out of 7 in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine


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 Pnra From S. Pneumoniae in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:37.5 occ:1.00 NE2 A:HIS9 1.9 41.8 1.0 NE2 A:HIS7 2.2 50.4 1.0 CE1 A:HIS7 2.3 53.6 1.0 CD2 A:HIS9 2.9 41.9 1.0 CE1 A:HIS9 3.0 40.8 1.0 ND1 A:HIS7 3.5 55.5 1.0 CD2 A:HIS7 3.6 54.5 1.0 CG A:HIS9 4.0 41.4 1.0 ND1 A:HIS9 4.0 39.5 1.0 CG A:HIS7 4.2 55.5 1.0

Nickel binding site 4 out of 7 in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine


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 Pnra From S. Pneumoniae in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:38.0 occ:1.00 O A:GLY2 2.0 29.7 1.0 CE1 A:HIS5 2.1 49.2 1.0 N A:GLY2 2.4 39.0 1.0 NE2 A:HIS5 2.9 47.0 1.0 C A:GLY2 2.9 35.9 1.0 CA A:GLY2 3.1 36.2 1.0 ND1 A:HIS5 3.2 45.8 1.0 CD2 A:HIS5 4.1 50.0 1.0 N A:SER3 4.2 32.8 1.0 CG A:HIS5 4.3 45.8 1.0 CA A:SER3 5.0 42.5 1.0

Nickel binding site 5 out of 7 in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:16.7 occ:1.00 NE2 B:HIS9 2.0 19.6 1.0 NE2 B:HIS7 2.1 21.1 1.0 CD2 B:HIS9 3.0 19.7 1.0 CE1 B:HIS9 3.0 22.8 1.0 CD2 B:HIS7 3.0 21.5 1.0 CE1 B:HIS7 3.1 20.4 1.0 ND1 B:HIS9 4.1 21.6 1.0 CG B:HIS9 4.1 21.5 1.0 CG B:HIS7 4.2 22.5 1.0 ND1 B:HIS7 4.2 20.8 1.0 C3 B:PEG403 4.8 46.0 1.0

Nickel binding site 6 out of 7 in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni402 b:25.8 occ:1.00 CE1 D:HIS7 1.8 26.6 1.0 CE1 D:HIS9 2.2 36.8 1.0 NE2 D:HIS7 2.6 27.2 1.0 ND1 D:HIS7 2.9 29.4 1.0 ND1 D:HIS9 3.1 35.8 1.0 NE2 D:HIS9 3.2 37.9 1.0 CD2 D:HIS7 3.9 25.9 1.0 CG D:HIS7 4.0 30.7 1.0 CG D:HIS9 4.3 39.2 1.0 CD2 D:HIS9 4.3 36.8 1.0

Nickel binding site 7 out of 7 in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Pnra From S. Pneumoniae in Complex with Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni403 b:99.7 occ:1.00 CE1 D:HIS8 2.8 34.1 1.0 O D:HOH513 2.9 44.0 1.0 CE1 D:HIS10 3.1 34.6 1.0 NE2 D:HIS8 3.3 28.6 1.0 ND1 D:HIS10 3.5 33.1 1.0 ND1 D:HIS8 3.9 30.0 1.0 O D:HOH544 4.3 47.8 1.0 NE2 D:HIS10 4.4 33.2 1.0 CD2 D:HIS8 4.5 32.1 1.0 CG D:HIS10 4.8 33.6 1.0 CG D:HIS8 4.8 31.5 1.0

M.R.Abdullah, M.T.Batuecas, F.Jennert, F.Voss, P.Westhoff, T.P.Kohler, R.Molina, S.Hirschmann, M.Lalk, J.A.Hermoso, S.Hammerschmidt. Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-Binding Protein Pnra. J.Mol.Biol. V. 433 66723 2021.
ISSN: ESSN 1089-8638
PubMed: 33242497
DOI: 10.1016/J.JMB.2020.11.022