Nickel in PDB 6yag: Crystal Structure of Pnra From S. Pneumoniae in Complex with Thymidine

The structure of Crystal Structure of Pnra From S. Pneumoniae in Complex with Thymidine, PDB code: 6yag 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)	49.21 / 2.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.966, 303.818, 128.417, 90, 90, 90
R / Rfree (%)	20.9 / 25.5

The binding sites of Nickel atom in the Crystal Structure of Pnra From S. Pneumoniae in Complex with Thymidine (pdb code 6yag). 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 Thymidine, PDB code: 6yag:
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 Thymidine


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 Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni501 b:18.5 occ:1.00 CE1 C:HIS7 2.2 26.8 1.0 CE1 C:HIS9 2.2 23.0 1.0 NE2 C:HIS9 2.7 20.9 1.0 NE2 C:HIS7 2.7 24.3 1.0 ND1 C:HIS7 3.3 27.9 1.0 ND1 C:HIS9 3.4 23.8 1.0 CD2 C:HIS7 4.0 24.2 1.0 CD2 C:HIS9 4.0 19.4 1.0 CG C:HIS7 4.3 25.1 1.0 CG C:HIS9 4.3 19.6 1.0

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


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 Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:46.1 occ:1.00 NE2 A:HIS10 1.9 56.0 1.0 CD2 A:HIS10 2.9 52.5 1.0 CE1 A:HIS10 3.0 54.7 1.0 CE1 A:HIS8 3.8 98.9 1.0 ND1 A:HIS8 3.8 95.5 1.0 ND1 A:HIS10 4.0 52.2 1.0 CG A:HIS10 4.0 54.3 1.0

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


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 Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:18.0 occ:1.00 NE2 B:HIS7 1.9 21.2 1.0 NE2 B:HIS9 2.0 20.1 1.0 CD2 B:HIS7 2.8 21.9 1.0 CE1 B:HIS7 2.9 20.6 1.0 CE1 B:HIS9 2.9 19.4 1.0 CD2 B:HIS9 3.1 19.8 1.0 CG B:HIS7 4.0 22.4 1.0 ND1 B:HIS7 4.0 20.2 1.0 ND1 B:HIS9 4.1 19.6 1.0 CG B:HIS9 4.1 20.1 1.0

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


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 Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:26.3 occ:1.00 NE2 B:HIS10 2.1 18.1 1.0 CE1 B:HIS8 2.2 22.1 1.0 NE2 B:HIS8 3.0 21.2 1.0 CD2 B:HIS10 3.1 18.8 1.0 CE1 B:HIS10 3.1 17.6 1.0 ND1 B:HIS8 3.2 21.6 1.0 CD2 B:HIS8 4.2 20.7 1.0 ND1 B:HIS10 4.2 18.9 1.0 CG B:HIS10 4.3 19.9 1.0 CG B:HIS8 4.3 22.9 1.0

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


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 Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:48.6 occ:1.00 CE1 D:HIS7 1.9 26.0 1.0 NE2 D:HIS7 2.2 24.2 1.0 NE2 D:HIS9 2.7 68.5 1.0 ND1 D:HIS7 3.1 34.6 1.0 CE1 D:HIS9 3.1 66.5 1.0 CD2 D:HIS7 3.5 31.9 1.0 CD2 D:HIS9 3.7 66.4 1.0 CG D:HIS7 4.0 36.2 1.0 ND1 D:HIS9 4.2 66.2 1.0 CG D:HIS9 4.5 62.5 1.0

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


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 Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni402 b:47.0 occ:1.00 NE2 D:HIS10 2.0 33.5 1.0 NE2 D:HIS8 2.3 45.3 1.0 CE1 D:HIS10 2.9 35.7 1.0 CE1 D:HIS8 3.0 48.9 1.0 CD2 D:HIS10 3.1 40.0 1.0 CD2 D:HIS8 3.5 44.7 1.0 ND1 D:HIS10 4.1 37.2 1.0 CG D:HIS10 4.2 40.3 1.0 ND1 D:HIS8 4.2 44.2 1.0 CG D:HIS8 4.5 42.3 1.0

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


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 Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni404 b:100.5 occ:1.00 OE1 D:GLU282 3.4 40.0 1.0 CD2 D:HIS52 3.4 50.2 1.0 CB D:HIS52 3.7 52.0 1.0 OE2 D:GLU282 3.7 38.4 1.0 CG D:HIS52 3.8 50.0 1.0 CD D:GLU282 3.9 45.5 1.0 CA D:GLY20 4.1 61.6 1.0 O D:HIS52 4.2 71.6 1.0 CD2 D:LEU54 4.4 62.4 1.0 CD1 D:LEU54 4.4 59.0 1.0 NE2 D:HIS52 4.6 46.9 1.0 O D:ALA21 4.6 55.2 1.0 CA D:HIS52 4.7 55.1 1.0 CG D:LEU54 4.7 60.6 1.0 N D:GLY20 4.7 58.2 1.0 C D:GLY20 4.8 62.5 1.0 C D:HIS52 4.9 60.5 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