Magnesium in PDB 4lj0: NAB2 Zn Fingers Complexed with Polyadenosine

The structure of NAB2 Zn Fingers Complexed with Polyadenosine, PDB code: 4lj0 was solved by M.Stewart, S.I.Kuhlmann, E.Valkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.58 / 2.15
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.929, 90.929, 54.081, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 20.7

The structure of NAB2 Zn Fingers Complexed with Polyadenosine also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium atom in the NAB2 Zn Fingers Complexed with Polyadenosine (pdb code 4lj0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the NAB2 Zn Fingers Complexed with Polyadenosine, PDB code: 4lj0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:94.6 occ:1.00 OP1 C:A3 2.1 81.7 1.0 H3' C:A3 2.2 0.8 1.0 OP2 C:A4 2.4 0.1 1.0 C3' C:A3 3.1 99.8 1.0 H5'' C:A4 3.1 0.4 1.0 P C:A4 3.3 0.3 1.0 O5' C:A4 3.3 0.8 1.0 P C:A3 3.3 79.2 1.0 C5' C:A4 3.6 1.0 1.0 O3' C:A3 3.6 0.3 1.0 HO2' C:A3 3.8 0.2 1.0 H5' C:A4 3.8 0.4 1.0 H5'' C:A3 3.8 0.8 1.0 OP2 C:A3 3.8 85.6 1.0 H2' C:A3 3.9 0.4 1.0 C2' C:A3 3.9 0.3 1.0 O5' C:A3 4.0 93.1 1.0 HO2' C:A2 4.1 73.8 1.0 C4' C:A3 4.1 96.4 1.0 C5' C:A3 4.1 95.7 1.0 O2' C:A3 4.3 0.7 1.0 H4' C:A3 4.5 0.7 1.0 H3' C:A2 4.5 73.4 1.0 O3' C:A2 4.6 65.3 1.0 OP1 C:A4 4.7 0.4 1.0 O2' C:A2 4.8 61.5 1.0 C3' C:A2 5.0 61.2 1.0

Magnesium binding site 2 out of 4 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:89.0 occ:1.00 OP2 C:A3 2.3 85.6 1.0 OP2 D:A3 2.4 82.8 1.0 P D:A3 3.8 88.7 1.0 O D:HOH201 3.8 64.2 1.0 P C:A3 3.8 79.2 1.0 H3' D:A3 4.1 0.9 1.0 O5' D:A3 4.2 0.3 1.0 H2' D:A3 4.3 0.7 1.0 HO2' D:A3 4.4 0.2 1.0 H2' C:A3 4.5 0.4 1.0 OP1 D:A3 4.5 88.0 1.0 O3' C:A2 4.6 65.3 1.0 OP2 D:A4 4.6 0.4 1.0 OP1 C:A3 4.6 81.7 1.0 O5' C:A3 4.7 93.1 1.0 O3' D:A2 4.9 65.4 1.0 C2' D:A3 4.9 96.4 1.0 C3' D:A3 4.9 0.6 1.0 HZ1 A:LYS447 4.9 0.4 1.0

Magnesium binding site 3 out of 4 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:86.1 occ:1.00 OP1 C:A2 2.2 65.9 1.0 P C:A2 3.7 63.0 1.0 H3' C:A1 3.7 68.8 1.0 H4' C:A3 4.1 0.7 1.0 OP2 C:A2 4.4 65.2 1.0 H5' C:A3 4.4 0.8 1.0 O5' C:A2 4.5 72.1 1.0 C3' C:A1 4.6 57.4 1.0 O3' C:A1 4.7 63.7 1.0 H5'' C:A1 4.9 64.4 1.0 C4' C:A3 4.9 96.4 1.0

Magnesium binding site 4 out of 4 in the NAB2 Zn Fingers Complexed with Polyadenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of NAB2 Zn Fingers Complexed with Polyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:90.7 occ:1.00 O D:HOH203 2.3 69.5 1.0 OP2 D:A4 2.6 0.4 1.0 OP1 D:A3 2.9 88.0 1.0 P D:A4 3.8 0.8 1.0 P D:A3 4.0 88.7 1.0 OP1 D:A4 4.1 0.8 1.0 H5' D:A4 4.2 0.4 1.0 O2' D:A2 4.2 71.6 1.0 OP2 D:A3 4.2 82.8 1.0 H3' D:A3 4.3 0.9 1.0 H5'' D:A4 4.3 0.4 1.0 H3' D:A2 4.4 80.3 1.0 C5' D:A4 4.6 0.0 1.0 O5' D:A4 4.7 0.8 1.0 HO2' D:A2 4.8 85.9 1.0 O3' D:A2 4.8 65.4 1.0 C3' D:A2 4.9 67.0 1.0 O3' D:A3 4.9 0.6 1.0 C2' D:A2 5.0 70.3 1.0

S.I.Kuhlmann, E.Valkov, M.Stewart. Structural Basis For the Molecular Recognition of Polyadenosine Rna By NAB2 Zn Fingers. Nucleic Acids Res. V. 42 672 2014.
ISSN: ISSN 0305-1048
PubMed: 24071581
DOI: 10.1093/NAR/GKT876