Magnesium in PDB 6jxm: Crystal Structure of PHI29 Prna Domain II

The structure of Crystal Structure of PHI29 Prna Domain II, PDB code: 6jxm was solved by R.Cai, I.R.Price, F.Ding, F.Wu, T.Chen, Y.Zhang, G.Liu, P.J.Jardine, C.Lu, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.18 / 3.32
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.178, 120.178, 187.494, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 26.5

The structure of Crystal Structure of PHI29 Prna Domain II also contains other interesting chemical elements:

Barium

(Ba)

15 atoms

The binding sites of Magnesium atom in the Crystal Structure of PHI29 Prna Domain II (pdb code 6jxm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of PHI29 Prna Domain II, PDB code: 6jxm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:0.2 occ:1.00 O6 B:G15 3.3 0.9 1.0 OP1 B:G7 3.6 0.2 1.0 N7 B:G15 3.6 0.4 1.0 C6 B:G15 4.0 0.6 1.0 C5 B:G15 4.1 0.1 1.0 O4 B:U8 4.2 0.5 1.0 OP2 B:A14 4.2 0.8 1.0 OP2 B:G15 4.5 0.4 1.0 C4 B:U8 4.6 0.8 1.0 C8 B:G15 4.7 0.7 1.0 P B:G7 5.0 0.7 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:0.8 occ:1.00 N7 B:G53 2.7 0.8 1.0 O6 B:G53 3.1 0.7 1.0 C5 B:G53 3.5 0.7 1.0 C6 B:G53 3.6 0.2 1.0 C8 B:G53 3.8 0.2 1.0 O4 B:U56 4.0 0.1 1.0 O6 B:G36 4.7 0.6 1.0 C4 B:G53 4.8 0.4 1.0 N1 B:G36 4.8 0.5 1.0 N9 B:G53 4.9 0.3 1.0 N1 B:G53 5.0 0.3 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:0.0 occ:1.00 OP2 B:G41 2.4 0.9 1.0 O4' B:C42 2.8 0.5 1.0 N3 B:U43 3.0 0.0 1.0 C5' B:C42 3.2 0.4 1.0 O5' B:C42 3.3 0.5 1.0 P B:G41 3.4 0.8 1.0 C2 B:U43 3.5 0.3 1.0 C4 B:U43 3.5 0.0 1.0 O5' B:G41 3.5 0.4 1.0 C4' B:C42 3.6 0.3 1.0 O2 B:U43 3.8 0.4 1.0 O4 B:U43 3.8 0.4 1.0 C1' B:C42 4.0 0.9 1.0 OP1 B:G41 4.0 0.8 1.0 N1 B:C42 4.1 0.5 1.0 C2 B:C42 4.3 0.1 1.0 N1 B:U43 4.3 0.7 1.0 C8 B:G41 4.3 0.2 1.0 C5 B:U43 4.3 0.8 1.0 O2 B:C42 4.4 1.0 1.0 N7 B:G41 4.4 0.3 1.0 C6 B:C42 4.6 0.2 1.0 C6 B:U43 4.6 0.3 1.0 C3' B:C42 4.7 0.6 1.0 O3' B:C40 4.8 0.6 1.0 C3' B:G41 4.9 0.3 1.0 P B:C42 4.9 1.0 1.0 C5' B:G41 4.9 0.3 1.0 N3 B:C42 4.9 0.3 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:0.9 occ:1.00 OP2 B:U58 4.3 0.9 1.0 OP1 B:U58 4.6 0.3 1.0 P B:U58 5.0 0.0 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:0.2 occ:1.00 N7 B:G66 3.0 0.9 1.0 O5' B:G65 3.3 0.9 1.0 OP2 B:G66 3.4 0.1 1.0 OP2 B:G65 3.6 0.4 1.0 C8 B:G66 3.7 0.6 1.0 MG B:MG107 3.9 0.3 1.0 P B:G65 3.9 0.1 1.0 C5 B:G66 4.1 0.2 1.0 OP1 B:G65 4.4 0.1 1.0 O6 B:G66 4.4 0.1 1.0 C5' B:G65 4.4 0.0 1.0 C8 B:G65 4.6 0.3 1.0 C3' B:G65 4.6 0.6 1.0 C6 B:G66 4.7 0.4 1.0 P B:G66 4.8 0.8 1.0 N7 B:G65 4.9 0.5 1.0 N9 B:G66 5.0 0.6 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:0.7 occ:1.00 O6 B:G3 3.6 0.8 1.0 N7 B:G3 3.6 0.7 1.0 O6 B:G4 3.7 0.5 1.0 C6 B:G3 4.1 0.9 1.0 C5 B:G3 4.1 0.1 1.0 N7 B:G4 4.1 0.1 1.0 C6 B:G4 4.5 0.5 1.0 C8 B:G3 4.6 0.3 1.0 C5 B:G4 4.7 0.1 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:0.3 occ:1.00 C5' B:G67 3.1 0.6 1.0 O5' B:G67 3.2 0.3 1.0 OP2 B:G66 3.6 0.1 1.0 C8 B:G66 3.6 0.6 1.0 O5' B:G66 3.7 0.2 1.0 N7 B:G66 3.9 0.9 1.0 MG B:MG105 3.9 0.2 1.0 C3' B:G66 4.1 0.9 1.0 P B:G66 4.3 0.8 1.0 N9 B:G66 4.5 0.6 1.0 P B:G67 4.5 0.1 1.0 C4' B:G67 4.6 0.5 1.0 OP2 B:G67 4.7 0.8 1.0 O3' B:G66 4.7 1.0 1.0 C2' B:G66 4.8 0.7 1.0 C5' B:G66 4.8 0.3 1.0 C5 B:G66 4.8 0.2 1.0 C4' B:G66 4.9 0.6 1.0 C8 B:G67 5.0 0.4 1.0 O4' B:G67 5.0 0.4 1.0

R.Cai, I.R.Price, F.Ding, F.Wu, T.Chen, Y.Zhang, G.Liu, P.J.Jardine, C.Lu, A.Ke. Atp/Adp Modulates GP16-Prna Conformational Change in the PHI29 Dna Packaging Motor. Nucleic Acids Res. V. 47 9818 2019.
ISSN: ESSN 1362-4962
PubMed: 31396619
DOI: 10.1093/NAR/GKZ692