Magnesium in PDB 7p9w: Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3

The structure of Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3, PDB code: 7p9w was solved by C.D.Suraweera, M.G.Hinds, M.Kvansakul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.25 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.772, 62.772, 92.592, 90, 90, 120
R / Rfree (%)	22 / 25.7

The structure of Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Magnesium atom in the Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3 (pdb code 7p9w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3, PDB code: 7p9w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg212 b:43.0 occ:1.00 HH11 A:ARG15 2.2 54.3 1.0 NH1 A:ARG15 3.0 45.0 1.0 HG3 A:ARG18 3.0 51.4 1.0 HD3 A:ARG15 3.2 44.7 1.0 HD2 A:ARG15 3.2 44.7 1.0 HH12 A:ARG15 3.3 54.3 1.0 HB2 A:PRO42 3.5 43.8 1.0 HG2 A:PRO42 3.6 48.8 1.0 HB2 A:ARG18 3.6 45.8 1.0 CD A:ARG15 3.6 37.0 1.0 HD2 A:ARG18 3.6 63.4 1.0 HB2 A:GLU43 3.6 69.6 1.0 HA A:ARG15 3.7 34.0 1.0 HB3 A:ARG18 3.7 45.8 1.0 CG A:ARG18 3.7 42.6 1.0 CB A:ARG18 3.9 37.9 1.0 CZ A:ARG15 4.0 46.9 1.0 CD A:ARG18 4.2 52.5 1.0 NE A:ARG15 4.3 40.4 1.0 CB A:PRO42 4.3 36.2 1.0 CG A:PRO42 4.3 40.4 1.0 HA A:GLU43 4.3 49.9 1.0 HE A:ARG18 4.4 63.5 1.0 N A:GLU43 4.5 35.0 1.0 CB A:GLU43 4.5 57.8 1.0 C A:PRO42 4.5 35.1 1.0 HG3 A:PRO42 4.6 48.8 1.0 HG2 A:ARG18 4.6 51.4 1.0 CA A:ARG15 4.6 28.1 1.0 O A:PRO42 4.6 34.2 1.0 HB2 A:ARG15 4.6 37.6 1.0 H A:GLU43 4.7 42.3 1.0 CA A:GLU43 4.7 41.3 1.0 HG3 A:GLU43 4.7 98.1 1.0 NE A:ARG18 4.7 52.7 1.0 CG A:ARG15 4.9 34.6 1.0 HG22 A:ILE14 4.9 39.0 1.0 CB A:ARG15 4.9 31.1 1.0 HD3 A:ARG18 5.0 63.4 1.0 OE1 A:GLU43 5.0 111.3 1.0

Magnesium binding site 2 out of 5 in the Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg213 b:46.8 occ:1.00 HH11 A:ARG131 2.6 35.4 1.0 HH22 A:ARG6 2.7 119.1 1.0 HG2 A:ARG131 2.7 28.9 1.0 HH12 A:ARG6 2.9 132.1 1.0 NH1 A:ARG131 3.2 29.3 1.0 HH12 A:ARG131 3.3 35.4 1.0 HB3 A:ARG131 3.4 31.3 1.0 OE2 A:GLU135 3.4 35.8 1.0 HA A:ARG131 3.5 31.8 1.0 NH2 A:ARG6 3.5 99.0 1.0 CG A:ARG131 3.5 23.9 1.0 NH1 A:ARG6 3.6 109.8 1.0 HD3 A:ARG131 3.7 35.0 1.0 HG3 A:GLU135 3.7 38.8 1.0 O A:HOH306 3.7 49.1 1.0 CB A:ARG131 3.8 25.9 1.0 CD A:ARG131 4.0 28.9 1.0 CZ A:ARG6 4.0 99.2 1.0 CD A:GLU135 4.1 29.6 1.0 CZ A:ARG131 4.1 26.1 1.0 CA A:ARG131 4.1 26.2 1.0 HH21 A:ARG6 4.2 119.1 1.0 CG A:GLU135 4.2 32.1 1.0 HG2 A:GLU135 4.3 38.8 1.0 HG3 A:ARG131 4.3 28.9 1.0 HH11 A:ARG6 4.3 132.1 1.0 NE A:ARG131 4.5 25.2 1.0 O A:ARG131 4.6 27.5 1.0 HB2 A:ARG131 4.7 31.3 1.0 C A:ARG131 4.9 25.3 1.0 HB2 A:LEU134 4.9 33.1 1.0 HD21 A:LEU31 4.9 77.8 1.0 HD2 A:ARG131 4.9 35.0 1.0 HD12 A:LEU134 5.0 35.9 1.0 OE1 A:GLU135 5.0 30.3 1.0

Magnesium binding site 3 out of 5 in the Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg214 b:37.1 occ:1.00 HE1 A:TRP69 2.5 37.2 1.0 HD23 A:LEU115 2.8 50.8 1.0 HG22 A:THR114 3.1 50.0 1.0 NE1 A:TRP69 3.3 30.8 1.0 HO1 A:EDO207 3.4 66.1 1.0 HD21 A:LEU115 3.5 50.8 1.0 CD2 A:LEU115 3.6 42.1 1.0 HG21 A:ILE73 3.6 41.9 1.0 HA A:LEU115 3.7 39.1 1.0 HG21 A:THR114 3.8 50.0 1.0 CG2 A:THR114 3.9 41.5 1.0 HG12 A:ILE73 3.9 44.0 1.0 HG A:LEU115 4.0 47.3 1.0 HG1 A:THR121 4.0 54.9 1.0 O1 A:EDO207 4.0 54.9 1.0 HZ2 A:TRP69 4.0 35.4 1.0 CD1 A:TRP69 4.2 28.9 1.0 HD1 A:TRP69 4.2 34.9 1.0 HB A:THR114 4.2 45.2 1.0 CE2 A:TRP69 4.3 28.8 1.0 HD22 A:LEU115 4.3 50.8 1.0 CG A:LEU115 4.3 39.1 1.0 HD22 A:ASN118 4.4 101.4 1.0 OG1 A:THR121 4.4 45.5 1.0 CA A:LEU115 4.5 32.4 1.0 O A:THR114 4.5 31.2 1.0 CZ2 A:TRP69 4.5 29.3 1.0 C A:THR114 4.6 29.6 1.0 N A:LEU115 4.6 30.8 1.0 HG23 A:THR114 4.6 50.0 1.0 CG2 A:ILE73 4.6 34.7 1.0 HG21 A:THR121 4.6 45.2 1.0 HG23 A:THR121 4.6 45.2 1.0 CB A:THR114 4.6 37.4 1.0 CG1 A:ILE73 4.9 36.5 1.0 HB3 A:ASN118 5.0 81.6 1.0 H A:LEU115 5.0 37.3 1.0 CB A:LEU115 5.0 33.4 1.0 HG23 A:ILE73 5.0 41.9 1.0

Magnesium binding site 4 out of 5 in the Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg215 b:45.4 occ:1.00 HA A:PHE91 2.5 65.3 1.0 HH11 A:ARG100 2.8 146.0 1.0 N A:ARG93 3.0 110.7 1.0 HA A:PRO96 3.2 108.5 1.0 CA A:PHE91 3.3 54.2 1.0 O A:HOH335 3.3 79.1 1.0 CA A:ARG93 3.4 122.7 1.0 HD1 A:PHE91 3.4 55.7 1.0 NH1 A:ARG100 3.5 121.5 1.0 HG3 A:PRO96 3.5 109.9 1.0 C A:PHE91 3.5 68.7 1.0 HB3 A:PHE91 3.5 61.4 1.0 HH12 A:ARG100 3.6 146.0 1.0 N A:HIS92 3.7 81.0 1.0 N A:PRO96 3.9 92.4 1.0 CB A:PHE91 3.9 50.9 1.0 O A:ILE90 3.9 46.9 1.0 CA A:PRO96 3.9 90.2 1.0 HD3 A:PRO96 3.9 111.5 1.0 HD2 A:ARG100 4.0 111.9 1.0 C A:HIS92 4.1 98.0 1.0 HD3 A:ARG100 4.1 111.9 1.0 O A:PHE91 4.1 67.2 1.0 CD1 A:PHE91 4.2 46.2 1.0 CG A:PRO96 4.2 91.3 1.0 CG A:ARG93 4.2 132.3 1.0 CD A:PRO96 4.3 92.7 1.0 HO1 A:EDO210 4.3 73.8 1.0 O1 A:EDO210 4.3 61.3 1.0 CB A:ARG93 4.4 130.3 1.0 HB3 A:PRO96 4.4 109.0 1.0 CA A:HIS92 4.4 89.7 1.0 N A:PHE91 4.4 45.1 1.0 C A:ARG93 4.5 122.4 1.0 CB A:PRO96 4.5 90.6 1.0 CD A:ARG100 4.5 93.0 1.0 CG A:PHE91 4.5 45.6 1.0 O A:ARG93 4.5 121.0 1.0 C A:ILE90 4.6 43.9 1.0 CZ A:ARG100 4.7 119.0 1.0 HB2 A:PHE91 4.8 61.4 1.0 CB A:HIS92 4.9 91.5 1.0

Magnesium binding site 5 out of 5 in the Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Epstein-Barr Virus Encoded Apoptosis Regulator BHRF1 in Complex with Puma BH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg216 b:48.1 occ:1.00 H11 A:EDO210 2.4 78.8 1.0 C1 A:EDO210 3.4 65.5 1.0 H12 A:EDO210 3.6 78.8 1.0 H22 A:EDO210 4.1 82.2 1.0 HO1 A:EDO210 4.1 73.8 1.0 ND1 A:HIS92 4.3 99.0 1.0 O1 A:EDO210 4.3 61.3 1.0 C2 A:EDO210 4.4 68.2 1.0 CG A:HIS92 4.5 97.1 1.0 CB A:HIS92 4.6 91.5 1.0 H21 A:EDO210 4.7 82.2 1.0 CE1 A:HIS92 4.8 99.7 1.0

C.D.Suraweera, M.G.Hinds, M.Kvansakul. Crystal Structures of Epstein-Barr Virus Bcl-2 Homolog BHRF1 Bound to Bid and Puma BH3 Motif Peptides. Viruses V. 14 2022.
ISSN: ESSN 1999-4915
PubMed: 36298777
DOI: 10.3390/V14102222