Magnesium in PDB 5y9e: Crystal Structure of HPV58 Pentamer

The structure of Crystal Structure of HPV58 Pentamer, PDB code: 5y9e was solved by S.W.Li, Z.H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.78 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	187.213, 101.804, 136.195, 90.00, 95.68, 90.00
R / Rfree (%)	16.8 / 19.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of HPV58 Pentamer (pdb code 5y9e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 29 binding sites of Magnesium where determined in the Crystal Structure of HPV58 Pentamer, PDB code: 5y9e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 29 in the Crystal Structure of HPV58 Pentamer


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 HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:42.5 occ:1.00 O A:HOH825 2.8 36.2 1.0 OE1 A:GLN305 2.9 38.1 1.0 ND2 A:ASN308 2.9 33.7 1.0 O B:HOH808 3.0 41.0 1.0 NH2 A:ARG338 3.0 35.6 1.0 CG A:GLN305 3.4 34.0 1.0 CD A:GLN305 3.5 36.1 1.0 CB A:ASN308 3.6 32.6 1.0 O A:PHE307 3.6 35.2 1.0 CB A:GLN305 3.6 33.1 1.0 CG A:ASN308 3.7 36.1 1.0 NH2 B:ARG251 4.0 41.6 1.0 C A:PHE307 4.0 33.9 1.0 CZ A:ARG338 4.1 35.8 1.0 NH1 A:ARG338 4.3 36.1 1.0 O B:HOH702 4.4 41.2 1.0 N A:ASN308 4.5 35.0 1.0 CA A:ASN308 4.7 35.5 1.0 CZ B:ARG251 4.7 46.4 1.0 CB A:PHE307 4.7 32.2 1.0 NE2 A:GLN305 4.8 30.6 1.0 CA A:PHE307 4.8 35.9 1.0 N A:PHE307 4.9 32.7 1.0 OD1 A:ASN308 4.9 38.4 1.0

Magnesium binding site 2 out of 29 in the Crystal Structure of HPV58 Pentamer


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 HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:42.3 occ:1.00 C A:ARG338 2.6 26.5 1.0 O A:ASP335 2.7 27.4 1.0 N A:SER339 2.9 28.1 1.0 O A:ARG338 2.9 28.1 1.0 N A:ARG338 3.0 24.8 1.0 CA A:ARG338 3.1 24.9 1.0 OE2 A:GLU367 3.2 36.3 1.0 CA A:SER339 3.3 29.0 1.0 CB A:ARG338 3.5 25.2 1.0 C A:ASP335 3.7 24.5 1.0 C A:THR336 3.7 24.6 1.0 CA A:GLY68 3.8 35.6 1.0 CB A:SER339 3.8 29.9 1.0 CA A:THR336 3.8 24.5 1.0 NH2 A:ARG110 3.9 36.2 1.0 N A:THR337 4.0 24.9 1.0 CD A:GLU367 4.0 41.2 1.0 OE1 A:GLU367 4.0 40.4 1.0 O A:THR336 4.1 24.6 1.0 C A:THR337 4.2 25.1 1.0 N A:THR336 4.2 25.0 1.0 O A:GLY68 4.4 33.3 1.0 CE1 A:HIS365 4.4 33.4 1.0 NE2 A:HIS365 4.4 33.0 1.0 O A:HOH692 4.5 27.0 1.0 C A:GLY68 4.6 37.1 1.0 CG A:ARG338 4.6 26.2 1.0 C A:SER339 4.7 31.3 1.0 CA A:THR337 4.7 25.2 1.0 OG A:SER339 4.7 31.2 1.0 O A:HOH641 4.8 31.2 1.0 CG A:ASP335 4.8 28.6 1.0 N A:GLY68 4.8 36.6 1.0 OD2 A:ASP335 4.9 30.4 1.0 CA A:ASP335 5.0 26.4 1.0

Magnesium binding site 3 out of 29 in the Crystal Structure of HPV58 Pentamer


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 HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:69.0 occ:1.00 CD A:ARG41 2.6 39.0 1.0 NH1 A:ARG41 2.9 53.2 1.0 OE2 A:GLU368 3.0 39.7 1.0 OD2 B:ASP233 3.1 37.2 1.0 NE A:ARG41 3.6 45.7 1.0 OD1 B:ASP233 3.6 36.0 1.0 CZ A:ARG41 3.7 51.0 1.0 CG B:ASP233 3.7 38.7 1.0 CG A:ARG41 3.7 41.8 1.0 CD A:GLU368 3.9 36.5 1.0 OE1 B:GLU168 4.1 40.3 1.0 CD2 B:LEU190 4.2 43.6 1.0 O A:HOH667 4.2 33.8 1.0 OE1 A:GLU368 4.4 36.8 1.0 CB A:ARG41 4.5 36.7 1.0 CG A:GLU368 4.8 36.7 1.0 OD1 B:ASN192 4.8 42.0 1.0 O A:HOH608 5.0 41.7 1.0 NH2 A:ARG41 5.0 49.2 1.0 ND2 B:ASN192 5.0 36.2 1.0

Magnesium binding site 4 out of 29 in the Crystal Structure of HPV58 Pentamer


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 HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:65.6 occ:1.00 OE1 A:GLU107 2.6 45.8 1.0 NZ A:LYS466 2.8 44.0 1.0 O A:HOH822 3.2 43.6 1.0 O A:ASN308 3.3 33.0 1.0 CD A:GLU107 3.6 46.5 1.0 C A:ASN308 3.9 35.3 1.0 OE2 A:GLU107 4.0 43.9 1.0 O A:HOH685 4.0 31.9 1.0 O B:HOH819 4.1 44.2 1.0 CE A:LYS466 4.2 44.0 1.0 O A:HOH840 4.2 39.6 1.0 O A:HOH644 4.5 41.2 1.0 CA A:ASN308 4.6 35.5 1.0 N A:LYS309 4.7 33.8 1.0 CB A:ASN308 4.7 32.6 1.0 CA A:LYS309 4.8 37.4 1.0 CG A:GLU107 5.0 39.8 1.0

Magnesium binding site 5 out of 29 in the Crystal Structure of HPV58 Pentamer


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 HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:45.4 occ:1.00 C3 A:GOL503 2.6 60.0 1.0 N A:ARG251 3.0 29.0 1.0 C3 A:GOL504 3.1 55.7 1.0 O3 A:GOL503 3.3 62.9 1.0 O A:ARG251 3.4 29.6 1.0 CA A:LEU250 3.4 37.3 1.0 C A:LEU250 3.7 34.7 1.0 C2 A:GOL503 3.9 62.5 1.0 CD2 A:LEU250 3.9 35.7 1.0 CG A:ARG251 3.9 30.4 1.0 O3 A:GOL504 3.9 54.1 1.0 CB A:LEU250 4.0 35.1 1.0 O2 A:GOL504 4.0 62.5 1.0 CA A:ARG251 4.0 28.7 1.0 O2 A:GOL503 4.1 59.2 1.0 C A:ARG251 4.1 30.8 1.0 C2 A:GOL504 4.2 62.2 1.0 O A:PHE249 4.4 37.0 1.0 CB A:ARG251 4.5 27.6 1.0 N A:LEU250 4.6 34.1 1.0 CG A:LEU250 4.6 37.9 1.0 O A:LEU250 4.9 29.9 1.0 C A:PHE249 4.9 36.9 1.0 CE1 A:PHE249 5.0 39.2 1.0

Magnesium binding site 6 out of 29 in the Crystal Structure of HPV58 Pentamer


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 HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:76.3 occ:1.00 O A:HOH702 2.5 37.1 1.0 O A:HOH717 2.8 42.0 1.0 OD2 A:ASP370 3.1 55.2 1.0 O B:HOH698 3.3 39.5 1.0 OD1 A:ASP370 3.4 49.8 1.0 CG A:ASP370 3.6 50.8 1.0 CB B:SER239 3.9 48.0 1.0 OH A:TYR36 4.0 41.5 1.0 CG A:GLN372 4.1 40.0 1.0 O A:HOH616 4.2 32.4 1.0 CD A:GLN372 4.2 45.4 1.0 OE1 A:GLN372 4.4 40.6 1.0 OG B:SER239 4.7 58.8 1.0 O A:HOH608 4.7 41.7 1.0 NE2 A:GLN372 4.7 44.2 1.0 CD A:PRO462 4.9 36.1 1.0 CG A:PRO462 4.9 39.4 1.0

Magnesium binding site 7 out of 29 in the Crystal Structure of HPV58 Pentamer


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 HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg511 b:45.9 occ:1.00 OD1 A:ASN356 2.7 34.7 1.0 O B:HOH740 2.7 26.8 1.0 N B:ASN144 2.8 37.2 1.0 ND2 A:ASN356 3.4 35.8 1.0 CB B:ALA264 3.4 32.4 1.0 CG A:ASN356 3.4 39.7 1.0 N B:ARG145 3.4 33.6 1.0 CA B:ASN144 3.5 35.2 1.0 C B:ASN144 3.6 38.7 1.0 CG B:ARG145 3.7 33.7 1.0 CB B:ASN144 3.7 36.2 1.0 C B:ASP143 3.7 41.2 1.0 CA B:ASP143 3.8 39.1 1.0 CE1 A:TYR354 4.0 37.7 1.0 OD1 B:ASP143 4.1 35.2 1.0 OD1 B:ASN125 4.2 31.6 1.0 OD1 B:ASN144 4.2 51.0 1.0 CA B:ARG145 4.2 41.0 1.0 O B:ASN144 4.3 33.3 1.0 CG B:ASN144 4.4 47.0 1.0 CB B:ARG145 4.6 31.8 1.0 N B:ASP143 4.6 41.0 1.0 CD1 A:TYR354 4.7 41.1 1.0 CD B:ARG145 4.7 38.3 1.0 CZ A:TYR354 4.7 44.0 1.0 OH A:TYR354 4.8 48.5 1.0 O B:SER142 4.8 40.6 1.0 CA B:ALA264 4.8 34.7 1.0 O B:ASP143 4.9 36.2 1.0 CB A:ASN356 4.9 38.3 1.0 C B:SER142 5.0 45.2 1.0 CG B:ASP143 5.0 38.1 1.0 CB B:ASP143 5.0 38.9 1.0

Magnesium binding site 8 out of 29 in the Crystal Structure of HPV58 Pentamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:52.6 occ:1.00 O B:HOH753 2.7 34.0 1.0 OD1 B:ASP244 2.8 40.8 1.0 NE1 B:TRP325 3.0 43.4 1.0 SD B:MET393 3.1 46.2 1.0 ND2 B:ASN320 3.5 41.5 1.0 CD1 B:TRP325 3.6 40.9 1.0 O B:HOH612 3.6 40.7 1.0 CG B:ASP244 3.7 44.0 1.0 CB B:TYR242 3.8 46.5 1.0 OD2 B:ASP244 3.8 45.2 1.0 CE B:MET393 3.8 47.9 1.0 CB B:ASN320 3.9 41.5 1.0 CG B:ASN320 4.0 39.0 1.0 O B:TYR242 4.1 40.6 1.0 CE2 B:TRP325 4.1 43.9 1.0 CD1 B:TYR242 4.2 48.2 1.0 CG B:MET393 4.3 45.7 1.0 O B:HOH676 4.3 32.8 1.0 CG B:TYR242 4.3 45.5 1.0 OH B:TYR27 4.5 46.6 1.0 CZ2 B:TRP325 4.7 48.0 1.0 C B:TYR242 4.7 44.3 1.0 CG2 B:THR24 4.7 41.6 1.0 CA B:TYR242 4.7 44.4 1.0 CA B:ASN320 4.8 43.1 1.0 CG B:TRP325 4.9 42.1 1.0 OD1 B:ASN320 4.9 39.8 1.0

Magnesium binding site 9 out of 29 in the Crystal Structure of HPV58 Pentamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg507 b:52.2 occ:1.00 O B:HOH652 2.8 37.5 1.0 NH1 B:ARG72 2.8 36.2 1.0 CG B:GLU367 3.0 43.6 1.0 O B:SER67 3.1 29.9 1.0 CG B:ARG72 3.5 37.3 1.0 CD B:ARG72 3.5 37.1 1.0 CD B:GLU367 3.5 47.1 1.0 CZ B:ARG72 3.9 41.0 1.0 OE2 B:GLU367 3.9 47.4 1.0 O B:HOH695 3.9 32.2 1.0 CB B:GLU367 4.0 43.8 1.0 OE1 B:GLU367 4.0 42.6 1.0 C B:SER67 4.1 35.3 1.0 NE B:ARG72 4.1 40.4 1.0 OE1 B:GLN70 4.3 31.3 1.0 O B:GLN70 4.4 31.3 1.0 CB B:GLN70 4.4 31.8 1.0 CA B:GLY68 4.6 29.5 1.0 N B:GLY68 4.7 32.6 1.0 N B:SER67 4.7 38.1 1.0 OH B:TYR369 4.7 46.1 1.0 CE1 B:TYR369 4.8 41.9 1.0 CG1 B:VAL66 4.9 33.8 1.0 N B:GLN70 5.0 27.9 1.0 CB B:ARG72 5.0 37.4 1.0 C B:GLN70 5.0 28.2 1.0

Magnesium binding site 10 out of 29 in the Crystal Structure of HPV58 Pentamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of HPV58 Pentamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg508 b:50.8 occ:1.00 O B:HOH823 2.3 53.6 1.0 OD2 B:ASP209 2.7 42.0 1.0 NE2 B:HIS169 3.0 39.2 1.0 O B:HOH665 3.1 35.9 1.0 O B:HOH735 3.2 44.2 1.0 CB B:ASP209 3.4 38.1 1.0 CG B:ASP209 3.5 41.5 1.0 CD2 B:HIS169 3.8 36.9 1.0 O B:HOH605 3.9 44.4 1.0 CE1 B:HIS169 4.0 40.0 1.0 CA B:GLY171 4.3 34.2 1.0 O B:HOH835 4.4 55.8 1.0 OG1 B:THR228 4.5 41.1 1.0 CD2 B:PHE191 4.5 39.5 1.0 OD1 B:ASP209 4.7 40.6 1.0 CE2 B:PHE191 4.7 40.3 1.0 O B:HOH832 4.8 47.9 1.0 CA B:ASP209 4.8 36.7 1.0 OG1 B:THR212 4.8 44.1 1.0 O B:HOH831 5.0 55.0 1.0 CG B:HIS169 5.0 35.2 1.0

Z.Li, D.Wang, Y.Gu, S.Song, M.He, J.Shi, X.Liu, S.Wei, J.Li, H.Yu, Q.Zheng, X.Yan, T.S.Baker, J.Zhang, J.S.Mclellan, S.Li, N.Xia. Crystal Structures of Two Immune Complexes Identify Determinants For Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus. Mbio V. 8 2017.
ISSN: ESSN 2150-7511
PubMed: 28951471
DOI: 10.1128/MBIO.00787-17