Magnesium in PDB 7kfr: Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution

The binding sites of Magnesium atom in the Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution (pdb code 7kfr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution, PDB code: 7kfr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2000 b:0.0 occ:1.00 NE2 A:HIS290 1.9 0.0 1.0 SG A:CYS363 2.2 12.5 1.0 HD3 A:ARG288 2.7 0.0 1.0 CD2 A:HIS290 2.8 0.0 1.0 HD3 A:PRO366 2.9 0.0 1.0 HD2 A:HIS290 2.9 0.0 1.0 CE1 A:HIS290 3.0 0.0 1.0 HG A:CYS363 3.0 12.6 1.0 HH11 A:ARG288 3.1 0.1 1.0 HE1 A:HIS290 3.3 0.0 1.0 NH1 A:ARG288 3.3 0.5 1.0 O A:LEU364 3.5 1.3 1.0 HB2 A:CYS363 3.5 8.8 1.0 CB A:CYS363 3.5 8.6 1.0 CD A:ARG288 3.6 0.0 1.0 HB2 A:ARG288 3.7 0.0 1.0 CZ A:ARG288 3.7 0.0 1.0 HH12 A:ARG288 3.8 0.1 1.0 NE A:ARG288 3.8 0.0 1.0 HA A:PRO365 3.9 0.0 1.0 CD A:PRO366 4.0 0.0 1.0 CG A:HIS290 4.0 0.0 1.0 HB3 A:CYS363 4.0 8.8 1.0 ND1 A:HIS290 4.0 0.0 1.0 HB3 A:ARG288 4.1 0.0 1.0 CB A:ARG288 4.2 0.0 1.0 HD2 A:ARG288 4.3 0.0 1.0 SG A:CYS291 4.3 0.8 1.0 HD2 A:PRO366 4.5 0.0 1.0 O A:HOH2163 4.5 21.6 1.0 HE A:ARG288 4.5 0.0 1.0 CG A:ARG288 4.5 0.0 1.0 N A:PRO366 4.5 0.0 1.0 C A:LEU364 4.5 0.0 1.0 HB3 A:PRO366 4.6 0.0 1.0 NH2 A:ARG288 4.6 0.0 1.0 HG A:CYS291 4.6 2.3 1.0 HG3 A:PRO366 4.7 0.0 1.0 CA A:PRO365 4.7 0.0 1.0 CA A:CYS363 4.8 4.0 1.0 C A:CYS363 4.8 1.3 1.0 CG A:PRO366 4.8 0.0 1.0 H1 A:HOH2163 4.8 21.6 1.0 HH22 A:ARG288 4.9 0.0 1.0 C A:PRO365 4.9 0.0 1.0 O A:CYS363 4.9 2.2 1.0 HD1 A:HIS290 4.9 0.0 1.0 H A:CYS363 4.9 1.8 1.0

Magnesium binding site 2 out of 3 in the Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:4.9 occ:1.00 NE2 A:HIS428 2.0 0.0 1.0 HE1 A:TYR426 2.7 3.0 1.0 CD2 A:HIS428 3.0 0.0 1.0 CE1 A:HIS428 3.1 0.0 1.0 OH A:TYR426 3.1 6.3 1.0 HD2 A:HIS428 3.1 0.0 1.0 HG3 A:ARG735 3.2 14.2 1.0 CE1 A:TYR426 3.3 3.2 1.0 HE1 A:HIS428 3.3 0.0 1.0 HH A:TYR426 3.4 5.4 1.0 CZ A:TYR426 3.5 5.0 1.0 H1 A:HOH2306 3.5 67.7 1.0 O A:ASN736 3.7 2.9 1.0 HA A:LEU737 3.7 11.4 1.0 HD3 A:ARG735 3.8 17.6 1.0 HG2 A:ARG735 3.9 14.2 1.0 CG A:ARG735 3.9 13.9 1.0 HD11 A:LEU737 4.1 11.8 1.0 CG A:HIS428 4.2 0.0 1.0 ND1 A:HIS428 4.2 0.0 1.0 CD1 A:TYR426 4.3 1.2 1.0 CD A:ARG735 4.3 17.4 1.0 O A:HOH2306 4.4 67.7 1.0 H2 A:HOH2306 4.5 67.7 1.0 HD13 A:LEU737 4.6 11.8 1.0 CE2 A:TYR426 4.6 3.3 1.0 HD1 A:TYR426 4.6 0.6 1.0 HE22 A:GLN609 4.6 4.3 1.0 NE A:ARG735 4.7 19.8 1.0 C A:ASN736 4.7 4.0 1.0 CA A:LEU737 4.8 11.3 1.0 CD1 A:LEU737 4.8 11.7 1.0 HE A:ARG735 4.9 20.1 1.0

Magnesium binding site 3 out of 3 in the Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Adeno-Associated Virus (Aav-Dj) - Cryo-Em Structure at 1.56 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:5.0 occ:1.00 NE2 A:HIS528 1.9 8.1 1.0 OD2 A:ASP563 2.0 10.9 1.0 OE1 A:GLU565 2.3 20.5 1.0 OD1 A:ASP563 2.5 9.4 1.0 CG A:ASP563 2.5 9.8 1.0 OE1 A:GLU533 2.6 29.6 1.0 CE1 A:HIS528 2.7 8.3 1.0 HB3 A:GLU565 2.7 14.1 1.0 HE1 A:HIS528 2.7 8.7 1.0 HG2 A:GLU565 2.8 17.4 1.0 CD2 A:HIS528 3.1 7.4 1.0 CD A:GLU565 3.1 19.7 1.0 CD A:GLU533 3.2 29.1 1.0 CG A:GLU565 3.2 17.1 1.0 CB A:GLU565 3.4 13.8 1.0 HD2 A:HIS528 3.5 7.7 1.0 HA A:GLU533 3.6 19.1 1.0 OE2 A:GLU533 3.8 30.0 1.0 ND1 A:HIS528 3.9 7.4 1.0 HB2 A:GLU565 3.9 14.1 1.0 CB A:ASP563 4.0 8.6 1.0 HG2 A:GLU533 4.0 27.0 1.0 CG A:HIS528 4.1 6.6 1.0 CG A:GLU533 4.1 26.8 1.0 H A:GLU565 4.3 8.8 1.0 HG3 A:GLU565 4.3 17.4 1.0 HB2 A:ASP563 4.3 8.7 1.0 OE2 A:GLU565 4.3 20.4 1.0 HB3 A:GLU533 4.4 23.2 1.0 HB3 A:ASP563 4.4 8.7 1.0 CA A:GLU533 4.5 19.0 1.0 CB A:GLU533 4.5 23.1 1.0 HB2 A:SER527 4.6 1.1 1.0 HD1 A:HIS528 4.7 7.6 1.0 HH12 A:ARG568 4.8 15.4 1.0 CA A:GLU565 4.8 9.9 1.0 N A:GLU565 4.9 8.8 1.0

Q.Xie, C.K.Yoshioka, M.S.Chapman. Adeno-Associated Virus (Aav-Dj)-Cryo-Em Structure at 1.56 Angstroms Resolution. Viruses V. 12 2020.
ISSN: ISSN 1999-4915
PubMed: 33092282
DOI: 10.3390/V12101194