Magnesium in PDB 8d8l: Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)

All present enzymatic activity of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3):
3.1.2.4;

The structure of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 72;

Binding sites:

The binding sites of Magnesium atom in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) (pdb code 8d8l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 72 binding sites of Magnesium where determined in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3), PDB code: 8d8l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ W:Mg502 b:6.7 occ:1.00 O W:HOH602 1.9 9.7 1.0 O W:HOH603 1.9 7.3 1.0 OG1 W:THR157 2.0 11.8 1.0 O2G W:ATP501 2.1 11.8 1.0 O W:HOH601 2.1 9.9 1.0 O2B W:ATP501 2.4 11.8 1.0 PG W:ATP501 3.3 11.8 1.0 CB W:THR157 3.3 11.8 1.0 O3B W:ATP501 3.3 11.8 1.0 PB W:ATP501 3.5 11.8 1.0 O1A W:ATP501 3.9 11.8 1.0 O3G W:ATP501 3.9 11.8 1.0 OD2 W:ASP292 4.0 6.9 1.0 OD1 W:ASP292 4.0 6.9 1.0 OD1 W:ASN293 4.0 6.5 1.0 N W:THR157 4.0 11.8 1.0 CA W:THR157 4.2 11.8 1.0 OG W:SER346 4.2 6.4 1.0 CG2 W:THR157 4.2 11.8 1.0 O3A W:ATP501 4.4 11.8 1.0 CB W:SER346 4.4 6.4 1.0 CG W:ASP292 4.4 6.9 1.0 O1G W:ATP501 4.5 11.8 1.0 O1B W:ATP501 4.6 11.8 1.0 O W:ILE345 4.7 5.6 1.0 PA W:ATP501 4.7 11.8 1.0 CA W:SER346 4.8 6.4 1.0

Magnesium binding site 2 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:6.8 occ:1.00 OD1 B:ASP363 2.1 4.1 1.0 OD1 B:ASP364 2.2 4.2 1.0 OD2 B:ASP347 2.3 4.7 1.0 OE1 B:GLN197 2.4 5.0 1.0 CG B:ASP364 2.9 4.2 1.0 OD2 B:ASP364 3.0 4.2 1.0 CG B:ASP363 3.1 4.1 1.0 CG B:ASP347 3.3 4.7 1.0 OD2 B:ASP363 3.4 4.1 1.0 CD B:GLN197 3.5 5.0 1.0 CB B:ASP347 3.6 4.7 1.0 OD1 B:ASP349 3.9 5.6 1.0 NE2 B:GLN197 4.0 5.0 1.0 NZ A:LYS51 4.1 4.7 1.0 CB B:ASP364 4.2 4.2 1.0 OD1 B:ASP347 4.4 4.7 1.0 N B:ASP364 4.4 4.2 1.0 NH2 B:ARG252 4.4 4.6 1.0 CB B:ASP363 4.4 4.1 1.0 CE A:LYS51 4.5 4.7 1.0 N B:ASP363 4.5 4.1 1.0 NH1 B:ARG252 4.6 4.6 1.0 C B:ASP363 4.6 4.1 1.0 CG B:ASP349 4.6 5.6 1.0 OD2 B:ASP349 4.7 5.6 1.0 CA B:ASP363 4.7 4.1 1.0 CA B:ASP364 4.8 4.2 1.0 CG B:GLN197 4.8 5.0 1.0 OD1 B:ASN362 4.9 4.1 1.0

Magnesium binding site 3 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1701 b:14.6 occ:1.00 O6 a:G75 4.1 28.5 1.0 N7 a:G75 4.2 28.5 1.0 O3' a:A71 4.3 18.3 1.0 O4 a:U99 4.3 23.1 1.0 C1' a:A71 4.5 18.3 1.0 OP2 a:U72 4.5 24.2 1.0 O4 a:U76 4.6 32.5 1.0 O4' a:A71 4.7 18.3 1.0 N3 a:A71 4.8 18.3 1.0 C6 a:G75 4.9 28.5 1.0 C5 a:G75 4.9 28.5 1.0

Magnesium binding site 4 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1702 b:15.5 occ:1.00 OP2 a:C70 4.1 14.4 1.0 N7 a:A71 4.4 18.3 1.0 C8 a:A71 4.9 18.3 1.0 OP2 a:A71 4.9 18.3 1.0 N7 a:A100 5.0 18.3 1.0

Magnesium binding site 5 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1703 b:15.2 occ:1.00 O2' a:A100 3.7 18.3 1.0 O6 a:G104 3.9 18.1 1.0 N7 a:G104 4.1 18.1 1.0 OP2 a:G102 4.2 25.0 1.0 C5 a:U103 4.2 23.4 1.0 OP2 a:U103 4.4 23.4 1.0 O4 a:U103 4.4 23.4 1.0 C1' a:A100 4.5 18.3 1.0 C6 a:G104 4.7 18.1 1.0 C4 a:U103 4.7 23.4 1.0 C2' a:A100 4.7 18.3 1.0 C5 a:G104 4.8 18.1 1.0 N3 a:A100 4.8 18.3 1.0

Magnesium binding site 6 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1704 b:10.1 occ:1.00 OP2 a:A110 2.0 11.8 1.0 P a:A110 3.3 11.8 1.0 OP1 a:A110 3.7 11.8 1.0 O5' a:A110 4.1 11.8 1.0 O6 a:G321 4.3 11.8 1.0 O3' a:A109 4.5 12.3 1.0 N6 a:A111 4.5 11.8 1.0 C4' a:A109 4.6 12.3 1.0 OP1 a:U336 4.7 11.8 1.0 N7 a:A111 4.8 11.8 1.0 N4 a:C112 4.8 11.8 1.0 N7 a:A110 4.9 11.8 1.0 C3' a:A109 4.9 12.3 1.0 C8 a:A110 5.0 11.8 1.0 C5' a:A109 5.0 12.3 1.0

Magnesium binding site 7 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1705 b:14.7 occ:1.00 O4 a:U114 3.4 11.8 1.0 N7 a:G113 3.5 11.8 1.0 C8 a:G113 4.2 11.8 1.0 C4 a:U114 4.3 11.8 1.0 OP2 a:G113 4.4 11.8 1.0 C5 a:G113 4.4 11.8 1.0 O6 a:G113 4.4 11.8 1.0 C5 a:U114 4.5 11.8 1.0 OP2 a:C112 4.7 11.8 1.0 C6 a:G113 4.7 11.8 1.0 C5 a:C112 4.8 11.8 1.0

Magnesium binding site 8 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1706 b:11.1 occ:1.00 OP1 a:A313 2.1 11.8 1.0 P a:A313 3.3 11.8 1.0 O3' a:A312 3.4 11.8 1.0 OP2 a:U114 3.7 11.8 1.0 O5' a:A313 4.1 11.8 1.0 OP1 a:A53 4.3 11.8 1.0 C5' a:A313 4.4 11.8 1.0 OP2 a:A313 4.5 11.8 1.0 OP1 a:U114 4.6 11.8 1.0 P a:U114 4.7 11.8 1.0 C3' a:A312 4.8 11.8 1.0 O2' a:A312 4.8 11.8 1.0 OP1 a:C54 4.9 11.8 1.0

Magnesium binding site 9 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1707 b:13.3 occ:1.00 N1 a:A38 3.6 11.8 1.0 N6 a:A38 4.0 11.8 1.0 C5' a:A312 4.2 11.8 1.0 C6 a:A38 4.2 11.8 1.0 O4' a:A55 4.4 11.8 1.0 OP1 a:A312 4.5 11.8 1.0 C2 a:A38 4.5 11.8 1.0 C4' a:A55 4.7 11.8 1.0 OP2 a:G115 4.8 11.8 1.0

Magnesium binding site 10 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg1708 b:9.8 occ:1.00 OP1 a:G115 2.0 11.8 1.0 OP2 a:A55 2.4 11.8 1.0 P a:G115 3.3 11.8 1.0 OP2 a:U56 3.6 11.8 1.0 P a:A55 3.7 11.8 1.0 O3' a:U114 3.7 11.8 1.0 O3' a:C54 3.8 11.8 1.0 OP2 a:G115 4.2 11.8 1.0 O5' a:G115 4.4 11.8 1.0 OP2 a:A58 4.6 11.8 1.0 O2' a:C54 4.6 11.8 1.0 C5' a:G115 4.6 11.8 1.0 OP1 a:A55 4.6 11.8 1.0 O5' a:A55 4.7 11.8 1.0 C5' a:A55 4.8 11.8 1.0 C3' a:C54 4.9 11.8 1.0 OP1 a:A58 5.0 11.8 1.0

N.J.Harper, C.Burnside, S.Klinge. Principles of Mitoribosomal Small Subunit Assembly in Eukaryotes. Nature 2022.
ISSN: ESSN 1476-4687
PubMed: 36482135
DOI: 10.1038/S41586-022-05621-0