Atomistry » Magnesium » PDB 8csu-8dba » 8d8k
Atomistry »
  Magnesium »
    PDB 8csu-8dba »
      8d8k »

Magnesium in PDB 8d8k: Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)

Other elements in 8d8k:

The structure of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2) also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

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 2) (pdb code 8d8k). 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 2), PDB code: 8d8k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 1 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg301

b:21.5
occ:1.00
O Q:LEU66 2.1 14.0 1.0
C Q:LEU66 3.2 14.0 1.0
OP2 a:G259 3.7 21.2 1.0
OP1 a:G259 3.8 21.2 1.0
OP1 a:G270 3.9 18.5 1.0
CA Q:LEU66 3.9 14.0 1.0
C5' a:A269 3.9 16.4 1.0
O3' a:A269 4.0 16.4 1.0
OP2 a:U260 4.0 26.4 1.0
P a:G259 4.2 21.2 1.0
CB Q:LEU66 4.3 14.0 1.0
N Q:SER67 4.3 14.6 1.0
C4' a:A269 4.4 16.4 1.0
P a:G270 4.4 18.5 1.0
CA Q:SER67 4.6 14.6 1.0
O5' a:G259 4.7 21.2 1.0
CB Q:SER67 4.7 14.6 1.0
C3' a:A269 4.8 16.4 1.0
O5' a:A269 4.8 16.4 1.0
OP2 a:G270 4.9 18.5 1.0
OP1 a:A269 4.9 16.4 1.0

Magnesium binding site 2 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 2 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg502

b:24.5
occ:1.00
O W:HOH602 2.0 24.3 1.0
O W:HOH601 2.0 15.8 1.0
OG1 W:THR157 2.0 9.6 1.0
O2B W:ATP501 2.0 10.4 1.0
O W:HOH603 2.1 14.4 1.0
O2G W:ATP501 2.1 10.4 1.0
O1A W:ATP501 2.6 10.4 1.0
O3B W:ATP501 2.9 10.4 1.0
PB W:ATP501 2.9 10.4 1.0
CB W:THR157 3.1 9.6 1.0
PG W:ATP501 3.1 10.4 1.0
O3A W:ATP501 3.4 10.4 1.0
PA W:ATP501 3.4 10.4 1.0
N W:THR157 3.6 9.6 1.0
CA W:THR157 3.9 9.6 1.0
O3G W:ATP501 4.0 10.4 1.0
O2A W:ATP501 4.1 10.4 1.0
CG2 W:THR157 4.2 9.6 1.0
O1G W:ATP501 4.2 10.4 1.0
O1B W:ATP501 4.3 10.4 1.0
OG W:SER346 4.3 10.6 1.0
C W:LYS156 4.7 9.4 1.0
OD1 W:ASP292 4.7 11.1 1.0
OD2 W:ASP292 4.8 11.1 1.0
O5' W:ATP501 4.8 10.4 1.0
CB W:LYS156 4.9 9.4 1.0
N W:LYS156 5.0 9.4 1.0

Magnesium binding site 3 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 3 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:7.2
occ:1.00
OD1 B:ASP364 2.2 8.6 1.0
OD2 B:ASP364 2.3 8.6 1.0
OD1 B:ASP363 2.4 6.3 1.0
CG B:ASP364 2.5 8.6 1.0
OE1 B:GLN197 2.8 9.1 1.0
OD2 B:ASP347 3.0 8.6 1.0
CG B:ASP363 3.2 6.3 1.0
OD2 B:ASP363 3.3 6.3 1.0
NH2 B:ARG252 3.5 9.4 1.0
CD B:GLN197 3.9 9.1 1.0
CG B:ASP347 4.0 8.6 1.0
CB B:ASP364 4.0 8.6 1.0
OD1 B:ASP349 4.0 13.5 1.0
NZ A:LYS51 4.1 8.0 1.0
CB B:ASP347 4.2 8.6 1.0
NE2 B:GLN197 4.2 9.1 1.0
N B:ASP364 4.4 8.6 1.0
CZ B:ARG252 4.5 9.4 1.0
OD2 B:ASP349 4.5 13.5 1.0
CB B:ASP363 4.6 6.3 1.0
CA B:ASP364 4.7 8.6 1.0
CG B:ASP349 4.7 13.5 1.0
NH1 B:ARG252 4.7 9.4 1.0
C B:ASP363 4.8 6.3 1.0

Magnesium binding site 4 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 4 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1701

b:10.9
occ:1.00
N7 a:G75 4.3 40.0 1.0
O3' a:A71 4.4 28.7 1.0
C1' a:A71 4.6 28.7 1.0
OP2 a:C74 4.6 34.4 1.0
O4' a:A71 4.7 28.7 1.0
N3 a:A71 4.7 28.7 1.0
O4 a:U76 4.8 47.6 1.0
O6 a:G75 4.8 40.0 1.0
C5' a:U72 4.9 29.3 1.0
OP2 a:U72 5.0 29.3 1.0

Magnesium binding site 5 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 5 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1702

b:21.3
occ:1.00
OP2 a:C70 4.1 19.5 1.0
O 2:LYS104 4.6 30.7 1.0
OP2 a:A71 4.7 28.7 1.0
OP1 a:C70 4.8 19.5 1.0
P a:C70 5.0 19.5 1.0

Magnesium binding site 6 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 6 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1703

b:8.5
occ:1.00
O6 a:G104 3.6 27.0 1.0
N3 a:A100 4.1 28.2 1.0
N7 a:G104 4.2 27.0 1.0
OP2 a:G102 4.3 36.8 1.0
O4 a:U103 4.4 35.2 1.0
C6 a:G104 4.5 27.0 1.0
O4' a:A100 4.5 28.2 1.0
C5 a:U103 4.5 35.2 1.0
C1' a:A100 4.6 28.2 1.0
C5 a:G104 4.7 27.0 1.0
O3' a:A100 4.7 28.2 1.0
C2 a:A100 4.9 28.2 1.0
C4 a:U103 4.9 35.2 1.0

Magnesium binding site 7 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 7 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1704

b:10.5
occ:1.00
OP2 a:A110 2.1 18.2 1.0
P a:A110 3.4 18.2 1.0
OP1 a:A110 4.1 18.2 1.0
O5' a:A110 4.2 18.2 1.0
O6 a:G321 4.2 24.1 1.0
N6 a:A111 4.3 20.6 1.0
OP1 a:U336 4.6 21.7 1.0
O3' a:A109 4.6 31.9 1.0
N4 a:C112 4.6 24.1 1.0
C4' a:A109 4.7 31.9 1.0
N7 a:A111 4.7 20.6 1.0
N7 a:A110 4.9 18.2 1.0
C5' a:A109 4.9 31.9 1.0
C3' a:A109 5.0 31.9 1.0

Magnesium binding site 8 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 8 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1705

b:10.1
occ:1.00
OP2 a:C112 3.6 24.1 1.0
OP2 a:G113 3.8 24.1 1.0
N7 a:G113 3.9 24.1 1.0
C8 a:G113 4.5 24.1 1.0
O5' a:C112 4.6 24.1 1.0
C5 a:C112 4.6 24.1 1.0
P a:C112 4.6 24.1 1.0
O4 a:U114 4.7 24.1 1.0
C6 a:C112 4.8 24.1 1.0

Magnesium binding site 9 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 9 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1706

b:12.8
occ:1.00
OP1 a:C54 3.0 15.6 1.0
OP1 a:A55 3.4 18.6 1.0
OP1 a:U114 3.5 24.1 1.0
OP1 a:A313 4.0 24.1 1.0
OP1 a:A53 4.2 18.9 1.0
O3' a:A312 4.2 24.1 1.0
P a:C54 4.3 15.6 1.0
OP2 a:U114 4.3 24.1 1.0
P a:U114 4.4 24.1 1.0
O5' a:C54 4.6 15.6 1.0
P a:A55 4.7 18.6 1.0
P a:A313 4.8 24.1 1.0
O2' a:A312 4.8 24.1 1.0

Magnesium binding site 10 out of 72 in 8d8k

Go back to Magnesium Binding Sites List in 8d8k
Magnesium binding site 10 out of 72 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1707

b:24.4
occ:1.00
N1 a:A38 3.7 20.7 1.0
OP2 a:G115 3.7 24.1 1.0
OP2 a:A55 3.7 18.6 1.0
C4' a:A55 3.8 18.6 1.0
OP1 a:G115 3.9 24.1 1.0
O4' a:A55 3.9 18.6 1.0
O5' a:A55 4.2 18.6 1.0
P a:G115 4.3 24.1 1.0
C2 a:A38 4.3 20.7 1.0
O3' a:A55 4.5 18.6 1.0
P a:A55 4.6 18.6 1.0
C5' a:A55 4.6 18.6 1.0
C6 a:A38 4.7 20.7 1.0
C5' a:A312 4.7 24.1 1.0
OP2 a:U56 4.7 18.5 1.0
N6 a:A38 4.7 20.7 1.0
C3' a:A55 4.8 18.6 1.0
OP1 a:U56 4.8 18.5 1.0
P a:U56 4.9 18.5 1.0
O5' a:G115 4.9 24.1 1.0
C1' a:A55 4.9 18.6 1.0
MG a:MG1708 5.0 5.8 1.0

Reference:

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
Page generated: Thu Oct 3 23:41:30 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy