Magnesium in PDB 5it9: Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.

The structure of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. also contains other interesting chemical elements:

Zinc

(Zn)

3 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 - 80;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. (pdb code 5it9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 80 binding sites of Magnesium where determined in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires., PDB code: 5it9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:71.7 occ:1.00 OP1 2:C267 2.1 0.8 1.0 OE1 G:GLN176 2.6 0.9 1.0 P 2:C267 2.9 0.6 1.0 OP2 2:C267 3.1 0.1 1.0 O5' 2:C267 3.7 0.6 1.0 C5' 2:C267 3.7 0.7 1.0 CD G:GLN176 3.8 0.0 1.0 CD G:ARG183 3.8 0.3 1.0 NE G:ARG183 4.1 0.4 1.0 O3' 2:U266 4.3 0.7 1.0 CG G:ARG183 4.4 0.4 1.0 NE2 G:GLN176 4.6 0.2 1.0 N G:ARG177 4.7 0.9 1.0 CG G:GLN176 4.8 0.8 1.0 C4' 2:C267 4.9 0.8 1.0 C3' 2:C267 5.0 0.7 1.0

Magnesium binding site 2 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg201 b:2.0 occ:1.00 OP1 2:G1034 4.0 6.1 1.0 O N:LYS9 4.4 24.3 1.0 OP1 2:G865 4.4 10.0 1.0 O N:GLY10 4.5 24.2 1.0 CA N:GLY2 4.5 20.8 1.0 O2' 2:U863 4.6 11.4 1.0 C N:LYS9 4.7 24.3 1.0 CB N:LYS9 4.8 24.6 1.0 OP1 2:A1035 4.8 7.7 1.0

Magnesium binding site 3 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg201 b:36.5 occ:1.00 OD1 T:ASN85 2.6 79.3 1.0 OP1 2:A1467 2.6 51.4 1.0 CG T:ASN85 3.5 79.1 1.0 CE1 T:HIS91 3.8 68.5 1.0 NE2 T:HIS91 3.9 68.6 1.0 P 2:A1467 3.9 51.6 1.0 ND2 T:ASN85 4.0 79.2 1.0 O5' 2:A1467 4.2 52.3 1.0 OP1 2:G1540 4.2 87.7 1.0 OP1 2:G1539 4.4 86.2 1.0 CB T:ASN85 4.6 78.5 1.0 OP2 2:A1467 4.8 51.9 1.0 OP1 2:C1474 4.8 80.8 1.0 OP2 2:G1540 4.8 87.3 1.0 OP1 2:A1473 4.8 86.2 1.0

Magnesium binding site 4 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg201 b:39.4 occ:1.00 O X:PRO64 2.2 37.0 1.0 C X:PRO64 2.9 36.8 1.0 CA X:PRO64 3.1 37.4 1.0 O6 2:G576 3.2 58.4 1.0 O2' i:U6216 3.7 0.5 1.0 N X:PRO64 3.9 37.8 1.0 N X:ASN65 4.1 35.9 1.0 C6 2:G576 4.3 58.6 1.0 CB X:PRO64 4.3 37.4 1.0 CD X:PRO64 4.6 37.7 1.0 O3' i:U6216 4.6 0.6 1.0 N3 2:C564 4.6 45.6 1.0 OE1 X:GLN63 4.6 42.1 1.0 N1 2:G576 4.6 58.9 1.0 C4' i:U6216 4.8 1.0 1.0 N4 2:C564 4.8 46.1 1.0 CA X:ASN65 4.8 35.1 1.0 C X:GLN63 4.9 38.5 1.0 C2' i:U6216 4.9 0.6 1.0 CG X:PRO64 4.9 37.5 1.0

Magnesium binding site 5 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1801 b:7.3 occ:1.00 OP1 2:A940 1.8 6.0 1.0 NE2 a:HIS17 3.0 11.1 1.0 CE1 a:HIS17 3.2 11.1 1.0 P 2:A940 3.3 5.9 1.0 CD2 a:HIS17 3.3 11.1 1.0 C5' 2:A940 3.6 6.1 1.0 ND1 a:HIS17 3.6 11.1 1.0 CG a:HIS17 3.7 11.1 1.0 O2' 2:A1026 3.7 4.9 1.0 O5' 2:A940 3.8 6.0 1.0 OP2 2:G941 3.9 6.7 1.0 C a:GLY16 4.0 11.6 1.0 O3' 2:A939 4.0 5.9 1.0 CA a:GLY16 4.1 11.8 1.0 O a:GLY16 4.2 11.6 1.0 OP2 2:A940 4.4 6.0 1.0 N a:HIS17 4.4 11.4 1.0 OP1 2:U1028 4.5 4.8 1.0 CB a:HIS17 4.8 11.2 1.0 C4' 2:A940 5.0 6.1 1.0

Magnesium binding site 6 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1802 b:23.1 occ:1.00 OP1 2:G361 2.3 4.4 1.0 O2' 2:A359 3.3 4.7 1.0 P 2:G361 3.5 4.4 1.0 OP2 2:G361 3.8 4.4 1.0 OP2 2:G376 4.1 4.6 1.0 OP1 2:A377 4.3 4.7 1.0 O3' 2:C360 4.5 4.4 1.0 O5' 2:G361 4.5 4.4 1.0 C2' 2:A359 4.7 4.7 1.0 N7 2:G376 4.7 4.6 1.0 OP2 2:G362 4.8 4.4 1.0 C8 2:G376 4.9 4.6 1.0 O5' 2:G376 4.9 4.6 1.0

Magnesium binding site 7 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1803 b:5.2 occ:1.00 OP1 2:G402 2.4 6.3 1.0 O6 2:G95 3.3 5.0 1.0 OP2 2:A93 3.4 8.2 1.0 NH2 E:ARG3 3.7 6.5 1.0 P 2:G402 3.9 6.3 1.0 N7 2:G402 4.2 7.1 1.0 C6 2:G95 4.3 4.9 1.0 O5' 2:A93 4.3 7.7 1.0 O3' 2:C401 4.5 6.2 1.0 P 2:A93 4.5 8.2 1.0 C8 2:G402 4.6 7.1 1.0 O5' 2:G402 4.8 6.5 1.0 CZ E:ARG3 4.8 6.5 1.0 OP2 2:G402 4.8 6.3 1.0 O5' 2:C401 4.9 5.8 1.0

Magnesium binding site 8 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1804 b:2.0 occ:1.00 OP2 2:A555 2.3 22.9 1.0 OP1 2:G551 2.6 19.3 1.0 OP2 2:A554 2.9 17.3 1.0 P 2:A555 3.7 22.9 1.0 P 2:G551 3.8 19.2 1.0 O5' 2:G551 3.8 18.8 1.0 P 2:A554 4.0 17.2 1.0 O5' 2:A554 4.0 17.9 1.0 O5' 2:A555 4.2 24.6 1.0 N7 2:A555 4.4 27.4 1.0 C8 2:A555 4.5 27.5 1.0 C5' 2:G551 4.5 18.4 1.0 OP1 2:A555 4.5 22.7 1.0 O3' 2:C553 4.5 16.6 1.0 OP2 2:G552 4.5 16.8 1.0 OP2 2:G551 4.7 19.2 1.0 O3' 2:A554 4.8 21.3 1.0 O3' 2:G550 4.9 19.6 1.0 C3' 2:A554 4.9 19.7 1.0 O2' 2:C553 4.9 15.8 1.0

Magnesium binding site 9 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1805 b:2.0 occ:1.00 OP1 2:A100 2.3 4.4 1.0 P 2:A100 3.4 4.4 1.0 OP2 2:A100 3.7 4.4 1.0 OP1 2:C360 3.8 4.6 1.0 O3' 2:C99 4.1 4.4 1.0 C3' 2:C99 4.2 4.4 1.0 O2' 2:A43 4.6 5.9 1.0 C5' 2:U44 4.6 5.8 1.0 C4' 2:U44 4.6 5.8 1.0 O5' 2:A100 4.7 4.4 1.0 OP2 2:C360 4.7 4.6 1.0 P 2:C360 4.8 4.6 1.0

Magnesium binding site 10 out of 80 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1806 b:7.3 occ:1.00 OP2 2:A1024 2.3 6.8 1.0 OP2 2:G623 2.6 5.5 1.0 P 2:A1024 3.4 6.8 1.0 C5' 2:A1024 3.8 6.2 1.0 O5' 2:A1024 3.9 6.5 1.0 P 2:G623 3.9 5.5 1.0 OP1 2:A1024 4.0 6.8 1.0 N7 2:A1026 4.1 5.0 1.0 N6 2:A1026 4.1 5.0 1.0 OP2 2:A1025 4.1 5.5 1.0 OP1 2:G623 4.5 5.5 1.0 O3' 2:U1023 4.7 7.0 1.0 C5 2:A1026 4.8 5.0 1.0 C6 2:A1026 4.9 5.0 1.0 O5' 2:G623 4.9 5.6 1.0 O3' 2:A622 4.9 5.4 1.0 P 2:A1025 4.9 5.5 1.0 C4' 2:A1024 5.0 6.0 1.0

J.Murray, C.G.Savva, B.S.Shin, T.E.Dever, V.Ramakrishnan, I.S.Fernandez. Structural Characterization of Ribosome Recruitment and Translocation By Type IV Ires. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27159451
DOI: 10.7554/ELIFE.13567