Magnesium in PDB 5xyu: Small Subunit of Mycobacterium Smegmatis Ribosome

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>>> 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 - 48;

Binding sites:

The binding sites of Magnesium atom in the Small Subunit of Mycobacterium Smegmatis Ribosome (pdb code 5xyu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 48 binding sites of Magnesium where determined in the Small Subunit of Mycobacterium Smegmatis Ribosome, PDB code: 5xyu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:69.8 occ:1.00 OP1 A:U17 2.9 86.2 1.0 OP2 A:U18 3.8 89.5 1.0 C5 A:U18 4.0 86.1 1.0 P A:U17 4.3 86.3 1.0 C6 A:U18 4.4 86.5 1.0 O5' A:U17 4.5 86.1 1.0 OP2 A:A20 4.7 77.6 1.0 OP1 A:A20 4.8 77.9 1.0

Magnesium binding site 2 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:56.5 occ:1.00 N4 A:C47 3.7 96.6 1.0 N4 A:C395 3.7 0.9 1.0 O4 A:U49 3.8 88.5 1.0 O6 A:G396 4.0 0.6 1.0 C4 A:C47 4.6 96.0 1.0 C4 A:C395 4.7 0.5 1.0 C4 A:U49 4.7 88.4 1.0 O6 A:G48 4.7 94.5 1.0 N7 A:G48 4.9 93.9 1.0 C5 A:C395 4.9 0.7 1.0 C5 A:C47 5.0 95.8 1.0

Magnesium binding site 3 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:47.8 occ:1.00 C5 A:C355 3.9 90.6 1.0 N7 A:G357 4.0 0.9 1.0 N7 A:A356 4.1 98.7 1.0 O2 A:C352 4.1 90.8 1.0 OP2 A:C355 4.1 84.3 1.0 C6 A:C355 4.3 90.1 1.0 O6 A:G357 4.3 0.7 1.0 C8 A:A356 4.4 99.1 1.0 O2' A:C352 4.5 89.8 1.0 C4 A:C355 4.6 90.2 1.0 C5 A:G357 4.8 0.3 1.0 N4 A:C355 4.8 90.4 1.0 C6 A:G357 4.9 0.4 1.0 O5' A:C355 4.9 86.9 1.0 C8 A:G357 5.0 0.3 1.0

Magnesium binding site 4 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:81.1 occ:1.00 O2' A:A728 2.9 0.8 1.0 O4' A:A729 4.1 0.8 1.0 C2' A:A728 4.1 0.1 1.0 O3' A:A728 4.1 0.3 1.0 O5' A:A729 4.3 0.4 1.0 C3' A:A728 4.7 0.6 1.0 O2 A:U727 4.8 0.6 1.0 P A:A729 4.9 0.7 1.0 C1' A:A729 5.0 0.7 1.0

Magnesium binding site 5 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:67.4 occ:1.00 O6 A:G803 3.9 79.5 1.0 N7 A:G803 4.1 80.9 1.0 O4 A:U804 4.1 90.7 1.0 N7 A:G802 4.2 72.0 1.0 O6 A:G802 4.2 72.4 1.0 C6 A:G803 4.7 79.7 1.0 C5 A:G802 4.7 71.8 1.0 C6 A:G802 4.7 72.0 1.0 C5 A:G803 4.8 80.3 1.0

Magnesium binding site 6 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:60.3 occ:1.00 O6 A:G877 3.2 95.4 1.0 N7 A:G876 3.7 95.0 1.0 N7 A:G877 3.9 97.2 1.0 C6 A:G877 4.1 95.3 1.0 C5 A:G877 4.4 96.2 1.0 C8 A:G876 4.4 94.6 1.0 C5 A:C875 4.6 87.8 1.0 C5 A:G876 4.6 95.0 1.0 O6 A:G876 4.6 95.2 1.0 OP2 A:G876 4.9 93.0 1.0

Magnesium binding site 7 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:72.9 occ:1.00 OP1 A:G926 2.4 93.5 1.0 OP2 A:G927 2.7 0.7 1.0 P A:G926 3.5 92.5 1.0 P A:G927 3.7 0.5 1.0 OP1 A:G927 3.9 0.7 1.0 O5' A:G926 3.9 94.1 1.0 OP2 A:G926 4.0 92.2 1.0 C5' A:G926 4.0 95.8 1.0 OP2 A:A928 4.5 0.5 1.0 O3' A:G926 4.6 99.6 1.0 O3' A:C925 4.9 92.0 1.0 N7 A:A928 4.9 0.1 1.0 C3' A:G926 4.9 97.7 1.0 O5' A:G927 5.0 0.5 1.0

Magnesium binding site 8 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:57.6 occ:1.00 OP2 A:G935 4.1 94.7 1.0 N6 A:A946 4.1 0.7 1.0 O6 A:G945 4.2 1.0 1.0 OP1 A:U934 4.2 89.3 1.0 OP1 A:G935 4.3 95.1 1.0 N7 A:G945 4.4 0.3 1.0 C5' A:U934 4.4 90.5 1.0 C5 A:C944 4.4 0.9 1.0 P A:G935 4.6 94.9 1.0 N4 A:C944 4.7 0.7 1.0 O5' A:U934 4.9 89.4 1.0 C6 A:G945 5.0 0.6 1.0

Magnesium binding site 9 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:58.7 occ:1.00 OP1 A:C954 2.0 91.5 1.0 P A:C954 3.4 91.8 1.0 OP1 A:C1349 3.7 86.7 1.0 O5' A:C954 3.9 92.0 1.0 O2' A:G953 4.0 94.7 1.0 O3' A:G953 4.3 93.5 1.0 C5' A:C1349 4.3 84.2 1.0 OP2 A:C954 4.4 91.9 1.0 C3' A:G953 4.4 94.9 1.0 C2' A:G953 4.6 94.7 1.0 P A:C1349 4.9 86.6 1.0

Magnesium binding site 10 out of 48 in the Small Subunit of Mycobacterium Smegmatis Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Small Subunit of Mycobacterium Smegmatis Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:71.1 occ:1.00 N7 A:G1030 3.6 0.9 1.0 OP2 A:U1029 4.0 0.9 1.0 C8 A:G1030 4.1 0.7 1.0 C5 A:G1030 4.2 0.3 1.0 O6 A:G1030 4.7 0.3 1.0 C6 A:G1030 4.7 0.6 1.0 O4 A:U1186 4.7 0.9 1.0 N9 A:G1030 4.9 1.0 1.0 O2' A:C1181 5.0 99.0 1.0 C4 A:G1030 5.0 0.2 1.0

Z.Li, X.Ge, Y.Zhang, L.Zheng, S.Sanyal, N.Gao. Cryo-Em Structure of Mycobacterium Smegmatis Ribosome Reveals Two Unidentified Ribosomal Proteins Close to the Functional Centers. Protein Cell V. 9 384 2018.
ISSN: ESSN 1674-8018
PubMed: 28875450
DOI: 10.1007/S13238-017-0456-9