Magnesium in PDB 6az1: Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin (pdb code 6az1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin, PDB code: 6az1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:69.0 occ:1.00 NH2 C:ARG66 3.6 77.9 0.5 NH1 C:ARG66 3.8 77.9 0.5 CG2 C:ILE65 4.0 76.8 1.0 CZ C:ARG66 4.2 77.9 0.5 O C:LEU85 4.2 77.5 1.0 NE2 C:GLN84 4.3 79.6 1.0 CD2 C:LEU58 4.5 77.9 1.0 CD1 C:ILE65 4.5 76.8 1.0

Magnesium binding site 2 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:47.5 occ:1.00 OP2 1:G559 4.0 65.1 1.0 NH2 D:ARG131 4.4 58.9 1.0 CZ D:ARG131 4.6 58.9 1.0 OP1 1:C578 4.6 65.0 1.0 OP2 1:C578 4.7 65.0 1.0 NE D:ARG131 4.8 58.9 1.0 O D:ALA160 4.8 64.4 1.0 CD D:ARG131 4.9 58.9 1.0

Magnesium binding site 3 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg101 b:44.8 occ:1.00 OE1 S:GLU36 3.4 56.6 1.0 OP1 1:A1890 3.9 65.4 1.0 O S:ARG33 4.3 52.0 1.0 CD S:GLU36 4.7 56.6 1.0

Magnesium binding site 4 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg2301 b:38.5 occ:1.00 O 1:HOH2521 3.5 46.5 1.0 O L:THR145 3.8 45.5 1.0 OP2 1:A1548 4.0 45.6 1.0 OP1 1:C1549 4.6 47.3 1.0 C4' 1:OMC1866 4.8 45.8 1.0 CM2 1:OMG1865 5.0 46.3 1.0 CB L:PHE144 5.0 44.3 1.0 C L:THR145 5.0 45.5 1.0

Magnesium binding site 5 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg2308 b:83.4 occ:1.00 N6 1:A783 3.0 84.4 1.0 N4 1:C835 3.7 95.3 1.0 C6 1:A783 3.9 84.4 1.0 N4 1:C836 3.9 91.1 1.0 N4 1:C784 4.1 84.2 1.0 C5 1:A783 4.4 84.4 1.0 N7 1:A783 4.5 84.4 1.0 C5 1:C784 4.5 84.2 1.0 N1 1:A783 4.7 84.4 1.0 O6 1:G787 4.8 85.8 1.0 C4 1:C784 4.8 84.2 1.0 C4 1:C835 5.0 95.3 1.0

Magnesium binding site 6 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg2309 b:49.8 occ:1.00 OP1 1:A629 3.2 50.6 1.0 O2' 1:A629 3.7 50.6 1.0 O6 1:G611 3.9 54.4 1.0 C2' 1:A629 4.0 50.6 1.0 O6 1:G610 4.4 56.1 1.0 O4 1:U609 4.5 56.5 1.0 P 1:A629 4.6 50.6 1.0 C3' 1:A629 4.6 50.6 1.0 OP1 1:U631 4.8 47.6 1.0 N7 1:G610 4.8 56.1 1.0 O5' 1:A629 4.9 50.6 1.0 C4 1:U609 4.9 56.5 1.0 N4 1:C632 5.0 50.0 1.0 C6 1:G611 5.0 54.4 1.0

Magnesium binding site 7 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg2310 b:37.5 occ:1.00 OP2 1:G1189 3.4 35.3 1.0 O b:GLY18 3.8 37.3 1.0 O3' 1:G2192 3.9 35.8 1.0 O2' 1:G2192 4.0 35.8 1.0 OP2 1:A1274 4.3 35.4 1.0 N1 1:A1272 4.4 35.9 1.0 OP1 1:C2193 4.6 35.8 1.0 C2 1:A1272 4.6 35.9 1.0 C4' 1:G2192 4.6 35.8 1.0 C3' 1:G2192 4.7 35.8 1.0 C5' 1:G1188 4.7 35.9 1.0 P 1:G1189 4.8 35.3 1.0 C b:GLY18 4.8 37.3 1.0 CB b:ARG19 4.8 36.2 1.0 P 1:C2193 4.9 35.8 1.0 C5' 1:C2193 4.9 35.8 1.0 OP1 1:G1188 4.9 35.9 1.0 NZ b:LYS12 5.0 40.6 1.0 C2' 1:G2192 5.0 35.8 1.0

Magnesium binding site 8 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg2311 b:38.6 occ:1.00 OP2 1:A1109 3.4 41.5 1.0 O2 1:C1210 3.9 37.9 1.0 N3 1:C1209 3.9 38.9 1.0 N6 1:A1112 3.9 38.3 1.0 O2' 1:A1108 4.1 40.3 1.0 N4 1:C1209 4.2 38.9 1.0 O6 1:G1111 4.3 40.4 1.0 N7 1:G1111 4.3 40.4 1.0 N3 1:C1210 4.4 37.9 1.0 N7 1:A1112 4.5 38.3 1.0 C4 1:C1209 4.6 38.9 1.0 C2 1:C1210 4.6 37.9 1.0 O2 1:C1209 4.8 38.9 1.0 C2 1:C1209 4.8 38.9 1.0 C6 1:A1112 4.9 38.3 1.0 P 1:A1109 4.9 41.5 1.0

Magnesium binding site 9 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg2312 b:48.1 occ:1.00 N3 1:G432 3.4 50.3 1.0 O2 1:C452 3.7 55.4 1.0 O2' 1:G432 3.9 50.3 1.0 N2 1:G432 3.9 50.3 1.0 C2 1:G432 4.1 50.3 1.0 C1' 1:G432 4.3 50.3 1.0 OP1 1:U2135 4.3 60.3 1.0 C4 1:G432 4.4 50.3 1.0 C2' 1:G432 4.4 50.3 1.0 O2' 1:C452 4.6 55.4 1.0 N2 1:G431 4.6 49.5 1.0 N9 1:G432 4.8 50.3 1.0 C2 1:C452 4.9 55.4 1.0 C5' 1:U2135 4.9 60.3 1.0 C1' 1:C452 5.0 55.4 1.0

Magnesium binding site 10 out of 24 in the Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of the Small Subunit of Leishmania Ribosome Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg2313 b:45.0 occ:1.00 O6 1:G472 3.7 52.6 1.0 OP2 1:C470 3.8 46.0 1.0 C5 1:C470 4.2 46.0 1.0 N7 1:G472 4.3 52.6 1.0 O2' 1:C467 4.4 49.2 1.0 C6 1:G472 4.6 52.6 1.0 N7 1:A471 4.6 49.3 1.0 C6 1:C470 4.6 46.0 1.0 O 1:HOH2528 4.8 47.2 1.0 C5 1:G472 4.8 52.6 1.0 O2 1:C467 4.8 49.2 1.0 OP2 1:A468 4.8 45.1 1.0 C2' 1:C467 4.8 49.2 1.0 OP2 1:A471 4.9 49.3 1.0 P 1:C470 5.0 46.0 1.0

M.Shalev-Benami, Y.Zhang, H.Rozenberg, Y.Nobe, M.Taoka, D.Matzov, E.Zimmerman, A.Bashan, T.Isobe, C.L.Jaffe, A.Yonath, G.Skiniotis. Atomic Resolution Snapshot of Leishmania Ribosome Inhibition By the Aminoglycoside Paromomycin. Nat Commun V. 8 1589 2017.
ISSN: ESSN 2041-1723
PubMed: 29150609
DOI: 10.1038/S41467-017-01664-4