Magnesium in PDB 7pwf: Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution

The structure of Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution also contains other interesting chemical elements:

Potassium

(K)

266 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution (pdb code 7pwf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 37 binding sites of Magnesium where determined in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution, PDB code: 7pwf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg208 b:24.1 occ:1.00 NH2 N:ARG3 3.3 16.2 1.0 CG2 N:ILE11 4.2 0.4 1.0 K 2:K1705 4.3 52.0 1.0 OP1 2:A618 4.4 5.1 1.0 O2' 2:G616 4.4 7.9 1.0 OP1 2:G787 4.5 0.0 1.0 CZ N:ARG3 4.6 19.5 1.0 OP2 2:G617 4.7 5.1 1.0 CD N:ARG3 4.9 9.2 1.0 OP1 2:C788 4.9 2.7 1.0 O N:GLY10 5.0 7.7 1.0

Magnesium binding site 2 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg201 b:9.9 occ:1.00 NH1 I:ARG102 2.6 17.1 1.0 CZ I:ARG102 3.7 19.9 1.0 CD I:ARG102 3.8 24.0 1.0 NE I:ARG102 4.1 24.9 1.0 NH2 I:ARG102 4.7 21.8 1.0

Magnesium binding site 3 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1740 b:5.8 occ:1.00 OP1 2:G315 2.6 2.8 1.0 OP2 2:A80 3.8 3.6 1.0 P 2:G315 3.9 0.0 1.0 O6 2:G82 4.1 13.2 1.0 O3' 2:C314 4.1 2.5 1.0 NH2 E:ARG3 4.1 10.5 1.0 O5' 2:C314 4.7 0.0 1.0 N7 2:G315 4.7 4.8 1.0 O5' 2:G315 4.8 3.9 1.0 P 2:A80 4.9 4.0 1.0 OP1 2:A80 4.9 1.1 1.0 C8 2:G315 5.0 3.5 1.0

Magnesium binding site 4 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1741 b:9.4 occ:1.00 MG 2:MG1742 2.5 12.6 1.0 OP2 2:A742 2.6 1.5 1.0 O5' 2:U741 3.6 1.4 1.0 N7 2:A742 3.7 0.0 1.0 OP2 2:U741 3.7 1.0 1.0 C8 2:A742 3.9 0.0 1.0 P 2:A742 4.0 0.0 1.0 P 2:U741 4.0 2.6 1.0 OP1 2:U741 4.0 5.1 1.0 O6 2:G743 4.1 0.0 1.0 C3' 2:U741 4.3 2.1 1.0 O5' 2:A742 4.4 0.6 1.0 C5' 2:U741 4.6 0.0 1.0 O3' 2:U741 4.6 2.8 1.0 N7 2:G743 4.7 0.0 1.0 C6 2:G743 4.8 0.0 1.0 K 2:K1529 4.8 23.9 1.0

Magnesium binding site 5 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1742 b:12.6 occ:1.00 MG 2:MG1741 2.5 9.4 1.0 O6 2:G743 2.7 0.0 1.0 OP2 2:G763 2.9 3.8 1.0 K 2:K1529 3.0 23.9 1.0 C6 2:G743 3.7 0.0 1.0 N7 2:G763 3.9 0.0 1.0 C8 2:G763 4.0 0.0 1.0 N7 2:G743 4.1 0.0 1.0 C5 2:G743 4.3 0.0 1.0 P 2:G763 4.3 5.3 1.0 OP2 2:A742 4.4 1.5 1.0 OP1 2:G763 4.8 4.3 1.0 C5' 2:G763 4.9 2.1 1.0 N1 2:G743 4.9 0.0 1.0 K 2:K1530 4.9 25.9 1.0 C5 2:G763 5.0 0.0 1.0

Magnesium binding site 6 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1743 b:10.2 occ:1.00 O G:ASN95 2.7 8.7 1.0 O2 2:U307 3.4 6.8 1.0 C G:ASN95 3.7 1.3 1.0 N G:ASN95 3.8 0.0 1.0 CB G:ASN95 4.0 0.0 1.0 O2' 2:U307 4.0 6.5 1.0 CA G:ASN95 4.0 0.0 1.0 C1' 2:U307 4.1 3.7 1.0 K G:K301 4.2 27.4 1.0 CB G:ARG94 4.3 0.0 1.0 C2 2:U307 4.4 2.1 1.0 O6 2:G79 4.4 3.8 1.0 C G:ARG94 4.5 0.0 1.0 N6 2:A311 4.6 0.0 1.0 C2' 2:U307 4.6 0.4 1.0 N6 2:A313 4.7 0.0 1.0 CG G:ARG94 4.8 0.0 1.0 N1 2:U307 4.8 3.3 1.0 N G:GLY96 4.9 0.0 1.0 CA G:ARG94 4.9 0.0 1.0 O4' 2:U307 4.9 3.9 1.0

Magnesium binding site 7 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1744 b:12.9 occ:1.00 N7 2:G861 2.4 2.1 1.0 MG 2:MG1745 2.7 12.1 1.0 C8 2:G861 3.3 3.5 1.0 C5 2:G861 3.4 1.1 1.0 O6 2:G861 3.6 5.1 1.0 N7 2:G860 3.7 2.7 1.0 C6 2:G861 3.9 3.6 1.0 C5 2:G860 4.0 2.2 1.0 C8 2:G860 4.1 4.5 1.0 N4 2:C862 4.3 1.8 1.0 C6 2:G860 4.4 3.9 1.0 N9 2:G861 4.5 1.4 1.0 C4 2:G861 4.6 3.2 1.0 O6 2:G860 4.6 4.5 1.0 C4 2:G860 4.6 4.5 1.0 N9 2:G860 4.7 2.5 1.0 OP2 2:G861 4.9 6.8 1.0

Magnesium binding site 8 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1745 b:12.1 occ:1.00 MG 2:MG1744 2.7 12.9 1.0 K 2:K1579 3.3 32.4 1.0 N7 2:G860 4.2 2.7 1.0 K 2:K1578 4.6 24.6 1.0 C8 2:G860 4.9 4.5 1.0 OP2 2:G860 4.9 6.7 1.0 O6 2:G861 4.9 5.1 1.0 N7 2:G861 4.9 2.1 1.0 C5 2:U859 4.9 1.7 1.0

Magnesium binding site 9 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1746 b:13.7 occ:1.00 N7 2:A257 2.6 1.9 1.0 C8 2:A257 3.5 4.7 1.0 C5 2:A257 3.6 1.4 1.0 N6 2:A257 3.8 3.3 1.0 C6 2:A257 4.2 1.8 1.0 K 2:K1580 4.3 24.6 1.0 N7 2:G256 4.4 3.9 1.0 N9 2:A257 4.7 5.6 1.0 C4 2:A257 4.8 5.8 1.0 C8 2:G256 4.8 2.4 1.0 C5 2:G256 4.9 2.2 1.0

Magnesium binding site 10 out of 37 in the Cryo-Em Structure of Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution


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 Small Subunit of Giardia Lamblia Ribosome at 2.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1747 b:8.3 occ:1.00 OP2 2:A778 2.4 5.5 1.0 OP1 2:C780 2.5 1.2 1.0 MG 2:MG1764 3.6 9.2 1.0 P 2:A778 3.6 0.0 1.0 C8 2:A779 3.7 0.0 1.0 O5' 2:A778 3.8 4.2 1.0 C3' 2:A779 3.8 4.5 1.0 C5' 2:A779 3.8 1.1 1.0 P 2:C780 3.9 4.2 1.0 C5' 2:G505 4.1 0.0 1.0 C4' 2:A779 4.3 0.0 1.0 N7 2:A779 4.3 0.0 1.0 OP1 2:A778 4.3 4.7 1.0 O3' 2:A779 4.4 2.1 1.0 C4' 2:G505 4.6 0.7 1.0 N9 2:A779 4.6 0.0 1.0 O4' 2:A779 4.6 3.9 1.0 OP2 2:G505 4.8 6.4 1.0 C2' 2:A779 4.8 1.3 1.0 C5 2:C780 4.8 0.1 1.0 O3' 2:A777 4.9 8.2 1.0 OP2 2:C780 4.9 3.1 1.0 O5' 2:C780 4.9 5.2 1.0 O5' 2:A779 4.9 1.0 1.0 C1' 2:A779 4.9 0.0 1.0 O4' 2:G505 5.0 3.5 1.0

D.G.Hiregange, A.Rivalta, T.Bose, E.Breiner-Goldstein, S.Samiya, G.Cimicata, L.Kulakova, E.Zimmerman, A.Bashan, O.Herzberg, A.Yonath. Cryo-Em Structure of the Ancient Eukaryotic Ribosome From the Human Parasite Giardia Lamblia. Nucleic Acids Res. V. 50 1770 2022.
ISSN: ESSN 1362-4962
PubMed: 35100413
DOI: 10.1093/NAR/GKAC046