Magnesium in PDB 4wfn: Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin

The structure of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin, PDB code: 4wfn was solved by I.Wekselman, E.Zimmerman, H.Rozenberg, A.Bashan, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 3.54
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	170.092, 411.588, 695.883, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 28.2

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;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin (pdb code 4wfn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 70 binding sites of Magnesium where determined in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin, PDB code: 4wfn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:54.6 occ:1.00 OP1 X:A2577 2.3 63.6 1.0 O A:HIS233 2.8 65.2 1.0 O A:GLY234 3.3 52.8 1.0 C A:HIS233 3.4 65.6 1.0 P X:A2577 3.6 63.8 1.0 O3' X:G2576 3.7 55.2 1.0 O A:PRO232 3.9 55.7 1.0 CA A:HIS233 3.9 67.0 1.0 CA A:GLY241 3.9 1.0 1.0 O A:GLY235 4.0 80.5 1.0 C A:GLY234 4.2 52.0 1.0 N A:GLY234 4.4 53.4 1.0 O A:THR240 4.4 87.5 1.0 N A:ALA242 4.5 67.9 1.0 OP2 X:A2577 4.6 63.5 1.0 O5' X:A2577 4.6 63.2 1.0 C5' X:A2577 4.6 63.2 1.0 C A:GLY235 4.8 80.1 1.0 C A:PRO232 4.8 56.0 1.0 C A:GLY241 4.8 0.3 1.0 N A:GLY241 4.8 0.3 1.0 CA A:GLY234 4.8 52.2 1.0 N A:HIS233 4.9 67.5 1.0 CB A:HIS233 4.9 67.1 1.0 C A:THR240 4.9 88.0 1.0

Magnesium binding site 2 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:34.7 occ:1.00 O B:LYS152 3.7 33.9 1.0 C5' X:G2621 3.8 35.8 1.0 C B:LYS152 4.1 33.4 1.0 C4' X:G2621 4.2 35.0 1.0 N G:TYR106 4.2 57.1 1.0 N B:GLY153 4.4 33.5 1.0 CA B:GLY153 4.4 33.2 1.0 CB G:TYR106 4.4 56.4 1.0 CG B:LYS152 4.6 34.2 1.0 CB B:LYS152 4.6 34.4 1.0 CD B:LYS152 4.7 35.0 1.0 O G:TYR106 4.7 58.0 1.0 O2' X:G2620 4.8 48.1 1.0 CA G:TYR106 4.9 57.1 1.0

Magnesium binding site 3 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg201 b:27.4 occ:1.00 CG K:LYS5 3.0 27.4 1.0 CB K:LYS5 3.0 27.2 1.0 CD2 K:HIS3 3.1 72.6 1.0 O K:HIS3 3.4 72.2 1.0 CG K:HIS3 3.6 72.4 1.0 C4' X:A2795 3.7 41.5 1.0 NE2 K:HIS3 3.8 72.6 1.0 O3' X:G2702 3.8 27.6 1.0 OP1 X:C2703 3.8 27.8 1.0 CB K:HIS3 4.1 72.3 1.0 CD K:LYS5 4.1 27.4 1.0 O3' X:A2795 4.2 41.6 1.0 O4' X:A2795 4.2 41.6 1.0 CA K:LYS5 4.4 27.0 1.0 ND1 K:HIS3 4.4 72.3 1.0 O5' X:A2795 4.4 41.3 1.0 C K:HIS3 4.4 72.1 1.0 O2' X:A2795 4.4 41.8 1.0 CE1 K:HIS3 4.5 72.4 1.0 P X:C2703 4.5 27.8 1.0 C3' X:A2795 4.5 41.7 1.0 C5' X:A2795 4.5 41.4 1.0 O2' X:G2702 4.6 27.3 1.0 N K:LYS5 4.7 26.9 1.0 C1' X:A2795 4.8 41.8 1.0 C2' X:A2795 4.9 41.8 1.0 CA K:HIS3 4.9 72.2 1.0 C K:GLY4 5.0 31.6 1.0 C5' X:C2703 5.0 27.5 1.0 C3' X:G2702 5.0 27.6 1.0

Magnesium binding site 4 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg202 b:27.0 occ:1.00 O K:GLY4 3.1 31.7 1.0 O6 X:G2797 3.8 31.8 1.0 OP1 X:A2795 3.8 41.1 1.0 CA K:LYS5 3.9 27.0 1.0 C K:GLY4 4.0 31.6 1.0 N K:ALA6 4.2 27.1 1.0 N K:LYS5 4.4 26.9 1.0 C K:LYS5 4.5 27.0 1.0 O K:ALA6 4.6 27.2 1.0 OP2 X:A2795 4.6 41.2 1.0 OP1 X:G1670 4.6 34.2 1.0 N1 X:G2797 4.6 31.8 1.0 C6 X:G2797 4.6 31.8 1.0 P X:A2795 4.7 41.3 1.0 CB K:LYS5 4.9 27.2 1.0

Magnesium binding site 5 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg201 b:35.7 occ:1.00 MG M:MG202 0.1 35.4 1.0 ND2 M:ASN58 2.9 43.9 1.0 OP1 X:G2699 4.0 31.1 1.0 CG M:ASN58 4.0 44.0 1.0 OP1 X:U2700 4.3 30.1 1.0 OP2 X:G2665 4.6 29.7 1.0 OD1 M:ASN58 4.7 43.9 1.0 OP2 X:G2664 4.8 31.4 1.0 CB M:ASN58 4.9 44.3 1.0 O5' X:G2699 4.9 30.5 1.0

Magnesium binding site 6 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg202 b:35.4 occ:1.00 MG M:MG201 0.1 35.7 1.0 ND2 M:ASN58 2.9 43.9 1.0 CG M:ASN58 4.0 44.0 1.0 OP1 X:G2699 4.1 31.1 1.0 OP1 X:U2700 4.4 30.1 1.0 OP2 X:G2665 4.6 29.7 1.0 OD1 M:ASN58 4.7 43.9 1.0 OP2 X:G2664 4.8 31.4 1.0 CB M:ASN58 4.9 44.3 1.0

Magnesium binding site 7 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2901 b:69.4 occ:1.00 OP2 X:A1167 1.8 70.5 1.0 NH1 N:ARG58 2.4 98.4 1.0 NH2 N:ARG58 3.1 0.7 1.0 CZ N:ARG58 3.1 99.6 1.0 P X:A1167 3.3 69.3 1.0 C3' X:A1166 4.0 66.8 1.0 O3' X:A1166 4.1 66.0 1.0 O5' X:A1166 4.1 67.0 1.0 OP1 X:A1167 4.1 68.2 1.0 O5' X:A1167 4.2 69.9 1.0 OP2 X:A1166 4.3 68.7 1.0 NE N:ARG58 4.4 99.7 1.0 C5' X:A1167 4.5 70.7 1.0 P X:A1166 4.8 67.2 1.0 N4 X:C1009 4.9 85.8 1.0 O6 X:G1008 5.0 74.7 1.0 C5' X:A1166 5.0 65.7 1.0

Magnesium binding site 8 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2903 b:30.8 occ:1.00 OP2 X:A1681 2.3 30.1 1.0 N6 X:A1682 3.1 30.7 1.0 P X:A1681 3.8 30.2 1.0 O6 X:G1975 3.9 29.4 1.0 N7 X:G1975 3.9 29.3 1.0 N7 X:A1681 3.9 30.0 1.0 O6 X:G1683 4.1 30.9 1.0 OP1 X:G1975 4.2 29.7 1.0 O6 X:G1684 4.2 31.1 1.0 C6 X:A1682 4.3 31.0 1.0 C6 X:G1975 4.4 29.4 1.0 C2' X:U1680 4.4 29.3 1.0 C5 X:G1975 4.4 29.3 1.0 OP2 X:G1975 4.5 30.3 1.0 C3' X:U1680 4.5 29.5 1.0 C8 X:A1681 4.6 30.1 1.0 O5' X:A1681 4.6 30.3 1.0 N7 X:A1682 4.6 31.1 1.0 O3' X:U1680 4.7 29.9 1.0 OP1 X:A1681 4.7 30.6 1.0 C8 X:G1975 4.8 29.3 1.0 C6 X:G1683 4.9 31.3 1.0 C5 X:A1682 4.9 31.2 1.0 P X:G1975 4.9 29.9 1.0 N7 X:G1683 4.9 31.7 1.0 C5 X:A1681 4.9 30.3 1.0

Magnesium binding site 9 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2904 b:32.6 occ:1.00 OP2 X:C1340 1.9 32.1 1.0 P X:C1340 3.2 31.9 1.0 N7 X:G1337 3.4 43.9 1.0 O5' X:C1340 3.8 31.9 1.0 OP1 X:C1340 4.0 32.3 1.0 C8 X:G1337 4.1 43.5 1.0 OP2 X:U1339 4.1 31.2 1.0 OP1 X:U1339 4.1 31.4 1.0 N7 X:G1341 4.2 34.1 1.0 C5 X:G1337 4.4 43.9 1.0 O3' X:U1339 4.5 31.4 1.0 O6 X:G1337 4.6 44.6 1.0 P X:U1339 4.6 31.1 1.0 OP2 X:G1341 4.8 35.0 1.0 C6 X:G1337 4.8 44.3 1.0 C6 X:C1340 5.0 31.3 1.0 C8 X:G1341 5.0 34.4 1.0

Magnesium binding site 10 out of 70 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22 in Complex with Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2905 b:31.4 occ:1.00 OP2 X:A1682 2.0 31.4 1.0 OP1 X:A1681 2.4 30.6 1.0 P X:A1682 3.4 31.7 1.0 OP1 X:A1682 3.8 32.0 1.0 P X:A1681 3.8 30.2 1.0 O5' X:A1682 4.4 32.1 1.0 O5' X:A1681 4.4 30.3 1.0 O3' X:A1681 4.5 31.4 1.0 C5' X:A1681 4.5 30.4 1.0 OP2 X:A1681 4.7 30.1 1.0 OP2 X:G1683 4.7 32.7 1.0 O3' X:U1680 4.8 29.9 1.0 C3' X:A1681 4.9 31.0 1.0

I.Wekselman, E.Zimmerman, C.Davidovich, M.Belousoff, D.Matzov, M.Krupkin, H.Rozenberg, A.Bashan, G.Friedlander, J.Kjeldgaard, H.Ingmer, L.Lindahl, J.M.Zengel, A.Yonath. The Ribosomal Protein UL22 Modulates the Shape of the Protein Exit Tunnel. Structure V. 25 1233 2017.
ISSN: ISSN 1878-4186
PubMed: 28689968
DOI: 10.1016/J.STR.2017.06.004