Magnesium in PDB 4u67: Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22

The structure of Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22, PDB code: 4u67 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 / 3.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.720, 412.591, 696.974, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27

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 - 51;

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 (pdb code 4u67). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 51 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, PDB code: 4u67:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg201 b:25.8 occ:1.00 O K:GLY4 2.7 40.4 1.0 C K:GLY4 3.7 40.4 1.0 OP1 X:A2795 3.9 50.3 1.0 O6 X:G2797 4.0 41.8 1.0 CA K:LYS5 4.1 25.9 1.0 N K:ALA6 4.1 25.8 1.0 N K:LYS5 4.4 25.8 1.0 OP2 X:A2795 4.4 50.4 1.0 OP1 X:G1670 4.5 27.2 1.0 C K:LYS5 4.7 25.9 1.0 CA K:GLY4 4.7 40.2 1.0 P X:A2795 4.7 50.4 1.0 O K:ALA6 4.8 25.9 1.0 N1 X:G2797 4.9 41.8 1.0 C6 X:G2797 4.9 41.9 1.0

Magnesium binding site 2 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2901 b:37.8 occ:1.00 OP1 X:U800 2.0 39.1 1.0 OP2 X:C803 2.0 0.8 1.0 P X:C803 2.9 0.8 1.0 OP1 X:C803 2.9 0.4 1.0 P X:U800 3.3 39.9 1.0 C5' X:A802 3.5 51.3 1.0 C4' X:A802 3.6 50.3 1.0 OP2 X:U800 3.7 40.0 1.0 O3' X:A802 4.0 49.8 1.0 C3' X:A802 4.1 50.1 1.0 O5' X:C803 4.1 0.7 1.0 O3' X:C799 4.2 39.5 1.0 N6 X:A1771 4.2 43.4 1.0 N7 X:A1771 4.4 42.3 1.0 O5' X:U800 4.4 41.0 1.0 C6 X:A1771 4.7 42.5 1.0 OP2 X:C804 4.8 42.3 1.0 C5 X:A1771 4.8 42.0 1.0 O5' X:A802 4.8 51.3 1.0 O4' X:A802 4.9 49.6 1.0 C5' X:A801 5.0 40.5 1.0

Magnesium binding site 3 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2902 b:33.5 occ:1.00 OP2 X:G2039 2.4 33.7 1.0 OP2 X:A2040 2.5 45.0 1.0 N6 X:A2041 3.0 36.3 1.0 P X:G2039 3.6 34.2 1.0 P X:A2040 3.9 45.0 1.0 O5' X:G2039 4.0 33.7 1.0 N7 X:A2040 4.1 42.9 1.0 OP1 X:G2039 4.1 35.1 1.0 C6 X:A2041 4.2 36.0 1.0 N7 X:A2041 4.3 36.1 1.0 OP1 X:G2484 4.4 44.5 1.0 C8 X:A2040 4.5 43.0 1.0 O5' X:A2040 4.5 44.3 1.0 C5 X:A2041 4.6 35.9 1.0 OP1 X:A2040 4.6 45.8 1.0 O5' X:U2483 4.9 43.3 1.0 O2' X:A2482 4.9 35.1 1.0 N6 X:A2042 4.9 41.1 1.0 C5' X:G2039 5.0 33.1 1.0 O3' X:C2038 5.0 48.5 1.0

Magnesium binding site 4 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2903 b:30.3 occ:1.00 OP2 X:A2684 2.2 42.4 1.0 P X:A2684 3.7 42.8 1.0 N7 X:A2685 3.7 50.4 1.0 O5' X:A2684 4.1 42.7 1.0 OP2 X:C2683 4.1 53.9 1.0 N6 X:A2685 4.2 50.0 1.0 N7 X:A2684 4.2 42.1 1.0 C8 X:A2684 4.3 42.3 1.0 OP1 X:A2684 4.6 42.9 1.0 C5 X:A2685 4.6 50.1 1.0 OP1 X:C2683 4.7 54.3 1.0 O3' X:C2683 4.7 54.7 1.0 OP2 X:A2685 4.7 50.8 1.0 C8 X:A2685 4.7 50.4 1.0 P X:C2683 4.8 54.3 1.0 C6 X:A2685 4.9 50.0 1.0 C3' X:C2683 4.9 54.8 1.0 O5' X:C2683 5.0 54.6 1.0

Magnesium binding site 5 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2904 b:29.3 occ:1.00 OP2 X:A1682 1.8 29.4 1.0 OP1 X:A1681 2.8 28.5 1.0 P X:A1682 3.3 29.7 1.0 O5' X:A1681 3.4 28.5 1.0 P X:A1681 3.8 28.3 1.0 C5' X:A1681 3.9 28.5 1.0 OP1 X:A1682 3.9 29.9 1.0 O5' X:A1682 4.2 30.0 1.0 O3' X:A1681 4.4 29.4 1.0 OP2 X:A1681 4.6 28.2 1.0 C3' X:A1681 4.7 29.0 1.0 OP2 X:G1683 4.7 30.6 1.0 C4' X:A1681 4.9 28.6 1.0 O3' X:U1680 5.0 27.9 1.0

Magnesium binding site 6 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2905 b:27.6 occ:1.00 OP2 X:G2661 2.1 38.9 1.0 OP1 X:A2701 2.3 30.8 1.0 P X:G2661 3.5 39.1 1.0 P X:A2701 3.6 30.6 1.0 O5' X:G2661 4.0 39.5 1.0 OP2 X:G2702 4.1 26.9 1.0 O5' X:A2701 4.2 30.3 1.0 O3' X:C2660 4.2 27.8 1.0 OP2 X:A2701 4.3 30.5 1.0 C5' X:A2701 4.3 30.4 1.0 OP2 X:C2662 4.4 28.4 1.0 C5' X:G2661 4.6 39.7 1.0 OP1 X:G2661 4.7 39.2 1.0 O3' X:U2700 4.8 27.2 1.0

Magnesium binding site 7 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2906 b:27.2 occ:1.00 OP2 X:G2557 4.0 33.5 1.0 N7 X:A2593 4.2 28.1 1.0 OP2 X:A2034 4.4 30.7 1.0 OP2 X:C2033 4.4 29.9 1.0 N7 X:A2034 4.5 31.3 1.0 OP1 X:G2557 4.5 34.0 1.0 C8 X:A2034 4.7 31.3 1.0 OP2 X:A2593 4.7 27.5 1.0 P X:G2557 4.8 33.8 1.0 C8 X:A2593 4.9 28.2 1.0 NH1 B:ARG137 5.0 47.3 1.0

Magnesium binding site 8 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2907 b:42.5 occ:1.00 OP2 X:C2431 4.0 41.5 1.0 O6 X:G2434 4.1 52.9 1.0 OP1 X:A2430 4.2 46.7 1.0 N4 X:C2475 4.3 45.8 1.0 N1 X:A2476 4.3 55.7 1.0 N7 X:A2432 4.6 41.8 1.0 OP2 X:A2430 4.7 46.0 1.0 N7 X:G2433 4.7 49.0 1.0 OP2 X:A2432 4.8 41.8 1.0 C2 X:A2476 4.8 55.7 1.0 P X:A2430 4.9 46.3 1.0 O6 X:G2433 4.9 50.9 1.0

Magnesium binding site 9 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2908 b:31.9 occ:1.00 OP2 X:C1340 1.9 31.4 1.0 P X:C1340 3.1 31.3 1.0 O5' X:C1340 3.6 31.3 1.0 OP1 X:C1340 3.7 31.7 1.0 N7 X:G1337 4.1 32.3 1.0 N7 X:G1341 4.1 37.3 1.0 OP2 X:U1339 4.2 30.5 1.0 C8 X:G1337 4.4 32.0 1.0 OP1 X:U1339 4.4 30.7 1.0 O3' X:U1339 4.5 30.7 1.0 OP2 X:G1341 4.5 38.2 1.0 O6 X:G1341 4.7 36.7 1.0 P X:U1339 4.8 30.3 1.0 C5' X:C1340 5.0 31.2 1.0

Magnesium binding site 10 out of 51 in the Crystal Structure of the Large Ribosomal Subunit (50S) of Deinococcus Radiodurans Containing A Three Residue Insertion in L22


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2909 b:51.2 occ:1.00 OP1 X:A576 2.1 51.1 1.0 O4 X:U823 3.1 52.4 1.0 P X:A576 3.3 50.6 1.0 O3' X:U575 3.6 49.6 1.0 N7 X:G822 4.1 50.2 1.0 C4 X:U823 4.3 52.5 1.0 OP2 X:A576 4.3 51.4 1.0 OP2 X:A821 4.3 51.1 1.0 O5' X:A576 4.4 50.0 1.0 OP2 X:G822 4.5 47.7 1.0 C5' X:A576 4.6 49.3 1.0 O I:SER39 4.7 54.8 1.0 C8 X:G822 4.7 49.4 1.0 C5 X:U823 4.9 51.6 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