Magnesium in PDB 4io9: Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans

The structure of Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans, PDB code: 4io9 was solved by S.Han, E.S.Marr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.940, 409.690, 694.790, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans (pdb code 4io9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans, PDB code: 4io9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2901 b:50.4 occ:1.00 O4 X:U2222 3.6 72.7 1.0 N7 X:G2217 3.9 88.4 1.0 O4 X:U2057 4.1 76.0 1.0 C8 X:G2217 4.2 88.6 1.0 O4 X:U2058 4.3 79.8 1.0 O6 X:G2221 4.3 79.5 1.0 N7 X:A2220 4.4 79.7 1.0 C4 X:U2222 4.5 70.9 1.0 N6 X:A2220 4.6 78.1 1.0 N7 X:G2221 4.7 79.1 1.0 N6 X:A2060 4.7 77.0 1.0 C5 X:U2222 4.8 69.8 1.0 C5 X:U2057 4.8 76.0 1.0 C4 X:U2057 4.8 75.8 1.0 C5 X:A2220 4.9 78.9 1.0

Magnesium binding site 2 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2902 b:94.5 occ:1.00 OP1 X:G2415 3.5 75.7 1.0 OP2 X:G2415 3.7 75.5 1.0 P X:G2415 4.1 75.3 1.0 OP2 X:G2225 4.1 82.1 1.0 O2' X:U2224 4.6 77.5 1.0

Magnesium binding site 3 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2903 b:89.4 occ:1.00 O4 X:U1370 2.5 97.4 1.0 OP2 X:C1385 3.7 0.3 1.0 C4 X:U1370 3.7 97.5 1.0 O6 X:G1369 3.8 0.9 1.0 N1 X:G1371 4.2 0.2 1.0 N7 X:G1369 4.5 0.4 1.0 N3 X:U1370 4.6 97.7 1.0 C5 X:U1370 4.6 97.6 1.0 C6 X:G1369 4.7 0.0 1.0 O6 X:G1371 4.7 0.6 1.0 P X:C1385 4.7 0.1 1.0 C6 X:G1371 4.8 0.2 1.0 OP1 X:C1385 4.8 0.9 1.0 C2 X:G1371 4.8 0.0 1.0 N2 X:G1371 4.8 0.9 1.0 C5 X:G1369 4.9 0.1 1.0

Magnesium binding site 4 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2904 b:0.5 occ:1.00 OP1 X:G746 3.9 70.3 1.0 OP2 X:C771 4.0 69.5 1.0 OP2 X:G772 4.0 71.5 1.0 O5' X:C771 4.2 70.0 1.0 OP1 X:A747 4.3 71.3 1.0 P X:C771 4.4 70.5 1.0 OP1 X:C771 4.4 71.2 1.0 P X:G746 5.0 69.6 1.0

Magnesium binding site 5 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2905 b:65.1 occ:1.00 OP1 X:G772 2.6 74.2 1.0 OP2 X:G773 3.3 66.4 1.0 OP1 X:C745 3.7 68.7 1.0 P X:G772 3.7 72.4 1.0 OP2 X:G772 3.9 71.5 1.0 OP2 X:G746 4.0 69.4 1.0 OP1 X:G773 4.1 68.4 1.0 P X:G773 4.1 66.8 1.0 O5' X:G772 4.3 69.9 1.0 C5' X:G772 4.6 68.1 1.0 O3' X:G772 4.7 66.9 1.0 P X:C745 4.8 69.1 1.0 OP1 X:G746 5.0 70.3 1.0 O3' X:C771 5.0 71.6 1.0

Magnesium binding site 6 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2906 b:58.4 occ:1.00 OP2 X:G1767 1.9 66.9 1.0 P X:G1767 3.3 67.0 1.0 O5' X:G1767 3.8 66.8 1.0 N7 X:G1767 3.9 52.5 1.0 OP1 X:G1767 4.1 68.0 1.0 C8 X:G1767 4.3 53.5 1.0 OP2 X:U1766 4.4 66.6 1.0 OP1 X:U1766 4.4 66.5 1.0 O5' X:U1766 4.5 64.0 1.0 O3' X:U1766 4.5 65.7 1.0 P X:U1766 4.6 66.2 1.0 C5' X:U1766 4.7 63.0 1.0 OP1 X:A1964 4.7 75.8 1.0 C3' X:U1766 4.8 64.0 1.0 O4 X:U1768 4.9 61.5 1.0

Magnesium binding site 7 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2907 b:51.7 occ:1.00 OP1 X:C1765 2.3 72.9 1.0 P X:C1765 3.7 72.0 1.0 OP1 X:A1777 3.7 64.9 1.0 O2' X:G1763 3.7 70.3 1.0 N2 X:G1763 3.7 73.8 1.0 N3 X:G1763 3.8 72.3 1.0 OP2 X:A1777 3.9 64.8 1.0 OP2 X:C1765 4.2 72.8 1.0 P X:A1777 4.3 65.2 1.0 C2 X:G1763 4.3 72.3 1.0 O6 X:G1767 4.3 53.0 1.0 OP2 X:U1766 4.6 66.6 1.0 O3' X:A1764 4.7 70.2 1.0 C2' X:G1763 4.7 70.4 1.0 O5' X:C1765 4.7 70.1 1.0 C5' X:A1777 4.8 67.9 1.0 C1' X:G1763 4.8 69.8 1.0 C4 X:G1763 4.9 70.9 1.0

Magnesium binding site 8 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2908 b:37.8 occ:1.00 OP2 X:A2034 4.1 50.7 1.0 OP1 X:G2557 4.1 52.4 1.0 N7 X:A2034 4.3 60.0 1.0 OP1 X:C2033 4.3 57.3 1.0 OP2 X:A2593 4.6 55.4 1.0 N7 X:A2593 4.6 54.1 1.0 OP1 X:U2592 4.8 58.8 1.0 C8 X:A2034 4.8 60.2 1.0 OP2 X:C2033 4.8 58.1 1.0 OP2 X:G2557 4.8 51.5 1.0 P X:G2557 4.9 52.3 1.0

Magnesium binding site 9 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2909 b:96.1 occ:1.00 OP2 X:G2743 3.1 96.3 1.0 OP2 X:G2742 3.8 0.9 1.0 N7 X:G2743 4.0 94.4 1.0 O5' X:G2742 4.0 1.0 1.0 P X:G2742 4.3 0.1 1.0 OP2 X:A2718 4.4 0.0 1.0 P X:G2743 4.5 97.4 1.0 C8 X:G2743 4.5 94.2 1.0 OP1 X:G2742 4.6 0.6 1.0 C3' X:G2742 4.7 98.5 1.0 C5' X:G2742 4.9 0.9 1.0

Magnesium binding site 10 out of 35 in the Crystal Structure of Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


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 Compound 4D Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2910 b:42.1 occ:1.00 OP1 X:A2556 2.2 52.8 1.0 OP1 X:G2555 2.2 61.9 1.0 P X:G2555 3.5 61.1 1.0 OP2 X:G2036 3.6 55.9 1.0 O3' X:C2554 3.6 60.3 1.0 P X:A2556 3.6 52.0 1.0 OP1 X:G2036 3.9 57.2 1.0 OP2 X:G2035 4.0 56.7 1.0 O3' X:G2555 4.2 53.6 1.0 P X:G2036 4.2 56.2 1.0 OP2 X:G2555 4.3 61.2 1.0 OP2 X:A2556 4.6 51.9 1.0 C3' X:G2555 4.6 54.3 1.0 O5' X:A2556 4.6 49.7 1.0 O5' X:G2555 4.7 57.7 1.0 C3' X:C2554 4.9 58.2 1.0 O3' X:G2035 4.9 54.9 1.0 C5' X:G2555 4.9 55.2 1.0

T.V.Magee, S.Han, S.P.Mccurdy, T.T.Nguyen, K.Granskog, E.S.Marr, B.A.Maguire, M.D.Huband, J.M.Chen, T.A.Subashi, V.Shanmugasundaram. Novel 3-O-Carbamoyl Erythromycin A Derivatives (Carbamolides) with Activity Against Resistant Staphylococcal and Streptococcal Isolates. Bioorg.Med.Chem.Lett. V. 23 1727 2013.
ISSN: ISSN 0960-894X
PubMed: 23414806
DOI: 10.1016/J.BMCL.2013.01.067