Magnesium in PDB 1m90: Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit

The structure of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit, PDB code: 1m90 was solved by J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.661, 299.773, 573.684, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.2

The structure of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

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; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 119;

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit (pdb code 1m90). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 119 binding sites of Magnesium where determined in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit, PDB code: 1m90:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8001 b:27.1 occ:1.00 OP2 A:C2534 1.9 32.3 1.0 O A:HOH7309 2.0 16.4 1.0 OP2 A:C2533 2.1 29.7 1.0 O A:HOH8697 2.2 25.9 1.0 OP2 A:A2483 2.2 33.0 1.0 O A:HOH3144 2.2 22.0 1.0 O3' A:G2482 3.2 32.7 1.0 P A:A2483 3.2 31.8 1.0 P A:C2534 3.4 32.0 1.0 P A:C2533 3.5 29.4 1.0 O A:HOH9160 4.0 24.6 1.0 O2' A:A2532 4.0 29.3 1.0 O3' A:A2532 4.0 28.9 1.0 OP1 A:A2483 4.1 33.0 1.0 O2' A:G2482 4.1 34.5 1.0 O3' A:C2533 4.2 30.6 1.0 OP1 A:C2534 4.2 31.0 1.0 O5' A:C2533 4.3 28.0 1.0 O A:HOH3858 4.3 38.9 1.0 OP2 A:U2484 4.3 35.8 1.0 O5' A:C2534 4.3 28.7 1.0 O A:HOH7013 4.4 35.0 1.0 C3' A:C2533 4.4 28.1 1.0 O5' A:A2483 4.5 33.5 1.0 O A:HOH5908 4.5 94.5 1.0 C3' A:G2482 4.5 32.6 1.0 OP1 A:C2533 4.6 27.5 1.0 C5' A:A2483 4.7 30.2 1.0 C2' A:G2482 4.8 31.8 1.0 MG A:MG8002 4.8 28.8 1.0

Magnesium binding site 2 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8002 b:28.8 occ:1.00 O A:HOH3858 1.9 38.9 1.0 OP1 A:A2483 2.0 33.0 1.0 O A:HOH7287 2.0 29.8 1.0 O6 A:G627 2.0 28.9 1.0 O A:HOH7288 2.1 19.8 1.0 OP1 A:C2534 2.1 31.0 1.0 P A:A2483 3.2 31.8 1.0 C6 A:G627 3.2 27.9 1.0 P A:C2534 3.4 32.0 1.0 OP2 A:A2483 3.6 33.0 1.0 OP2 A:C2534 3.9 32.3 1.0 N1 A:G627 3.9 26.5 1.0 O4 A:U626 3.9 30.1 1.0 O A:HOH6633 3.9 47.4 1.0 O A:HOH5414 4.1 37.9 1.0 O A:HOH8782 4.1 20.2 1.0 O5' A:A2483 4.1 33.5 1.0 O2' A:U625 4.2 24.0 1.0 O3' A:C2533 4.2 30.6 1.0 O3' A:G2482 4.3 32.7 1.0 O A:HOH3054 4.4 45.8 1.0 OP2 A:U2535 4.4 30.0 1.0 C5 A:U626 4.4 29.8 1.0 C5 A:G627 4.4 27.5 1.0 C4 A:U626 4.4 29.9 1.0 O5' A:C2534 4.5 28.7 1.0 C3' A:G2482 4.8 32.6 1.0 MG A:MG8001 4.8 27.1 1.0 N7 A:G627 4.9 26.6 1.0 C5' A:C2534 5.0 30.2 1.0

Magnesium binding site 3 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8003 b:26.8 occ:1.00 OP1 A:A2624 1.9 25.3 1.0 O A:HOH3194 2.0 34.4 1.0 O A:HOH8541 2.0 15.4 1.0 OP2 A:G877 2.1 22.5 1.0 OP2 A:A876 2.2 24.5 1.0 O C:HOH8536 2.4 26.2 1.0 P A:A2624 3.3 26.8 1.0 P A:G877 3.3 21.9 1.0 P A:A876 3.6 26.5 1.0 OP1 A:G877 3.8 23.2 1.0 O3' A:G2623 3.9 26.3 1.0 O A:HOH8540 4.1 19.5 1.0 OD1 C:ASN195 4.1 23.7 1.0 O5' A:A876 4.1 23.7 1.0 O3' A:A875 4.1 24.5 1.0 O3' A:A876 4.1 22.7 1.0 O A:HOH6691 4.1 47.9 1.0 OP2 A:A2624 4.2 25.8 1.0 O C:HOH8617 4.2 40.2 1.0 O A:HOH5810 4.2 32.6 1.0 O C:HOH8566 4.3 39.4 1.0 O5' A:A2624 4.4 27.9 1.0 O C:ALA193 4.4 28.1 1.0 C5' A:A876 4.4 22.0 1.0 O C:HOH8545 4.5 37.7 1.0 O5' A:G877 4.6 22.4 1.0 C5' A:A2624 4.6 28.6 1.0 C3' A:A876 4.7 24.4 1.0 OP1 A:A876 4.7 27.0 1.0 CG C:ASN195 5.0 23.1 1.0 O A:HOH7318 5.0 11.7 1.0

Magnesium binding site 4 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8004 b:26.1 occ:1.00 O A:HOH3311 1.9 19.2 1.0 O6 A:G456 2.0 31.9 1.0 OP1 A:A459 2.0 23.2 1.0 O A:HOH8566 2.0 17.5 1.0 O A:HOH9298 2.0 16.4 1.0 O A:HOH7294 2.0 18.9 1.0 C6 A:G456 3.1 33.2 1.0 P A:A459 3.3 26.2 1.0 C5 A:G456 3.9 33.0 1.0 N7 A:G456 3.9 31.8 1.0 OP2 A:A459 4.0 28.9 1.0 O5' A:A459 4.0 25.0 1.0 O A:HOH5497 4.1 46.6 1.0 O A:HOH3231 4.2 35.2 1.0 C5' A:A459 4.2 27.0 1.0 N1 A:G456 4.2 34.5 1.0 CE E:LYS85 4.2 24.7 1.0 O A:HOH3040 4.3 42.0 1.0 O A:HOH8853 4.3 20.5 1.0 NZ E:LYS85 4.4 24.0 1.0 N7 A:A455 4.4 32.1 1.0 OP1 A:A460 4.4 29.6 1.0 OP2 A:A455 4.5 29.5 1.0 O3' A:G458 4.5 25.1 1.0 OP1 A:A477 4.7 26.4 1.0 O A:HOH4942 4.8 36.6 1.0 CD E:LYS85 4.9 25.8 1.0 N6 A:A455 5.0 29.5 1.0

Magnesium binding site 5 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8005 b:33.5 occ:1.00 O A:HOH7311 1.9 24.5 1.0 O A:HOH7310 2.0 32.0 1.0 O A:HOH3140 2.0 20.6 1.0 OP2 A:A1839 2.0 27.6 1.0 OP1 A:A1836 2.1 22.6 1.0 OP1 A:U1838 2.1 26.9 1.0 P A:A1839 3.5 26.8 1.0 P A:A1836 3.5 24.4 1.0 P A:U1838 3.5 25.1 1.0 O A:HOH5097 3.8 52.0 1.0 O A:HOH8528 3.9 13.7 1.0 O5' A:A1836 4.2 27.0 1.0 OP2 A:U1838 4.2 26.0 1.0 O5' A:A1839 4.3 26.5 1.0 O5' A:U1838 4.3 25.7 1.0 O A:HOH5038 4.3 45.1 1.0 OP2 A:A1836 4.3 26.5 1.0 O A:HOH9156 4.3 33.2 1.0 OP1 A:A1839 4.3 27.3 1.0 O3' A:U1838 4.3 26.4 1.0 C2' A:U1835 4.4 24.5 1.0 O A:HOH9034 4.4 41.1 1.0 C3' A:G1837 4.4 27.2 1.0 OP2 A:G1837 4.5 27.5 1.0 O3' A:U1835 4.5 22.9 1.0 O3' A:G1837 4.5 24.4 1.0 C3' A:U1835 4.6 23.4 1.0 C3' A:U1838 4.6 25.6 1.0 C5' A:U1838 4.6 23.8 1.0 N7 A:A1839 4.6 27.7 1.0 C8 A:A1839 4.7 28.0 1.0 O A:HOH7386 4.7 32.0 1.0 O2' A:U1835 4.8 25.6 1.0

Magnesium binding site 6 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8006 b:30.3 occ:1.00 O A:HOH9330 1.8 27.8 1.0 OP2 A:C822 1.9 35.3 1.0 OP2 A:U821 2.0 35.3 1.0 O A:HOH3146 2.0 26.8 1.0 OP1 A:G854 2.1 33.9 1.0 O A:HOH3282 2.3 38.0 1.0 P A:C822 3.3 36.1 1.0 P A:G854 3.3 33.4 1.0 P A:U821 3.4 35.0 1.0 O5' A:U821 3.7 38.8 1.0 OP1 A:G856 3.8 37.8 1.0 OP2 A:G854 3.9 33.5 1.0 O3' A:U821 4.0 36.8 1.0 O5' A:G854 4.0 32.7 1.0 C3' A:U821 4.0 37.2 1.0 O A:HOH9729 4.1 38.2 1.0 NA A:NA8327 4.1 41.5 1.0 OP1 A:U855 4.1 34.7 1.0 O A:HOH4533 4.1 40.8 1.0 OP1 A:C822 4.2 38.4 1.0 O3' A:G820 4.2 35.1 1.0 O5' A:C822 4.4 34.7 1.0 C5' A:G854 4.4 30.6 1.0 OP1 A:U821 4.5 34.4 1.0 O3' A:C853 4.6 31.8 1.0 C5' A:U821 4.9 39.1 1.0 C4' A:U821 5.0 38.2 1.0 O A:HOH9249 5.0 44.5 1.0 C5 A:C822 5.0 34.3 1.0

Magnesium binding site 7 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8007 b:16.6 occ:1.00 O A:HOH7299 1.9 19.3 1.0 OP2 A:U832 1.9 30.0 1.0 OP1 A:A1839 2.0 27.3 1.0 OP2 A:A1840 2.1 22.6 1.0 O A:HOH8528 2.2 13.7 1.0 O A:HOH9883 2.2 18.9 1.0 P A:A1840 3.3 24.9 1.0 P A:U832 3.3 29.1 1.0 P A:A1839 3.4 26.8 1.0 OP1 A:A1840 3.6 26.1 1.0 O A:HOH9156 3.6 33.2 1.0 O A:HOH8621 3.7 34.5 1.0 OP1 A:U832 3.9 29.1 1.0 O A:HOH5886 3.9 48.6 1.0 OP2 A:A1839 4.1 27.6 1.0 O5' A:U832 4.2 28.7 1.0 O3' A:A1839 4.2 23.8 1.0 O A:HOH7417 4.3 54.0 1.0 O3' A:U1838 4.3 26.4 1.0 O3' A:U831 4.3 28.8 1.0 O5' A:A1839 4.4 26.5 1.0 O5' A:A1840 4.5 24.9 1.0 C3' A:A1839 4.6 25.1 1.0 C5' A:A1839 4.6 25.9 1.0 C5' A:U832 4.7 29.7 1.0 OP2 A:G833 4.8 32.4 1.0 C3' A:U831 4.8 28.9 1.0 O A:HOH7310 4.8 32.0 1.0 O A:HOH7386 5.0 32.0 1.0

Magnesium binding site 8 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8008 b:35.7 occ:1.00 O A:HOH7387 1.8 35.7 1.0 O A:HOH7303 2.0 24.9 1.0 OP1 A:U919 2.0 26.1 1.0 O A:HOH3158 2.1 35.5 1.0 OP1 A:C2464 2.1 29.9 1.0 OP1 A:A2465 2.2 33.4 1.0 P A:U919 3.0 25.4 1.0 P A:C2464 3.5 28.4 1.0 OP2 A:U919 3.5 25.6 1.0 P A:A2465 3.5 33.7 1.0 O5' A:U919 3.7 22.8 1.0 O A:HOH5427 4.0 58.0 1.0 O5' A:A2465 4.0 32.9 1.0 OP2 A:A2465 4.1 33.2 1.0 O5' A:C2464 4.1 30.4 1.0 O A:HOH8970 4.1 27.7 1.0 OP2 A:C2464 4.1 31.5 1.0 C5' A:C2464 4.2 31.1 1.0 C5' A:U919 4.2 26.1 1.0 O A:HOH9873 4.2 26.7 1.0 O3' A:G918 4.4 25.7 1.0 O A:HOH9068 4.4 49.7 1.0 OP1 A:G2466 4.4 30.1 1.0 O3' A:A2463 4.6 30.6 1.0 O A:HOH9441 4.6 47.7 1.0 C3' A:A2465 4.6 31.2 1.0 O3' A:C2464 4.8 32.6 1.0 C2' A:A2465 4.9 31.5 1.0 C5' A:A2465 4.9 31.0 1.0

Magnesium binding site 9 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8009 b:26.2 occ:1.00 O A:HOH7305 1.8 23.8 1.0 OP1 A:A2612 1.8 24.6 1.0 O A:HOH6964 2.0 32.7 1.0 OP1 A:G2611 2.1 27.1 1.0 O A:HOH7304 2.2 25.9 1.0 O A:HOH3268 2.2 24.3 1.0 P A:A2612 3.3 26.3 1.0 P A:G2611 3.3 28.3 1.0 O3' A:U2610 3.5 29.6 1.0 OP2 A:G2093 3.6 26.8 1.0 NA A:NA8358 3.7 82.2 1.0 O A:HOH8854 3.8 33.2 1.0 C5' A:G2611 4.0 27.4 1.0 O5' A:G2611 4.0 28.2 1.0 OP2 A:A2612 4.0 28.5 1.0 O3' A:G2611 4.1 26.2 1.0 O A:HOH8989 4.1 39.1 1.0 OP2 A:G2094 4.1 26.4 1.0 O5' A:A2612 4.2 28.0 1.0 OP1 A:G2094 4.3 28.6 1.0 O A:HOH8825 4.3 28.2 1.0 C3' A:G2611 4.5 26.4 1.0 OP2 A:G2611 4.6 27.9 1.0 P A:G2094 4.7 28.3 1.0 C3' A:U2610 4.8 29.9 1.0 C4' A:G2611 4.8 26.0 1.0 P A:G2093 5.0 29.1 1.0 O2' A:U2610 5.0 30.4 1.0 C4' A:U2610 5.0 28.9 1.0

Magnesium binding site 10 out of 119 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8010 b:35.3 occ:1.00 O A:HOH8792 1.8 29.5 1.0 OP1 A:G836 1.8 29.1 1.0 O A:HOH3368 1.9 34.8 1.0 O A:HOH8882 2.2 19.7 1.0 OP1 A:U2615 2.2 27.8 1.0 OE1 D:GLN230 2.3 25.2 1.0 P A:G836 3.2 31.9 1.0 CD D:GLN230 3.4 24.4 1.0 P A:U2615 3.6 28.0 1.0 O A:HOH4579 3.7 44.8 1.0 CG D:GLN230 4.0 23.8 1.0 CB D:GLN230 4.0 25.1 1.0 OP2 A:G836 4.0 32.4 1.0 O5' A:G836 4.1 30.0 1.0 C5' A:G836 4.1 29.2 1.0 O A:HOH6363 4.2 41.1 1.0 O3' A:U835 4.2 28.9 1.0 C3' A:U835 4.3 28.1 1.0 OP2 A:U2615 4.3 28.9 1.0 CA D:GLN230 4.5 25.6 1.0 O5' A:U2615 4.5 27.7 1.0 O A:HOH8727 4.5 26.0 1.0 O A:HOH3519 4.5 44.2 1.0 O3' A:C2614 4.5 25.7 1.0 NE2 D:GLN230 4.5 24.4 1.0 O D:GLN230 4.6 25.5 1.0 O A:HOH9070 4.7 32.0 1.0 OP2 A:G2616 4.7 28.4 1.0 C5' A:U835 4.7 28.4 1.0 N2 A:G2616 4.9 28.4 1.0 C5' A:U2615 4.9 25.7 1.0

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz. Structural Insights Into Peptide Bond Formation. Proc.Natl.Acad.Sci.Usa V. 99 11670 2002.
ISSN: ISSN 0027-8424
PubMed: 12185246
DOI: 10.1073/PNAS.172404099