Magnesium in PDB 3g6e: Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit

The structure of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit, PDB code: 3g6e was solved by G.Gurel, G.Blaha, 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)	49.90 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.863, 299.418, 574.087, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.9

The structure of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Strontium	(Sr)	108 atoms
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 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 - 93;

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit (pdb code 3g6e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 93 binding sites of Magnesium where determined in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit, PDB code: 3g6e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:32.1 occ:1.00 OP2 0:C2534 2.4 38.8 1.0 O 0:HOH8295 2.5 28.7 1.0 O 0:HOH3595 2.5 31.1 1.0 OP2 0:A2483 2.7 37.0 1.0 O 0:HOH7743 2.7 78.1 1.0 O3' 0:G2482 2.8 39.6 1.0 OP2 0:C2533 2.9 31.8 1.0 O2' 0:G2482 3.2 37.2 1.0 O 0:HOH5398 3.3 37.7 1.0 P 0:A2483 3.3 37.9 1.0 P 0:C2534 3.8 41.1 1.0 C3' 0:G2482 4.0 37.8 1.0 C2' 0:G2482 4.0 36.9 1.0 C1' 0:G2482 4.2 38.9 1.0 OP1 0:A2483 4.2 38.3 1.0 P 0:C2533 4.3 37.7 1.0 O5' 0:C2534 4.3 38.7 1.0 O2' 0:A2532 4.4 34.9 1.0 OP1 0:C2534 4.5 39.1 1.0 C5 0:C2534 4.5 45.5 1.0 O5' 0:A2483 4.5 36.4 1.0 N3 0:G2482 4.6 38.4 1.0 O 0:HOH5807 4.7 68.4 1.0 OP2 0:U2484 4.7 36.4 1.0 C5' 0:A2483 4.7 33.4 1.0 O3' 0:A2532 4.8 35.3 1.0 O 0:HOH2977 4.8 39.4 1.0 O3' 0:C2533 4.8 38.1 1.0 C6 0:C2534 4.8 45.0 1.0 OP2 0:U2535 4.9 38.5 1.0

Magnesium binding site 2 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:25.6 occ:1.00 O6 0:G627 2.2 39.1 1.0 OP1 0:A2483 2.2 38.3 1.0 O 0:HOH7721 2.4 58.2 1.0 OP1 0:C2534 2.5 39.1 1.0 O 0:HOH7722 2.5 29.8 1.0 O 0:HOH2977 2.5 39.4 1.0 P 0:A2483 3.2 37.9 1.0 O 0:HOH6837 3.3 36.0 1.0 C6 0:G627 3.4 37.1 1.0 OP2 0:A2483 3.6 37.0 1.0 P 0:C2534 3.7 41.1 1.0 O4 0:U626 3.8 39.4 1.0 O 0:HOH3928 3.9 31.7 1.0 O5' 0:A2483 4.0 36.4 1.0 O 0:HOH8207 4.1 52.0 1.0 C5 0:U626 4.1 36.7 1.0 O2' 0:U625 4.1 33.7 1.0 N1 0:G627 4.2 36.5 1.0 OP2 0:C2534 4.2 38.8 1.0 C4 0:U626 4.3 39.0 1.0 O 0:HOH5115 4.3 65.2 1.0 C5 0:G627 4.5 35.5 1.0 O3' 0:C2533 4.5 38.1 1.0 O3' 0:G2482 4.5 39.6 1.0 OP2 0:U2535 4.8 38.5 1.0 N7 0:G627 4.8 34.3 1.0 O5' 0:C2534 4.9 38.7 1.0

Magnesium binding site 3 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:34.5 occ:1.00 OP2 0:G877 2.2 29.2 1.0 OP1 0:A2624 2.2 29.6 1.0 O A:HOH241 2.3 32.5 1.0 OP2 0:A876 2.5 32.3 1.0 O 0:HOH8347 2.5 29.6 1.0 O A:HOH1054 2.5 54.2 1.0 P 0:G877 3.4 31.8 1.0 P 0:A2624 3.6 30.7 1.0 OP1 0:G877 3.8 32.2 1.0 OD1 A:ASN195 3.8 30.4 1.0 P 0:A876 3.8 34.4 1.0 O3' 0:G2623 4.2 30.4 1.0 O 0:HOH5679 4.2 39.3 1.0 O A:HOH1745 4.3 33.7 1.0 OP2 0:A2624 4.3 32.0 1.0 O A:ALA193 4.3 35.8 1.0 O3' 0:A875 4.3 31.8 1.0 O5' 0:A876 4.4 31.8 1.0 O 0:HOH6918 4.4 72.0 1.0 O3' 0:A876 4.4 31.9 1.0 O A:HOH7306 4.5 54.0 1.0 O5' 0:G877 4.5 30.2 1.0 MG 0:MG8009 4.6 31.4 1.0 CG A:ASN195 4.7 27.7 1.0 O5' 0:A2624 4.7 31.9 1.0 C5' 0:A876 4.7 31.7 1.0 O A:HOH7752 4.8 29.9 1.0 C3' 0:A876 4.9 32.8 1.0 O A:HOH3204 5.0 36.3 1.0 C5' 0:A2624 5.0 31.3 1.0

Magnesium binding site 4 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:29.1 occ:1.00 OP1 0:A459 2.2 32.1 1.0 O 0:HOH5899 2.3 36.1 1.0 O 0:HOH7728 2.3 30.4 1.0 O 0:HOH8472 2.4 45.2 1.0 O6 0:G456 2.4 42.0 1.0 O 0:HOH3100 2.4 30.1 1.0 C6 0:G456 3.4 43.0 1.0 P 0:A459 3.6 35.7 1.0 N7 0:G456 3.8 38.9 1.0 C5 0:G456 3.9 40.7 1.0 CE C:LYS85 4.0 34.0 1.0 OP2 0:A455 4.0 31.2 1.0 OP2 0:A459 4.1 38.2 1.0 N7 0:A455 4.2 38.1 1.0 NZ C:LYS85 4.4 34.1 1.0 CD C:LYS85 4.4 33.8 1.0 O5' 0:A459 4.4 34.5 1.0 O 0:HOH8384 4.4 45.8 1.0 N1 0:G456 4.6 44.1 1.0 C5' 0:A459 4.6 33.3 1.0 O3' 0:G458 4.6 33.3 1.0 O 0:HOH8193 4.6 53.6 1.0 O 0:HOH4457 4.6 50.8 1.0 O 0:HOH5232 4.6 59.8 1.0 C5' 0:U454 4.7 33.1 1.0 O 0:HOH4211 4.7 42.4 1.0 OP1 0:A477 4.8 33.2 1.0 OP1 0:A460 4.9 33.0 1.0 C8 0:A455 4.9 37.8 1.0

Magnesium binding site 5 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:34.2 occ:1.00 OP2 0:A1839 2.2 34.9 1.0 OP1 0:A1836 2.3 30.8 1.0 OP1 0:U1838 2.4 28.5 1.0 O 0:HOH7745 2.4 59.2 1.0 O 0:HOH8291 2.5 23.2 1.0 O 0:HOH7744 2.6 47.4 1.0 P 0:A1839 3.6 33.8 1.0 P 0:A1836 3.6 32.9 1.0 P 0:U1838 3.8 27.2 1.0 O 0:HOH4670 4.1 61.2 1.0 O5' 0:A1836 4.1 34.7 1.0 OP2 0:G1837 4.2 30.9 1.0 OP1 0:A1839 4.2 33.0 1.0 O 0:HOH2961 4.3 11.4 1.0 C3' 0:G1837 4.4 31.4 1.0 O 0:HOH7826 4.5 30.8 1.0 O3' 0:U1838 4.5 35.2 1.0 O5' 0:A1839 4.5 34.0 1.0 O5' 0:U1838 4.5 30.2 1.0 OP2 0:A1836 4.5 32.1 1.0 C2' 0:U1835 4.5 30.7 1.0 O 0:HOH5385 4.5 56.8 1.0 O 0:HOH4588 4.6 63.0 1.0 O3' 0:G1837 4.6 28.7 1.0 O3' 0:U1835 4.6 29.4 1.0 C5' 0:U1838 4.7 28.9 1.0 C3' 0:U1835 4.7 29.4 1.0 O 0:HOH4944 4.7 45.5 1.0 OP2 0:U1838 4.8 29.1 1.0 C3' 0:U1838 4.8 31.1 1.0 N7 0:A1839 4.9 30.0 1.0 C8 0:A1839 5.0 32.1 1.0 O2' 0:U1835 5.0 32.4 1.0

Magnesium binding site 6 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:30.9 occ:1.00 OP1 0:U919 2.3 31.0 1.0 OP1 0:C2464 2.4 37.9 1.0 OP1 0:A2465 2.4 41.5 1.0 O 0:HOH7737 2.6 41.8 1.0 O 0:HOH8310 2.7 27.4 1.0 O 0:HOH7827 2.8 86.2 1.0 P 0:U919 3.0 33.5 1.0 OP2 0:U919 3.1 31.6 1.0 P 0:C2464 3.6 38.0 1.0 O 0:HOH5075 3.6 51.4 1.0 P 0:A2465 3.6 42.4 1.0 O 0:HOH5129 3.7 71.3 1.0 O5' 0:U919 3.9 29.9 1.0 OP2 0:C2464 4.0 38.5 1.0 OP2 0:A2465 4.1 43.3 1.0 O5' 0:C2464 4.3 39.7 1.0 O5' 0:A2465 4.3 39.7 1.0 O 0:HOH6448 4.4 57.3 1.0 O3' 0:G918 4.4 34.3 1.0 O 0:HOH4701 4.5 46.4 1.0 C5' 0:C2464 4.5 40.8 1.0 O 0:HOH7942 4.6 31.9 1.0 C5' 0:U919 4.6 30.8 1.0 O3' 0:A2463 4.8 41.3 1.0 OP1 0:G2293 4.8 48.9 1.0 O3' 0:C2464 4.9 41.8 1.0

Magnesium binding site 7 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:31.1 occ:1.00 O 0:HOH7739 2.3 35.7 1.0 OP1 0:G2611 2.4 32.8 1.0 OP1 0:A2612 2.4 29.3 1.0 O 0:HOH7286 2.4 31.8 1.0 O 0:HOH7738 2.4 58.7 1.0 O 0:HOH8424 2.4 31.0 1.0 O3' 0:U2610 3.1 34.9 1.0 P 0:G2611 3.3 35.1 1.0 OP2 0:G2093 3.5 33.9 1.0 O 0:HOH4761 3.6 27.5 1.0 P 0:A2612 3.8 31.7 1.0 C5' 0:G2611 4.0 30.3 1.0 OP2 0:G2094 4.0 28.7 1.0 O5' 0:G2611 4.1 34.5 1.0 OP1 0:G2094 4.3 31.8 1.0 C3' 0:U2610 4.4 34.3 1.0 NA 0:NA8549 4.5 64.9 1.0 O3' 0:G2611 4.5 29.6 1.0 O2' 0:U2610 4.5 34.6 1.0 P 0:G2094 4.5 30.3 1.0 O 0:HOH4223 4.6 39.5 1.0 C4' 0:U2610 4.6 34.0 1.0 OP2 0:G2611 4.6 33.6 1.0 O5' 0:A2612 4.7 35.4 1.0 P 0:G2093 4.8 35.5 1.0 C3' 0:G2611 4.8 28.5 1.0 OP2 0:A2612 4.8 33.4 1.0 O 0:HOH4111 4.8 37.8 1.0 C4' 0:G2611 4.9 27.9 1.0 O3' 0:G2093 4.9 29.7 1.0 C5' 0:G2093 4.9 31.6 1.0

Magnesium binding site 8 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:29.5 occ:1.00 O 0:HOH5386 2.3 29.8 1.0 OP1 0:G28 2.4 39.3 1.0 O 0:HOH3066 2.4 33.1 1.0 O 0:HOH7828 2.6 63.2 1.0 O 0:HOH7535 2.7 40.2 1.0 O 0:HOH8329 2.7 31.2 1.0 P 0:G28 3.5 41.9 1.0 OP1 0:U1304 3.7 38.2 1.0 O3' 0:U27 3.9 37.1 1.0 OP2 0:G28 4.1 42.9 1.0 OP2 0:G1344 4.3 44.6 1.0 OP1 0:C1343 4.4 41.4 1.0 O 0:HOH8170 4.4 67.5 1.0 OP1 0:C1305 4.8 32.5 1.0 OP1 0:G1344 4.8 48.2 1.0 O5' 0:G28 4.9 42.0 1.0 P 0:G1344 4.9 46.3 1.0 O 0:HOH7176 4.9 34.4 1.0 OP2 0:C1305 4.9 39.8 1.0

Magnesium binding site 9 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:31.4 occ:1.00 OP1 0:G2623 2.4 29.4 1.0 OP1 0:G877 2.4 32.2 1.0 O A:HOH7752 2.5 29.9 1.0 O 0:HOH8323 2.5 41.8 1.0 O 0:HOH8336 2.7 24.5 1.0 O A:HOH1054 2.7 54.2 1.0 O 0:HOH7753 3.3 71.4 1.0 OP2 0:A2624 3.3 32.0 1.0 O 0:HOH8483 3.4 0.8 1.0 P 0:G2623 3.8 30.4 1.0 P 0:G877 3.8 31.8 1.0 P 0:A2624 4.2 30.7 1.0 O A:HOH240 4.2 60.2 1.0 OP2 0:G2623 4.4 31.7 1.0 OP1 0:A2624 4.4 29.6 1.0 OP2 0:G877 4.4 29.2 1.0 O5' 0:G2623 4.5 31.2 1.0 OD1 A:ASN195 4.5 30.4 1.0 OP2 0:C2475 4.5 38.3 1.0 O3' 0:G2623 4.6 30.4 1.0 O5' 0:G877 4.6 30.2 1.0 MG 0:MG8003 4.6 34.5 1.0 C5' 0:G2623 4.7 32.8 1.0 O6 0:G885 4.7 28.9 1.0 O 0:HOH5118 4.7 0.5 1.0 O 0:HOH3859 4.8 30.5 1.0 O3' 0:A876 4.8 31.9 1.0 O3' 0:A2622 4.8 28.8 1.0 C5' 0:G877 4.9 30.1 1.0 O A:HOH1745 5.0 33.7 1.0

Magnesium binding site 10 out of 93 in the Co-Crystal Structure of Homoharringtonine Bound to the Large 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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:52.9 occ:1.00 OP2 0:G2537 2.3 38.0 1.0 O 0:HOH7719 2.4 45.3 1.0 O 0:HOH8340 2.4 50.3 1.0 O 0:HOH3047 2.6 47.3 1.0 O5' 0:G2102 2.7 54.4 1.0 OP2 0:G2102 2.8 53.9 1.0 O 0:HOH9026 2.9 60.0 1.0 P 0:G2102 3.2 54.6 1.0 O3' 0:A2101 3.5 52.8 1.0 O2' 0:A2101 3.7 46.9 1.0 O 0:HOH8294 3.7 42.3 1.0 P 0:G2537 3.8 38.6 1.0 C5' 0:G2102 4.0 51.2 1.0 O 0:HOH4862 4.1 38.5 1.0 C3' 0:G2102 4.1 50.8 1.0 O3' 0:C2536 4.5 38.8 1.0 O 0:HOH6099 4.5 39.4 1.0 C2' 0:G2102 4.5 49.5 1.0 C5' 0:G2537 4.5 40.6 1.0 C2' 0:A2101 4.6 47.7 1.0 C3' 0:A2101 4.6 49.6 1.0 OP1 0:G2102 4.6 60.1 1.0 N7 0:G2480 4.6 33.9 1.0 OP1 0:G2537 4.6 38.5 1.0 C4' 0:G2102 4.7 50.4 1.0 O2' 0:C2536 4.7 35.7 1.0 O5' 0:G2537 4.7 39.2 1.0 C8 0:G2480 5.0 32.2 1.0 C1' 0:A2101 5.0 47.4 1.0

G.Gurel, G.Blaha, P.B.Moore, T.A.Steitz. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: the Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome. J.Mol.Biol. V. 389 146 2009.
ISSN: ISSN 0022-2836
PubMed: 19362093
DOI: 10.1016/J.JMB.2009.04.005