Magnesium in PDB 2qex: Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex was solved by S.J.Schroeder, G.Blaha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.92 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	214.620, 304.048, 578.647, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.1

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 - 116;

Binding sites:

The binding sites of Magnesium atom in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit (pdb code 2qex). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 116 binding sites of Magnesium where determined in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:25.9 occ:1.00 O 0:HOH7610 1.9 14.6 1.0 OP2 0:C2534 2.0 34.9 1.0 OP2 0:C2533 2.0 36.7 1.0 O 0:HOH3441 2.1 22.1 1.0 O 0:HOH8997 2.2 30.4 1.0 OP2 0:A2483 2.2 33.6 1.0 P 0:A2483 3.3 34.4 1.0 O3' 0:G2482 3.4 35.0 1.0 P 0:C2533 3.4 37.6 1.0 P 0:C2534 3.5 34.8 1.0 O3' 0:A2532 3.9 36.2 1.0 O2' 0:A2532 3.9 35.6 1.0 O 0:HOH4176 4.1 42.6 1.0 OP1 0:A2483 4.2 32.6 1.0 O3' 0:C2533 4.2 35.5 1.0 OP1 0:C2534 4.2 33.3 1.0 O 0:HOH9463 4.3 43.3 1.0 OP2 0:U2484 4.3 37.1 1.0 O5' 0:C2533 4.3 33.9 1.0 O 0:HOH7321 4.4 51.1 1.0 O2' 0:G2482 4.4 26.7 1.0 C3' 0:C2533 4.4 33.0 1.0 O5' 0:C2534 4.4 34.7 1.0 OP1 0:C2533 4.5 37.1 1.0 O5' 0:A2483 4.6 35.0 1.0 C3' 0:G2482 4.7 32.7 1.0 C5' 0:A2483 4.9 33.1 1.0 C3' 0:A2532 4.9 35.8 1.0 C2' 0:A2532 4.9 36.0 1.0 C5' 0:C2533 4.9 32.1 1.0 C5 0:C2534 5.0 43.8 1.0 O 0:HOH6219 5.0 69.2 1.0

Magnesium binding site 2 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:27.7 occ:1.00 OP1 0:A2483 2.0 32.6 1.0 O6 0:G627 2.0 31.9 1.0 O 0:HOH7588 2.1 19.9 1.0 OP1 0:C2534 2.1 33.3 1.0 O 0:HOH7589 2.1 22.9 1.0 O 0:HOH4176 2.3 42.6 1.0 C6 0:G627 3.2 29.6 1.0 P 0:A2483 3.3 34.4 1.0 P 0:C2534 3.5 34.8 1.0 O 0:HOH9085 3.5 30.2 1.0 O 0:HOH6949 3.7 72.8 1.0 OP2 0:A2483 3.8 33.6 1.0 N1 0:G627 3.8 29.6 1.0 O4 0:U626 4.0 33.9 1.0 OP2 0:C2534 4.1 34.9 1.0 O 0:HOH5727 4.1 45.6 1.0 O5' 0:A2483 4.1 35.0 1.0 O3' 0:C2533 4.3 35.5 1.0 O2' 0:U625 4.3 27.2 1.0 O 0:HOH3355 4.4 38.6 1.0 C5 0:G627 4.4 27.7 1.0 C5 0:U626 4.4 32.9 1.0 O3' 0:G2482 4.5 35.0 1.0 OP2 0:U2535 4.5 40.9 1.0 O5' 0:C2534 4.5 34.7 1.0 C4 0:U626 4.6 34.4 1.0 C5' 0:C2534 4.8 37.6 1.0 C3' 0:G2482 4.9 32.7 1.0 N7 0:G627 5.0 27.1 1.0

Magnesium binding site 3 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:29.9 occ:1.00 O 0:HOH9658 1.9 25.7 1.0 OP2 0:A876 2.0 25.0 1.0 OP1 0:A2624 2.1 27.2 1.0 O 0:HOH8843 2.3 11.2 1.0 OP2 0:G877 2.3 25.3 1.0 O 0:HOH3489 2.4 33.9 1.0 P 0:A876 3.4 26.6 1.0 P 0:A2624 3.5 25.0 1.0 P 0:G877 3.6 25.6 1.0 O5' 0:A876 4.0 24.2 1.0 O3' 0:A875 4.1 25.7 1.0 OD1 A:ASN195 4.1 23.1 1.0 O3' 0:G2623 4.2 26.1 1.0 OP1 0:G877 4.2 28.0 1.0 O 0:HOH4331 4.2 45.5 1.0 O 0:HOH3207 4.3 49.8 1.0 O A:ALA193 4.3 27.7 1.0 O3' 0:A876 4.3 26.4 1.0 OP2 0:A2624 4.3 25.0 1.0 C5' 0:A876 4.4 27.7 1.0 O 0:HOH6125 4.4 37.1 1.0 O5' 0:A2624 4.5 26.3 1.0 OP1 0:A876 4.5 25.5 1.0 C5' 0:A2624 4.5 25.9 1.0 O 0:HOH8842 4.6 28.1 1.0 C3' 0:A876 4.8 29.4 1.0 O5' 0:G877 4.8 24.4 1.0 CG A:ASN195 5.0 22.4 1.0

Magnesium binding site 4 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:23.1 occ:1.00 O 0:HOH9609 1.8 27.4 1.0 O 0:HOH8870 2.0 17.9 1.0 OP1 0:A459 2.0 24.6 1.0 O6 0:G456 2.1 32.3 1.0 O 0:HOH3611 2.2 13.2 1.0 O 0:HOH7595 2.2 19.6 1.0 C6 0:G456 3.3 34.5 1.0 P 0:A459 3.4 28.5 1.0 O 0:HOH3527 3.9 48.6 1.0 C5 0:G456 4.0 33.2 1.0 N7 0:G456 4.1 32.9 1.0 OP2 0:A459 4.1 32.4 1.0 O5' 0:A459 4.2 28.8 1.0 C5' 0:A459 4.2 29.1 1.0 O 0:HOH3341 4.3 43.5 1.0 CE C:LYS85 4.3 27.9 1.0 NZ C:LYS85 4.3 28.0 1.0 N1 0:G456 4.4 36.5 1.0 OP2 0:A455 4.5 30.9 1.0 O3' 0:G458 4.5 30.3 1.0 O 0:HOH9156 4.6 22.8 1.0 N7 0:A455 4.6 34.8 1.0 O 0:HOH5256 4.6 54.5 1.0 O 0:HOH5811 4.7 67.9 1.0 OP1 0:A460 4.7 33.0 1.0 CD C:LYS85 4.7 27.8 1.0 OP1 0:A477 4.7 30.3 1.0 OP2 0:A477 5.0 28.2 1.0

Magnesium binding site 5 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:32.6 occ:1.00 O 0:HOH7612 1.8 21.6 1.0 O 0:HOH3437 1.9 23.6 1.0 OP2 0:A1839 1.9 29.7 1.0 OP1 0:A1836 2.1 28.2 1.0 OP1 0:U1838 2.2 24.6 1.0 O 0:HOH7611 2.2 18.7 1.0 P 0:A1839 3.4 28.7 1.0 P 0:A1836 3.6 26.1 1.0 P 0:U1838 3.6 26.3 1.0 O 0:HOH5409 4.1 41.1 1.0 O 0:HOH5351 4.1 38.0 1.0 O5' 0:A1836 4.2 29.5 1.0 O5' 0:A1839 4.2 26.1 1.0 O 0:HOH9337 4.2 24.9 1.0 OP1 0:A1839 4.2 28.1 1.0 O 0:HOH8829 4.2 26.3 1.0 O3' 0:U1838 4.3 29.0 1.0 O5' 0:U1838 4.3 26.8 1.0 C2' 0:U1835 4.3 26.9 1.0 OP2 0:A1836 4.4 26.6 1.0 O 0:HOH9460 4.4 41.6 1.0 OP2 0:U1838 4.4 25.2 1.0 O 0:HOH7688 4.5 28.5 1.0 C3' 0:G1837 4.5 28.5 1.0 C5' 0:U1838 4.5 25.7 1.0 C3' 0:U1838 4.5 27.0 1.0 O3' 0:U1835 4.5 26.1 1.0 N7 0:A1839 4.5 26.1 1.0 O3' 0:G1837 4.6 25.9 1.0 C3' 0:U1835 4.6 26.6 1.0 OP2 0:G1837 4.6 26.2 1.0 C8 0:A1839 4.6 25.8 1.0 O2' 0:U1835 4.8 26.3 1.0

Magnesium binding site 6 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:32.5 occ:1.00 O 0:HOH3443 1.8 21.7 1.0 OP2 0:C822 1.9 36.4 1.0 OP1 0:G854 2.1 31.1 1.0 OP2 0:U821 2.4 34.4 1.0 O 0:HOH3580 2.6 30.1 1.0 O 0:HOH9639 2.7 45.3 1.0 P 0:G854 3.3 32.8 1.0 P 0:C822 3.4 38.3 1.0 OP1 0:U855 3.7 36.4 1.0 P 0:U821 3.8 33.9 1.0 O5' 0:G854 3.8 31.5 1.0 O 0:HOH3036 3.9 59.4 1.0 OP2 0:G854 3.9 33.6 1.0 OP1 0:G856 4.0 41.4 1.0 O5' 0:U821 4.1 36.5 1.0 OP1 0:C822 4.1 37.4 1.0 C5' 0:G854 4.2 31.7 1.0 O3' 0:U821 4.2 39.0 1.0 C3' 0:U821 4.3 36.9 1.0 O5' 0:C822 4.3 36.8 1.0 NA 0:NA8527 4.4 46.6 1.0 O3' 0:C853 4.5 31.0 1.0 O3' 0:G820 4.5 34.0 1.0 OP1 0:U821 4.8 31.8 1.0 C5 0:C822 4.9 35.0 1.0 O 0:HOH4850 4.9 36.0 1.0

Magnesium binding site 7 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:9.6 occ:1.00 O 0:HOH7600 1.7 14.1 1.0 O 0:HOH8829 1.9 26.3 1.0 OP2 0:U832 2.0 34.1 1.0 O 0:HOH3183 2.2 17.4 1.0 OP1 0:A1839 2.2 28.1 1.0 OP2 0:A1840 2.4 20.1 1.0 O 0:HOH8921 3.2 39.1 1.0 P 0:U832 3.4 33.7 1.0 P 0:A1840 3.6 23.8 1.0 P 0:A1839 3.6 28.7 1.0 OP1 0:A1840 3.9 22.5 1.0 OP1 0:U832 4.0 32.5 1.0 O 0:HOH9460 4.1 41.6 1.0 O 0:HOH6197 4.2 72.7 1.0 OP2 0:A1839 4.3 29.7 1.0 O5' 0:U832 4.3 32.7 1.0 O3' 0:U831 4.4 32.3 1.0 O3' 0:U1838 4.5 29.0 1.0 O 0:HOH7688 4.5 28.5 1.0 O3' 0:A1839 4.5 22.5 1.0 O5' 0:A1839 4.6 26.1 1.0 C3' 0:U831 4.7 34.9 1.0 O5' 0:A1840 4.8 22.7 1.0 O 0:HOH7611 4.8 18.7 1.0 C3' 0:A1839 4.9 24.6 1.0 C5' 0:A1839 4.9 25.4 1.0 O 0:HOH7612 5.0 21.6 1.0 C5' 0:U832 5.0 35.2 1.0

Magnesium binding site 8 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:27.0 occ:1.00 O 0:HOH7689 1.8 44.5 1.0 OP1 0:U919 2.0 27.2 1.0 OP1 0:A2465 2.1 34.2 1.0 O 0:HOH7604 2.2 33.1 1.0 OP1 0:C2464 2.2 30.8 1.0 O 0:HOH3454 2.3 38.0 1.0 P 0:U919 3.2 27.8 1.0 P 0:A2465 3.4 33.1 1.0 P 0:C2464 3.6 32.1 1.0 OP2 0:U919 3.6 28.0 1.0 O 0:HOH9372 3.9 46.6 1.0 O5' 0:U919 3.9 25.9 1.0 O5' 0:A2465 4.0 31.5 1.0 C5' 0:C2464 4.0 33.2 1.0 O5' 0:C2464 4.1 31.9 1.0 OP2 0:A2465 4.1 34.3 1.0 O 0:HOH5738 4.1 53.8 1.0 OP2 0:C2464 4.3 33.6 1.0 C5' 0:U919 4.4 27.9 1.0 O 0:HOH3174 4.4 25.4 1.0 OP1 0:G2466 4.4 35.6 1.0 O3' 0:G918 4.4 26.4 1.0 O 0:HOH9273 4.5 51.3 1.0 O3' 0:C2464 4.6 32.1 1.0 C3' 0:A2465 4.6 33.1 1.0 O3' 0:A2463 4.7 34.1 1.0 O 0:HOH6183 4.8 64.3 1.0 O 0:HOH9754 4.8 53.0 1.0 C2' 0:A2465 4.8 32.3 1.0 C5' 0:A2465 4.9 30.8 1.0 C3' 0:C2464 4.9 33.9 1.0 C4' 0:C2464 5.0 34.6 1.0

Magnesium binding site 9 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:31.1 occ:1.00 O 0:HOH7606 1.7 28.9 1.0 O 0:HOH3565 2.1 23.0 1.0 O 0:HOH7276 2.1 27.6 1.0 OP1 0:A2612 2.1 25.6 1.0 O 0:HOH7605 2.2 35.0 1.0 OP1 0:G2611 2.4 28.6 1.0 P 0:A2612 3.6 27.2 1.0 NA 0:NA8558 3.6 68.7 1.0 OP2 0:G2093 3.6 28.8 1.0 P 0:G2611 3.7 29.0 1.0 O3' 0:U2610 3.7 29.4 1.0 OP2 0:G2094 3.8 25.1 1.0 O 0:HOH9157 3.9 38.2 1.0 O 0:HOH9291 4.0 38.1 1.0 OP1 0:G2094 4.0 26.5 1.0 O 0:HOH9127 4.3 29.8 1.0 P 0:G2094 4.3 25.9 1.0 O5' 0:A2612 4.3 28.5 1.0 C5' 0:G2611 4.4 27.1 1.0 OP2 0:A2612 4.4 28.9 1.0 O3' 0:G2611 4.4 27.5 1.0 O5' 0:G2611 4.5 27.3 1.0 OP2 0:G2611 4.8 27.6 1.0 C3' 0:G2611 4.8 27.2 1.0 O 0:HOH8947 4.9 24.5 1.0 O3' 0:G2093 4.9 25.0 1.0 P 0:G2093 4.9 31.4 1.0 C3' 0:U2610 5.0 26.9 1.0

Magnesium binding site 10 out of 116 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:13.7 occ:1.00 O B:HOH8827 1.7 15.8 1.0 O 0:HOH3667 1.8 31.1 1.0 OP1 0:G836 2.0 29.2 1.0 O 0:HOH9185 2.1 33.6 1.0 OE1 B:GLN230 2.1 32.3 1.0 OP1 0:U2615 2.2 27.5 1.0 CD B:GLN230 3.3 30.5 1.0 P 0:G836 3.5 33.1 1.0 P 0:U2615 3.7 27.0 1.0 O 0:HOH4894 4.0 54.2 1.0 CG B:GLN230 4.0 29.5 1.0 CB B:GLN230 4.1 28.6 1.0 C5' 0:G836 4.3 32.6 1.0 O 0:HOH6675 4.3 64.6 1.0 O5' 0:G836 4.3 32.2 1.0 NE2 B:GLN230 4.3 29.8 1.0 O 0:HOH9029 4.3 47.5 1.0 OP2 0:G836 4.3 32.4 1.0 C3' 0:U835 4.4 31.8 1.0 O 0:HOH3830 4.4 52.6 1.0 O3' 0:U835 4.4 29.8 1.0 OP2 0:U2615 4.5 27.9 1.0 O 0:HOH9374 4.5 54.1 1.0 O3' 0:C2614 4.5 26.6 1.0 O5' 0:U2615 4.6 28.1 1.0 OP2 0:G2616 4.8 27.9 1.0 CA B:GLN230 4.8 28.8 1.0 C5' 0:U835 4.9 31.7 1.0 O B:GLN230 4.9 26.9 1.0 C5' 0:U2615 5.0 26.4 1.0 N2 0:G2616 5.0 30.6 1.0

S.J.Schroeder, G.Blaha, P.B.Moore. Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit. Antimicrob.Agents Chemother. V. 51 4462 2007.
ISSN: ISSN 0066-4804
PubMed: 17664317
DOI: 10.1128/AAC.00455-07