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Magnesium in PDB 2otl: Girodazole Bound to the Large Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Girodazole Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otl was solved by G.Blaha, S.J.Schroeder, J.Tirado-Rives, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.36 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.077, 300.598, 575.055, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.8

Other elements in 2otl:

The structure of Girodazole Bound to the Large Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 23 atoms
Sodium (Na) 85 atoms

Magnesium Binding Sites:

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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui (pdb code 2otl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 116 binding sites of Magnesium where determined in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 116 in 2otl

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Magnesium binding site 1 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8001

b:36.4
occ:1.00
 O 0:HOH7760 1.9 28.2 1.0
OP2 0:C2534 2.0 37.1 1.0
OP2 0:C2533 2.0 34.7 1.0
O 0:HOH3627 2.1 28.2 1.0
OP2 0:A2483 2.3 33.7 1.0
O 0:HOH9173 2.3 34.2 1.0
P 0:A2483 3.3 31.8 1.0
O3' 0:G2482 3.3 35.5 1.0
P 0:C2533 3.4 36.8 1.0
P 0:C2534 3.4 36.3 1.0
O3' 0:A2532 3.9 37.5 1.0
O 0:HOH9639 3.9 43.3 1.0
OP1 0:A2483 4.1 35.9 1.0
O3' 0:C2533 4.2 35.3 1.0
O2' 0:A2532 4.2 36.8 1.0
O 0:HOH4345 4.2 44.1 1.0
O5' 0:C2533 4.2 35.9 1.0
OP2 0:U2484 4.2 37.5 1.0
OP1 0:C2534 4.3 36.2 1.0
O 0:HOH6378 4.3 59.1 1.0
O5' 0:C2534 4.3 36.9 1.0
C3' 0:C2533 4.4 33.4 1.0
O2' 0:G2482 4.4 37.0 1.0
O 0:HOH7468 4.5 56.3 1.0
OP1 0:C2533 4.5 38.0 1.0
O5' 0:A2483 4.6 32.2 1.0
C3' 0:G2482 4.7 35.8 1.0
C5' 0:A2483 4.8 33.5 1.0
C5 0:C2534 4.9 38.8 1.0
C5' 0:C2533 4.9 33.3 1.0
C3' 0:A2532 4.9 37.2 1.0
MG 0:MG8002 5.0 34.4 1.0
C2' 0:G2482 5.0 36.3 1.0

Magnesium binding site 2 out of 116 in 2otl

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Magnesium binding site 2 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8002

b:34.4
occ:1.00
 O6 0:G627 1.9 37.9 1.0
O 0:HOH7738 2.0 33.5 1.0
O 0:HOH4345 2.1 44.1 1.0
OP1 0:A2483 2.2 35.9 1.0
OP1 0:C2534 2.2 36.2 1.0
O 0:HOH7739 2.3 30.3 1.0
C6 0:G627 3.1 34.8 1.0
P 0:A2483 3.4 31.8 1.0
P 0:C2534 3.4 36.3 1.0
O4 0:U626 3.6 33.4 1.0
N1 0:G627 3.8 34.0 1.0
OP2 0:A2483 3.8 33.7 1.0
O 0:HOH7104 3.8 59.0 1.0
OP2 0:C2534 3.9 37.1 1.0
O 0:HOH9261 4.0 27.7 1.0
O3' 0:C2533 4.1 35.3 1.0
C4 0:U626 4.2 34.8 1.0
C5 0:U626 4.2 33.5 1.0
O2' 0:U625 4.2 32.8 1.0
C5 0:G627 4.2 32.3 1.0
O5' 0:A2483 4.3 32.2 1.0
O 0:HOH5893 4.4 48.6 1.0
O3' 0:G2482 4.5 35.5 1.0
OP2 0:U2535 4.6 38.0 1.0
O 0:HOH3541 4.6 52.9 1.0
O5' 0:C2534 4.6 36.9 1.0
N7 0:G627 4.7 30.8 1.0
MG 0:MG8001 5.0 36.4 1.0
O 0:HOH7468 5.0 56.3 1.0

Magnesium binding site 3 out of 116 in 2otl

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Magnesium binding site 3 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8003

b:35.0
occ:1.00
 OP1 0:A2624 1.9 33.1 1.0
OP2 0:G877 2.0 31.8 1.0
O 0:HOH9021 2.1 26.4 1.0
O A:HOH8732 2.1 36.3 1.0
OP2 0:A876 2.3 30.3 1.0
O 0:HOH3677 2.3 26.5 1.0
P 0:G877 3.2 32.6 1.0
P 0:A2624 3.3 34.4 1.0
OP1 0:G877 3.6 32.5 1.0
P 0:A876 3.7 33.7 1.0
O3' 0:G2623 3.8 32.5 1.0
O 0:HOH9020 4.0 25.9 1.0
OD1 A:ASN195 4.1 30.5 1.0
O3' 0:A876 4.1 31.8 1.0
OP2 0:A2624 4.1 34.4 1.0
O5' 0:A876 4.2 31.7 1.0
O3' 0:A875 4.2 29.9 1.0
O 0:HOH6283 4.3 36.1 1.0
O 0:HOH7163 4.3 56.7 1.0
O5' 0:G877 4.3 31.4 1.0
O5' 0:A2624 4.4 35.7 1.0
C5' 0:A876 4.4 31.8 1.0
O A:HOH8743 4.5 54.1 1.0
C5' 0:A2624 4.6 35.5 1.0
C3' 0:A876 4.6 33.6 1.0
O A:ALA193 4.6 34.8 1.0
O A:HOH8764 4.7 36.4 1.0
O A:HOH8816 4.7 46.4 1.0
O 0:HOH7769 4.7 24.8 1.0
OP1 0:A876 4.9 31.9 1.0
MG 0:MG8013 4.9 38.2 1.0
CG A:ASN195 4.9 28.9 1.0

Magnesium binding site 4 out of 116 in 2otl

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Magnesium binding site 4 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8004

b:29.2
occ:1.00
 OP1 0:A459 1.8 31.7 1.0
O 0:HOH7745 2.0 26.6 1.0
O 0:HOH3794 2.0 25.6 1.0
O 0:HOH9048 2.0 32.6 1.0
O6 0:G456 2.0 36.9 1.0
O 0:HOH9783 2.1 31.0 1.0
C6 0:G456 3.1 38.1 1.0
P 0:A459 3.2 34.6 1.0
OP2 0:A459 3.8 35.8 1.0
C5 0:G456 3.9 36.9 1.0
N7 0:G456 3.9 35.2 1.0
O5' 0:A459 3.9 33.4 1.0
NZ C:LYS85 4.0 31.8 1.0
CE C:LYS85 4.1 30.7 1.0
C5' 0:A459 4.2 33.9 1.0
N1 0:G456 4.3 40.5 1.0
O3' 0:G458 4.3 34.2 1.0
O 0:HOH9333 4.3 37.8 1.0
O 0:HOH5976 4.3 43.6 1.0
OP2 0:A455 4.4 32.6 1.0
CD C:LYS85 4.5 32.0 1.0
OP1 0:A460 4.6 37.2 1.0
O 0:HOH3527 4.6 47.0 1.0
O 0:HOH3714 4.6 48.0 1.0
N7 0:A455 4.7 39.1 1.0
OP1 0:A477 4.7 36.3 1.0
O 0:HOH5422 4.9 43.5 1.0
OP2 0:A477 4.9 32.3 1.0

Magnesium binding site 5 out of 116 in 2otl

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Magnesium binding site 5 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8005

b:33.5
occ:1.00
 O 0:HOH3623 2.0 28.3 1.0
O 0:HOH7762 2.0 29.0 1.0
OP2 0:A1839 2.0 31.2 1.0
OP1 0:U1838 2.0 34.0 1.0
OP1 0:A1836 2.1 31.1 1.0
O 0:HOH7761 2.3 25.1 1.0
P 0:U1838 3.4 31.9 1.0
P 0:A1839 3.5 32.8 1.0
P 0:A1836 3.6 31.3 1.0
O 0:HOH5518 3.9 42.0 1.0
O 0:HOH9006 4.1 24.3 1.0
O 0:HOH5577 4.1 46.1 1.0
O5' 0:U1838 4.1 30.4 1.0
O5' 0:A1839 4.2 31.2 1.0
OP2 0:U1838 4.3 32.4 1.0
O5' 0:A1836 4.3 30.1 1.0
O3' 0:U1838 4.3 30.4 1.0
C3' 0:G1837 4.4 35.9 1.0
OP2 0:A1836 4.4 34.0 1.0
C2' 0:U1835 4.4 32.3 1.0
O 0:HOH7836 4.4 40.9 1.0
O3' 0:G1837 4.4 33.4 1.0
O 0:HOH9516 4.4 40.8 1.0
OP1 0:A1839 4.4 33.9 1.0
C5' 0:U1838 4.5 27.8 1.0
O3' 0:U1835 4.5 29.8 1.0
O 0:HOH9636 4.5 35.2 1.0
C3' 0:U1838 4.5 29.8 1.0
OP2 0:G1837 4.6 36.1 1.0
C3' 0:U1835 4.6 31.4 1.0
N7 0:A1839 4.6 33.4 1.0
C8 0:A1839 4.8 33.6 1.0
O2' 0:U1835 4.8 35.6 1.0

Magnesium binding site 6 out of 116 in 2otl

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Magnesium binding site 6 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8006

b:33.9
occ:1.00
 OP2 0:C822 1.9 44.4 1.0
O 0:HOH3629 2.0 37.8 1.0
OP2 0:U821 2.1 40.3 1.0
OP1 0:G854 2.1 37.6 1.0
O 0:HOH9815 2.1 40.7 1.0
O 0:HOH3766 2.5 37.0 1.0
P 0:C822 3.3 44.9 1.0
P 0:G854 3.4 37.9 1.0
P 0:U821 3.4 40.2 1.0
O 0:HOH3213 3.7 47.6 1.0
O5' 0:U821 3.7 42.1 1.0
OP1 0:G856 3.8 44.8 1.0
NA 0:NA8527 3.9 44.8 1.0
O5' 0:G854 3.9 35.7 1.0
O3' 0:U821 4.0 46.0 1.0
C3' 0:U821 4.0 43.4 1.0
OP2 0:G854 4.0 36.4 1.0
OP1 0:C822 4.1 43.7 1.0
O3' 0:G820 4.1 38.9 1.0
OP1 0:U855 4.2 39.5 1.0
C5' 0:G854 4.3 33.7 1.0
O5' 0:C822 4.4 42.2 1.0
O3' 0:C853 4.6 38.5 1.0
OP1 0:U821 4.6 39.5 1.0
O 0:HOH5016 4.7 41.0 1.0
C5' 0:U821 4.9 42.8 1.0
C4' 0:U821 5.0 43.2 1.0

Magnesium binding site 7 out of 116 in 2otl

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Magnesium binding site 7 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8007

b:22.1
occ:1.00
 OP2 0:U832 1.9 36.6 1.0
OP1 0:A1839 2.0 33.9 1.0
O 0:HOH7750 2.1 26.0 1.0
O 0:HOH3366 2.2 38.6 1.0
OP2 0:A1840 2.2 29.1 1.0
O 0:HOH9006 2.3 24.3 1.0
P 0:A1840 3.3 31.8 1.0
P 0:U832 3.4 34.5 1.0
P 0:A1839 3.5 32.8 1.0
OP1 0:A1840 3.7 32.4 1.0
O 0:HOH6356 3.7 57.8 1.0
O 0:HOH9636 3.9 35.2 1.0
O 0:HOH9100 3.9 39.2 1.0
O5' 0:U832 4.1 36.1 1.0
OP2 0:A1839 4.2 31.2 1.0
O3' 0:A1839 4.2 31.2 1.0
OP1 0:U832 4.3 35.7 1.0
O3' 0:U1838 4.3 30.4 1.0
O3' 0:U831 4.3 34.9 1.0
O5' 0:A1839 4.4 31.2 1.0
OP2 0:G833 4.5 39.6 1.0
O 0:HOH7836 4.6 40.9 1.0
O5' 0:A1840 4.6 33.4 1.0
C5' 0:U832 4.7 37.2 1.0
C3' 0:A1839 4.7 30.9 1.0
C5' 0:A1839 4.7 31.8 1.0
C3' 0:U831 4.9 36.9 1.0

Magnesium binding site 8 out of 116 in 2otl

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Magnesium binding site 8 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8008

b:37.3
occ:1.00
 OP1 0:U919 1.9 31.6 1.0
OP1 0:A2465 2.1 37.0 1.0
O 0:HOH7754 2.1 40.4 1.0
O 0:HOH3641 2.1 30.2 1.0
O 0:HOH7837 2.1 49.0 1.0
OP1 0:C2464 2.2 35.7 1.0
P 0:U919 3.1 32.1 1.0
P 0:A2465 3.4 38.9 1.0
OP2 0:U919 3.6 32.7 1.0
P 0:C2464 3.6 37.4 1.0
O5' 0:U919 3.8 29.0 1.0
O5' 0:A2465 3.8 37.5 1.0
O5' 0:C2464 4.0 38.3 1.0
O 0:HOH9550 4.1 43.1 1.0
C5' 0:C2464 4.1 39.5 1.0
O 0:HOH3357 4.1 30.8 1.0
OP2 0:A2465 4.1 39.0 1.0
O 0:HOH9454 4.2 57.3 1.0
C5' 0:U919 4.3 30.2 1.0
O3' 0:G918 4.3 32.7 1.0
C3' 0:A2465 4.4 36.5 1.0
OP1 0:G2466 4.4 37.9 1.0
O 0:HOH5906 4.5 59.8 1.0
OP2 0:C2464 4.5 39.1 1.0
O3' 0:C2464 4.6 38.5 1.0
O3' 0:A2463 4.6 38.6 1.0
C5' 0:A2465 4.7 34.3 1.0
C2' 0:A2465 4.7 36.6 1.0
O 0:HOH9930 4.9 77.4 1.0
C3' 0:C2464 4.9 38.7 1.0

Magnesium binding site 9 out of 116 in 2otl

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Magnesium binding site 9 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8009

b:35.4
occ:1.00
 O 0:HOH7422 1.9 35.9 1.0
O 0:HOH7756 1.9 30.9 1.0
O 0:HOH3750 2.1 21.7 1.0
OP1 0:A2612 2.1 28.8 1.0
OP1 0:G2611 2.2 31.9 1.0
O 0:HOH7755 2.3 29.5 1.0
NA 0:NA8558 3.0 82.4 1.0
P 0:G2611 3.4 30.8 1.0
O3' 0:U2610 3.4 30.6 1.0
P 0:A2612 3.6 31.4 1.0
OP2 0:G2093 3.7 31.0 1.0
OP2 0:G2094 4.0 27.9 1.0
O B:HOH8726 4.0 33.2 1.0
OP1 0:G2094 4.0 28.5 1.0
O 0:HOH9334 4.1 47.8 1.0
C5' 0:G2611 4.2 30.5 1.0
OP2 0:A2612 4.2 31.2 1.0
O5' 0:G2611 4.3 31.7 1.0
O 0:HOH9304 4.4 39.3 1.0
O5' 0:A2612 4.4 34.0 1.0
P 0:G2094 4.4 28.8 1.0
O3' 0:G2611 4.5 31.1 1.0
OP2 0:G2611 4.5 30.6 1.0
O 0:HOH7772 4.7 42.6 1.0
C3' 0:U2610 4.7 31.4 1.0
C3' 0:G2611 4.8 29.7 1.0
C4' 0:U2610 4.9 31.0 1.0

Magnesium binding site 10 out of 116 in 2otl

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Magnesium binding site 10 out of 116 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8010

b:33.9
occ:1.00
 O B:HOH8725 1.8 35.1 1.0
O 0:HOH3851 1.9 41.3 1.0
OP1 0:G836 1.9 27.6 1.0
OP1 0:U2615 2.1 30.7 1.0
OE1 B:GLN230 2.3 35.1 1.0
O 0:HOH9363 2.4 37.2 1.0
P 0:G836 3.4 30.8 1.0
CD B:GLN230 3.4 34.0 1.0
P 0:U2615 3.6 33.7 1.0
O 0:HOH5059 3.8 56.6 1.0
C5' 0:G836 4.1 31.4 1.0
CG B:GLN230 4.1 33.5 1.0
O B:HOH8842 4.1 50.7 1.0
OP2 0:G836 4.1 31.5 1.0
O5' 0:G836 4.2 30.3 1.0
CB B:GLN230 4.2 33.9 1.0
O3' 0:U835 4.3 27.6 1.0
C3' 0:U835 4.3 26.5 1.0
OP2 0:U2615 4.4 35.0 1.0
O 0:HOH4004 4.4 47.6 1.0
O 0:HOH9204 4.4 41.8 1.0
O5' 0:U2615 4.5 35.1 1.0
NE2 B:GLN230 4.5 34.3 1.0
O3' 0:C2614 4.5 32.7 1.0
C5' 0:U835 4.5 30.6 1.0
OP2 0:G2616 4.5 35.4 1.0
CA B:GLN230 4.7 34.9 1.0
N2 0:G2616 4.8 30.8 1.0
O B:GLN230 4.9 35.9 1.0
C5' 0:U2615 4.9 32.1 1.0
O 0:HOH9552 4.9 40.9 1.0

Reference:

S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, P.B.Moore. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula Marismortui: 13-Deoxytedanolide and Girodazole. J.Mol.Biol. V. 367 1471 2007.
ISSN: ISSN 0022-2836
PubMed: 17321546
DOI: 10.1016/J.JMB.2007.01.081
Page generated: Wed Aug 14 01:34:49 2024

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