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Magnesium in PDB 1kc8: Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit, PDB code: 1kc8 was solved by J.L.Hansen, N.Ban, P.Nissen, 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) 19.99 / 3.01
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.5

Other elements in 1kc8:

The structure of Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Potassium (K) 3 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 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 - 117;

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit (pdb code 1kc8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit, PDB code: 1kc8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in 1kc8

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Magnesium binding site 1 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8001

b:26.4
occ:1.00
O A:HOH3619 1.8 8.4 1.0
OP2 A:C2533 1.9 25.2 1.0
O A:HOH9178 1.9 37.0 1.0
OP2 A:C2534 2.0 28.5 1.0
O A:HOH7777 2.0 23.6 1.0
OP2 A:A2483 2.4 26.4 1.0
P A:C2533 3.3 24.9 1.0
P A:C2534 3.5 29.9 1.0
P A:A2483 3.6 25.6 1.0
O3' A:A2532 3.7 26.6 1.0
O3' A:G2482 3.7 26.8 1.0
O2' A:A2532 3.9 25.1 1.0
O A:HOH9639 4.1 29.6 1.0
OP2 A:U2484 4.1 31.1 1.0
O5' A:C2533 4.2 25.5 1.0
O A:HOH4325 4.2 27.5 1.0
O3' A:C2533 4.2 28.3 1.0
O A:HOH6372 4.2 59.5 1.0
C3' A:C2533 4.3 26.2 1.0
OP1 A:C2534 4.3 28.0 1.0
OP1 A:C2533 4.4 27.2 1.0
O5' A:C2534 4.4 28.2 1.0
O2' A:G2482 4.5 30.5 1.0
OP1 A:A2483 4.5 27.7 1.0
C5 A:C2534 4.7 31.0 1.0
O A:HOH7481 4.7 23.6 1.0
C3' A:A2532 4.7 27.7 1.0
O5' A:A2483 4.8 25.6 1.0
C2' A:A2532 4.8 26.5 1.0
C5' A:C2533 4.8 24.9 1.0
C5' A:A2483 4.9 25.9 1.0
C3' A:G2482 5.0 27.9 1.0

Magnesium binding site 2 out of 117 in 1kc8

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Magnesium binding site 2 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8002

b:24.2
occ:1.00
O A:HOH7757 1.9 20.9 1.0
OP1 A:A2483 2.0 27.7 1.0
O6 A:G627 2.0 24.7 1.0
OP1 A:C2534 2.0 28.0 1.0
O A:HOH7756 2.1 20.3 1.0
O A:HOH4325 2.4 27.5 1.0
P A:A2483 3.1 25.6 1.0
C6 A:G627 3.2 24.3 1.0
P A:C2534 3.3 29.9 1.0
OP2 A:A2483 3.5 26.4 1.0
N1 A:G627 3.8 24.0 1.0
O4 A:U626 3.9 25.0 1.0
OP2 A:C2534 3.9 28.5 1.0
O5' A:A2483 4.1 25.6 1.0
O A:HOH9262 4.1 25.4 1.0
O3' A:C2533 4.1 28.3 1.0
OP2 A:U2535 4.2 31.4 1.0
O A:HOH5870 4.2 22.7 1.0
O3' A:G2482 4.3 26.8 1.0
O A:HOH7100 4.4 30.9 1.0
C5 A:G627 4.4 24.1 1.0
O2' A:U625 4.4 22.2 1.0
O5' A:C2534 4.5 28.2 1.0
C4 A:U626 4.5 25.0 1.0
C5 A:U626 4.5 24.8 1.0
O A:HOH3529 4.6 49.7 1.0
C3' A:G2482 4.7 27.9 1.0
C5' A:C2534 4.8 29.0 1.0
N7 A:G627 4.9 24.5 1.0

Magnesium binding site 3 out of 117 in 1kc8

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Magnesium binding site 3 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8003

b:20.5
occ:1.00
OP2 A:G877 1.8 25.8 1.0
O A:HOH9024 2.0 15.1 1.0
OP1 A:A2624 2.0 22.3 1.0
OP2 A:A876 2.4 24.6 1.0
O C:HOH8536 2.5 25.3 1.0
O A:HOH3671 2.6 22.4 1.0
P A:G877 3.0 24.6 1.0
P A:A2624 3.3 23.7 1.0
OP1 A:G877 3.5 24.4 1.0
P A:A876 3.6 23.5 1.0
O3' A:G2623 3.8 22.6 1.0
O3' A:A876 3.9 22.8 1.0
OD1 C:ASN195 4.0 27.0 1.0
O5' A:A876 4.0 24.5 1.0
O A:HOH6274 4.1 19.2 1.0
O A:HOH9023 4.1 27.6 1.0
OP2 A:A2624 4.1 23.6 1.0
O3' A:A875 4.1 22.0 1.0
C5' A:A876 4.2 23.6 1.0
O5' A:G877 4.2 23.7 1.0
O A:HOH7162 4.3 78.4 1.0
O C:ALA193 4.4 29.6 1.0
C3' A:A876 4.4 22.6 1.0
O C:HOH8625 4.5 18.2 1.0
O5' A:A2624 4.5 24.6 1.0
O A:HOH4476 4.7 48.3 1.0
O A:HOH7786 4.7 15.9 1.0
C5' A:A2624 4.8 23.9 1.0
C4' A:A876 4.9 23.5 1.0
CG C:ASN195 4.9 25.2 1.0
OP1 A:A876 4.9 24.6 1.0

Magnesium binding site 4 out of 117 in 1kc8

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Magnesium binding site 4 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8004

b:27.8
occ:1.00
OP1 A:A459 1.7 23.0 1.0
O A:HOH9774 1.8 18.9 1.0
O A:HOH9050 1.9 18.0 1.0
O6 A:G456 2.0 28.0 1.0
O A:HOH3787 2.2 14.4 1.0
O A:HOH7762 2.3 20.0 1.0
P A:A459 3.1 24.6 1.0
C6 A:G456 3.2 29.1 1.0
O5' A:A459 3.7 24.5 1.0
OP2 A:A459 3.8 27.1 1.0
O A:HOH9335 3.9 51.8 1.0
C5' A:A459 4.0 24.9 1.0
C5 A:G456 4.0 27.3 1.0
N7 A:G456 4.1 26.2 1.0
O3' A:G458 4.2 22.9 1.0
CE E:LYS85 4.2 22.1 1.0
N1 A:G456 4.2 31.0 1.0
O A:HOH3708 4.3 47.0 1.0
NZ E:LYS85 4.4 22.0 1.0
O A:HOH5955 4.4 46.2 1.0
OP1 A:A460 4.5 27.4 1.0
O A:HOH3515 4.6 39.3 1.0
OP2 A:A455 4.7 20.8 1.0
N7 A:A455 4.8 31.3 1.0
CD E:LYS85 4.8 22.4 1.0
OP1 A:A477 4.9 22.4 1.0
OP2 A:A460 4.9 26.9 1.0
OP2 A:A477 4.9 19.4 1.0

Magnesium binding site 5 out of 117 in 1kc8

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Magnesium binding site 5 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8005

b:28.7
occ:1.00
O A:HOH7779 1.7 21.6 1.0
O A:HOH7778 1.7 17.8 1.0
OP2 A:A1839 1.8 21.6 1.0
OP1 A:A1836 2.1 21.3 1.0
OP1 A:U1838 2.2 22.8 1.0
O A:HOH3615 2.3 7.8 1.0
P A:A1839 3.3 20.5 1.0
P A:A1836 3.6 20.7 1.0
P A:U1838 3.6 19.7 1.0
O A:HOH5556 3.6 37.6 1.0
O A:HOH5499 4.0 38.5 1.0
O A:HOH9009 4.0 19.0 1.0
O5' A:A1839 4.1 20.1 1.0
O3' A:U1838 4.1 22.1 1.0
O A:HOH9636 4.3 49.3 1.0
O5' A:A1836 4.3 21.1 1.0
OP1 A:A1839 4.3 21.6 1.0
OP2 A:U1838 4.3 21.3 1.0
O5' A:U1838 4.3 18.9 1.0
C2' A:U1835 4.4 23.6 1.0
O3' A:U1835 4.4 20.9 1.0
O A:HOH7855 4.4 48.3 1.0
OP2 A:G1837 4.5 27.5 1.0
C3' A:G1837 4.5 25.8 1.0
OP2 A:A1836 4.5 21.1 1.0
C3' A:U1838 4.5 22.1 1.0
C3' A:U1835 4.5 23.0 1.0
O3' A:G1837 4.6 22.6 1.0
C5' A:U1838 4.6 20.2 1.0
N7 A:A1839 4.7 24.3 1.0
C8 A:A1839 4.8 24.1 1.0
O A:HOH9510 4.8 37.7 1.0
O2' A:U1835 4.9 25.1 1.0

Magnesium binding site 6 out of 117 in 1kc8

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Magnesium binding site 6 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8006

b:33.9
occ:1.00
OP2 A:C822 1.7 31.4 1.0
O A:HOH9806 1.9 31.8 1.0
OP2 A:U821 1.9 29.5 1.0
OP1 A:G854 2.1 29.5 1.0
O A:HOH3758 2.1 36.2 1.0
O A:HOH3621 2.2 14.6 1.0
P A:C822 2.9 30.9 1.0
P A:G854 3.3 29.4 1.0
P A:U821 3.3 30.0 1.0
O3' A:U821 3.6 33.7 1.0
OP1 A:C822 3.7 31.7 1.0
O5' A:U821 3.8 31.4 1.0
C3' A:U821 3.8 33.3 1.0
NA A:NA8327 3.9 23.1 1.0
OP2 A:G854 3.9 29.1 1.0
O A:HOH3202 3.9 37.9 1.0
O5' A:G854 3.9 29.0 1.0
OP1 A:G856 4.0 35.7 1.0
O5' A:C822 4.1 30.0 1.0
O3' A:G820 4.2 29.1 1.0
O A:HOH4996 4.3 23.5 1.0
C5' A:G854 4.3 28.1 1.0
OP1 A:U821 4.4 30.2 1.0
O3' A:C853 4.5 29.0 1.0
OP1 A:U855 4.6 29.2 1.0
C5' A:U821 4.9 33.5 1.0
C4' A:U821 4.9 34.5 1.0
C5 A:C822 4.9 25.7 1.0
O A:HOH9311 4.9 68.9 1.0
O A:HOH9728 5.0 53.1 1.0
C2' A:U821 5.0 32.8 1.0

Magnesium binding site 7 out of 117 in 1kc8

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Magnesium binding site 7 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8007

b:17.3
occ:1.00
O A:HOH9009 1.9 19.0 1.0
OP2 A:U832 1.9 27.2 1.0
O A:HOH7767 1.9 10.5 1.0
OP2 A:A1840 2.2 19.9 1.0
O A:HOH3356 2.3 26.9 1.0
OP1 A:A1839 2.3 21.6 1.0
P A:U832 3.3 26.6 1.0
O A:HOH9104 3.3 36.0 1.0
P A:A1840 3.4 20.5 1.0
P A:A1839 3.6 20.5 1.0
OP1 A:A1840 3.9 19.5 1.0
O A:HOH9636 3.9 49.3 1.0
OP1 A:U832 4.0 25.9 1.0
O A:HOH6350 4.0 44.8 1.0
OP2 A:A1839 4.1 21.6 1.0
O5' A:U832 4.2 27.6 1.0
O3' A:U831 4.2 28.4 1.0
O3' A:A1839 4.3 21.6 1.0
O3' A:U1838 4.5 22.1 1.0
O5' A:A1840 4.6 20.4 1.0
C3' A:U831 4.6 30.0 1.0
O5' A:A1839 4.6 20.1 1.0
C5' A:U832 4.7 28.4 1.0
C3' A:A1839 4.7 22.5 1.0
O A:HOH7855 4.8 48.3 1.0
OP2 A:G833 4.8 30.9 1.0
O A:HOH7885 4.9 49.4 1.0
C5' A:A1839 4.9 21.4 1.0
O A:HOH9893 4.9 34.0 1.0

Magnesium binding site 8 out of 117 in 1kc8

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Magnesium binding site 8 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8008

b:26.4
occ:1.00
OP1 A:U919 1.9 24.9 1.0
O A:HOH7856 1.9 38.0 1.0
OP1 A:A2465 2.1 41.3 1.0
OP1 A:C2464 2.1 31.3 1.0
O A:HOH7771 2.2 26.1 1.0
O A:HOH3634 2.8 2.1 1.0
P A:U919 3.1 24.5 1.0
P A:A2465 3.4 38.9 1.0
P A:C2464 3.5 31.9 1.0
O5' A:U919 3.7 23.5 1.0
O A:HOH3346 3.7 39.1 1.0
C5' A:C2464 3.8 35.8 1.0
O5' A:A2465 3.8 39.3 1.0
OP2 A:U919 3.8 23.1 1.0
O5' A:C2464 3.9 33.2 1.0
C5' A:U919 4.1 26.4 1.0
OP1 A:G2466 4.1 51.6 1.0
O A:HOH9544 4.1 32.6 1.0
O A:HOH5882 4.2 78.2 1.0
OP2 A:A2465 4.2 39.5 1.0
O A:HOH9451 4.3 61.7 1.0
C3' A:A2465 4.3 43.2 1.0
O3' A:G918 4.3 24.6 1.0
O3' A:A2463 4.5 33.4 1.0
C5' A:A2465 4.5 39.5 1.0
OP2 A:C2464 4.5 31.4 1.0
O A:HOH9918 4.5 77.7 1.0
O3' A:C2464 4.6 38.2 1.0
C2' A:A2465 4.6 43.2 1.0
C4' A:C2464 4.8 37.0 1.0
C5' A:G2466 4.9 50.1 1.0
C3' A:C2464 4.9 36.7 1.0
C4' A:A2465 5.0 41.2 1.0

Magnesium binding site 9 out of 117 in 1kc8

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Magnesium binding site 9 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8009

b:22.8
occ:1.00
O A:HOH7773 1.7 28.4 1.0
OP1 A:A2612 1.8 20.5 1.0
O A:HOH7432 2.0 30.8 1.0
O A:HOH7772 2.0 20.1 1.0
OP1 A:G2611 2.3 22.3 1.0
O A:HOH3745 2.4 17.3 1.0
P A:A2612 3.2 20.7 1.0
P A:G2611 3.5 22.7 1.0
O A:HOH9336 3.5 39.4 1.0
O3' A:U2610 3.5 23.9 1.0
OP2 A:G2093 3.7 24.1 1.0
NA A:NA8358 3.7 80.3 1.0
OP2 A:A2612 3.8 21.6 1.0
C5' A:G2611 4.1 22.5 1.0
O3' A:G2611 4.1 23.4 1.0
O5' A:A2612 4.2 23.9 1.0
OP1 A:G2094 4.2 19.8 1.0
O D:HOH8526 4.2 15.2 1.0
O5' A:G2611 4.2 23.5 1.0
OP2 A:G2094 4.3 20.4 1.0
O A:HOH9308 4.3 20.9 1.0
C3' A:G2611 4.4 23.1 1.0
OP2 A:G2611 4.7 23.1 1.0
P A:G2094 4.7 20.3 1.0
C4' A:G2611 4.8 22.5 1.0
C3' A:U2610 4.8 24.8 1.0

Magnesium binding site 10 out of 117 in 1kc8

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Magnesium binding site 10 out of 117 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8010

b:21.6
occ:1.00
O A:HOH3843 1.5 38.7 1.0
O A:HOH9274 1.6 35.4 1.0
OP1 A:G836 1.8 24.9 1.0
O A:HOH9364 2.4 21.5 1.0
OP1 A:U2615 2.4 24.0 1.0
OE1 D:GLN230 2.4 25.2 1.0
P A:G836 3.2 22.2 1.0
CD D:GLN230 3.6 23.8 1.0
P A:U2615 3.8 24.5 1.0
O A:HOH5042 3.9 53.2 1.0
OP2 A:G836 3.9 25.0 1.0
C5' A:G836 3.9 24.0 1.0
O5' A:G836 4.0 22.6 1.0
O A:HOH3996 4.0 37.8 1.0
O A:HOH6821 4.1 39.9 1.0
O3' A:U835 4.2 21.7 1.0
CG D:GLN230 4.2 22.8 1.0
C3' A:U835 4.2 20.0 1.0
CB D:GLN230 4.2 22.6 1.0
O A:HOH9206 4.3 31.1 1.0
OP2 A:U2615 4.5 25.9 1.0
O A:HOH9546 4.6 26.4 1.0
CA D:GLN230 4.6 23.4 1.0
O D:GLN230 4.6 23.3 1.0
NE2 D:GLN230 4.7 22.3 1.0
O3' A:C2614 4.7 24.4 1.0
C5' A:U835 4.8 20.4 1.0
O5' A:U2615 4.8 22.4 1.0
O A:HOH9065 4.9 18.6 1.0
OP2 A:U837 5.0 25.5 1.0
OP2 A:G2616 5.0 21.1 1.0

Reference:

J.Hansen, P.B.Moore, T.A.Steitz. Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit J.Mol.Biol. V. 330 1061 2003.
ISSN: ISSN 0022-2836
PubMed: 12860128
DOI: 10.1016/S0022-2836(03)00668-5
Page generated: Mon Dec 14 06:17:29 2020

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