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Magnesium in PDB 1kqs: The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis

Protein crystallography data

The structure of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis, PDB code: 1kqs was solved by T.M.Schmeing, A.C.Seila, J.L.Hansen, B.Freeborn, J.K.Soukup, S.A.Scaringe, S.A.Strobel, 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 / 3.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.784, 300.349, 574.961, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22

Other elements in 1kqs:

The structure of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis also contains other interesting chemical elements:

Potassium (K) 2 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 The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis (pdb code 1kqs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis, PDB code: 1kqs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in 1kqs

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Magnesium binding site 1 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8001

b:21.3
occ:1.00
O 0:HOH8694 1.9 38.9 1.0
OP2 0:C2533 1.9 20.9 1.0
O 0:HOH7262 1.9 27.1 1.0
OP2 0:C2534 2.0 23.1 1.0
O 0:HOH3123 2.1 12.7 1.0
OP2 0:A2483 2.3 27.4 1.0
P 0:C2533 3.3 21.8 1.0
P 0:A2483 3.4 27.0 1.0
O3' 0:G2482 3.4 27.8 1.0
P 0:C2534 3.5 23.2 1.0
O3' 0:A2532 3.9 24.1 1.0
O2' 0:A2532 4.0 20.4 1.0
O 0:HOH3825 4.0 23.2 1.0
OP2 0:U2484 4.1 27.6 1.0
O3' 0:C2533 4.1 20.8 1.0
O 0:HOH9154 4.1 45.5 1.0
O5' 0:C2533 4.2 21.3 1.0
OP1 0:A2483 4.3 27.6 1.0
OP1 0:C2534 4.3 20.7 1.0
O2' 0:G2482 4.3 31.4 1.0
O 0:HOH6966 4.3 28.4 1.0
C3' 0:C2533 4.3 19.3 1.0
O 0:HOH5872 4.4 74.9 1.0
OP1 0:C2533 4.4 24.7 1.0
O5' 0:C2534 4.4 21.8 1.0
O5' 0:A2483 4.6 26.0 1.0
C3' 0:G2482 4.7 28.9 1.0
C5' 0:A2483 4.8 25.8 1.0
C3' 0:A2532 4.9 23.5 1.0
C5 0:C2534 4.9 31.3 1.0
C2' 0:A2532 5.0 22.4 1.0
C5' 0:C2533 5.0 19.2 1.0

Magnesium binding site 2 out of 117 in 1kqs

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Magnesium binding site 2 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8002

b:33.4
occ:1.00
O 0:HOH7240 1.9 22.6 1.0
O 0:HOH7241 1.9 23.7 1.0
OP1 0:A2483 1.9 27.6 1.0
O6 0:G627 2.0 20.6 1.0
OP1 0:C2534 2.2 20.7 1.0
O 0:HOH3825 2.3 23.2 1.0
P 0:A2483 3.2 27.0 1.0
C6 0:G627 3.2 20.3 1.0
P 0:C2534 3.4 23.2 1.0
OP2 0:A2483 3.6 27.4 1.0
O4 0:U626 3.8 26.7 1.0
O 0:HOH8778 3.9 3.5 1.0
N1 0:G627 3.9 19.7 1.0
OP2 0:C2534 4.0 23.1 1.0
O5' 0:A2483 4.1 26.0 1.0
O 0:HOH5371 4.1 33.7 1.0
O2' 0:U625 4.1 20.7 1.0
O 0:HOH6595 4.2 34.3 1.0
O3' 0:C2533 4.2 20.8 1.0
O3' 0:G2482 4.3 27.8 1.0
O 0:HOH3037 4.3 39.3 1.0
OP2 0:U2535 4.3 27.4 1.0
C5 0:G627 4.4 19.6 1.0
C4 0:U626 4.4 24.7 1.0
C5 0:U626 4.4 24.1 1.0
O5' 0:C2534 4.6 21.8 1.0
C3' 0:G2482 4.7 28.9 1.0
N7 0:G627 4.8 19.2 1.0
C5' 0:C2534 5.0 23.4 1.0

Magnesium binding site 3 out of 117 in 1kqs

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Magnesium binding site 3 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8003

b:22.4
occ:1.00
OP1 0:A2624 1.8 23.9 1.0
O 0:HOH3174 2.0 24.1 1.0
OP2 0:G877 2.1 19.1 1.0
O 0:HOH8543 2.2 14.4 1.0
OP2 0:A876 2.2 19.9 1.0
O A:HOH8537 2.3 15.4 1.0
P 0:A2624 3.1 25.3 1.0
P 0:G877 3.2 21.9 1.0
P 0:A876 3.6 22.0 1.0
OP1 0:G877 3.6 21.3 1.0
O3' 0:G2623 3.7 23.7 1.0
O 0:HOH6654 4.0 77.1 1.0
OP2 0:A2624 4.0 27.0 1.0
O5' 0:A876 4.0 21.2 1.0
O3' 0:A876 4.0 21.1 1.0
O 0:HOH8542 4.2 12.6 1.0
O3' 0:A875 4.2 19.9 1.0
O5' 0:A2624 4.2 26.9 1.0
O A:HOH8613 4.3 33.7 1.0
OD1 A:ASN195 4.3 26.2 1.0
C5' 0:A876 4.3 19.9 1.0
O A:HOH8630 4.4 24.9 1.0
O 0:HOH3974 4.4 24.6 1.0
O A:ALA193 4.4 21.1 1.0
O5' 0:G877 4.5 20.8 1.0
C5' 0:A2624 4.5 27.2 1.0
C3' 0:A876 4.6 20.7 1.0
OP1 0:A876 4.8 22.0 1.0
O 0:HOH7271 5.0 34.4 1.0

Magnesium binding site 4 out of 117 in 1kqs

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Magnesium binding site 4 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8004

b:30.0
occ:1.00
OP1 0:A459 1.7 20.5 1.0
O6 0:G456 1.8 27.2 1.0
O 0:HOH8568 1.9 16.2 1.0
O 0:HOH9290 2.0 8.0 1.0
O 0:HOH3291 2.1 14.9 1.0
O 0:HOH7247 2.3 17.8 1.0
C6 0:G456 2.9 29.3 1.0
P 0:A459 3.1 22.3 1.0
O5' 0:A459 3.7 23.5 1.0
OP2 0:A459 3.8 25.4 1.0
C5 0:G456 3.8 27.6 1.0
N7 0:G456 3.9 26.3 1.0
C5' 0:A459 4.0 24.8 1.0
N1 0:G456 4.0 30.6 1.0
O 0:HOH8846 4.1 50.7 1.0
O3' 0:G458 4.2 20.9 1.0
CE C:LYS85 4.2 16.8 1.0
NZ C:LYS85 4.4 15.8 1.0
OP1 0:A460 4.5 26.5 1.0
O 0:HOH3212 4.5 32.2 1.0
OP2 0:A455 4.5 17.9 1.0
O 0:HOH3023 4.5 40.9 1.0
N7 0:A455 4.6 29.3 1.0
O 0:HOH5457 4.7 41.7 1.0
O 0:HOH4903 4.7 19.3 1.0
CD C:LYS85 4.9 19.2 1.0
OP1 0:A477 4.9 20.5 1.0
OP2 0:A460 5.0 25.4 1.0
O 0:HOH7248 5.0 1.0 1.0

Magnesium binding site 5 out of 117 in 1kqs

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Magnesium binding site 5 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8005

b:26.8
occ:1.00
O 0:HOH7264 1.9 27.6 1.0
O 0:HOH7263 1.9 16.6 1.0
OP1 0:A1836 1.9 24.8 1.0
OP1 0:U1838 1.9 20.4 1.0
O 0:HOH3119 2.0 18.0 1.0
OP2 0:A1839 2.1 21.3 1.0
P 0:U1838 3.4 21.2 1.0
P 0:A1836 3.4 23.7 1.0
P 0:A1839 3.6 21.6 1.0
O 0:HOH5056 3.8 58.1 1.0
O 0:HOH4998 3.9 40.7 1.0
OP2 0:U1838 4.1 21.2 1.0
O5' 0:A1836 4.1 21.9 1.0
OP2 0:A1836 4.2 25.8 1.0
O5' 0:U1838 4.2 18.7 1.0
C3' 0:G1837 4.2 24.5 1.0
O 0:HOH8529 4.3 23.2 1.0
O3' 0:U1835 4.3 21.8 1.0
O3' 0:U1838 4.3 21.4 1.0
O3' 0:G1837 4.3 21.6 1.0
O5' 0:A1839 4.3 21.2 1.0
C2' 0:U1835 4.4 22.8 1.0
C3' 0:U1835 4.5 22.5 1.0
C5' 0:U1838 4.5 16.9 1.0
OP1 0:A1839 4.5 22.1 1.0
O 0:HOH7338 4.5 34.4 1.0
OP2 0:G1837 4.5 24.4 1.0
O 0:HOH9024 4.5 23.8 1.0
C3' 0:U1838 4.6 19.0 1.0
O 0:HOH9151 4.6 25.6 1.0
N7 0:A1839 4.6 24.0 1.0
O2' 0:U1835 4.8 23.1 1.0
C8 0:A1839 4.8 23.7 1.0

Magnesium binding site 6 out of 117 in 1kqs

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Magnesium binding site 6 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8006

b:28.2
occ:1.00
OP2 0:C822 2.0 29.3 1.0
OP1 0:G854 2.0 26.7 1.0
O 0:HOH3125 2.0 9.8 1.0
O 0:HOH9322 2.0 36.8 1.0
OP2 0:U821 2.1 31.6 1.0
O 0:HOH3263 2.1 46.6 1.0
P 0:G854 3.2 27.4 1.0
P 0:C822 3.3 30.9 1.0
P 0:U821 3.5 31.2 1.0
O 0:HOH9712 3.8 24.9 1.0
O5' 0:G854 3.8 25.8 1.0
O5' 0:U821 3.8 31.2 1.0
OP1 0:G856 3.9 37.4 1.0
NA 0:NA8327 3.9 16.1 1.0
OP2 0:G854 3.9 27.8 1.0
O3' 0:U821 4.0 32.5 1.0
OP1 0:C822 4.0 32.6 1.0
C3' 0:U821 4.1 33.2 1.0
C5' 0:G854 4.2 25.5 1.0
O 0:HOH4493 4.2 29.0 1.0
O3' 0:G820 4.2 29.0 1.0
OP1 0:U855 4.4 24.6 1.0
O5' 0:C822 4.4 31.3 1.0
O3' 0:C853 4.5 24.4 1.0
OP1 0:U821 4.6 29.5 1.0

Magnesium binding site 7 out of 117 in 1kqs

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Magnesium binding site 7 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8007

b:18.7
occ:1.00
OP2 0:U832 1.9 24.2 1.0
O 0:HOH8529 2.0 23.2 1.0
O 0:HOH7252 2.0 12.2 1.0
OP2 0:A1840 2.1 22.6 1.0
OP1 0:A1839 2.1 22.1 1.0
O 0:HOH9866 2.1 10.3 1.0
P 0:U832 3.3 23.7 1.0
P 0:A1840 3.3 23.6 1.0
O 0:HOH8621 3.3 24.8 1.0
P 0:A1839 3.5 21.6 1.0
OP1 0:A1840 3.7 22.8 1.0
O 0:HOH9151 3.7 25.6 1.0
OP1 0:U832 3.9 24.1 1.0
O 0:HOH5850 4.0 36.0 1.0
O5' 0:U832 4.1 23.4 1.0
OP2 0:A1839 4.2 21.3 1.0
O3' 0:A1839 4.3 21.4 1.0
O3' 0:U831 4.3 23.2 1.0
O3' 0:U1838 4.4 21.4 1.0
O5' 0:A1840 4.5 21.7 1.0
O5' 0:A1839 4.5 21.2 1.0
O 0:HOH7338 4.6 34.4 1.0
C3' 0:A1839 4.7 21.9 1.0
C3' 0:U831 4.7 24.3 1.0
C5' 0:U832 4.8 23.2 1.0
C5' 0:A1839 4.8 21.4 1.0
O 0:HOH7368 4.8 25.4 1.0
OP2 0:G833 4.8 27.6 1.0
O 0:HOH7263 5.0 16.6 1.0

Magnesium binding site 8 out of 117 in 1kqs

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Magnesium binding site 8 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8008

b:42.2
occ:1.00
OP1 0:U919 2.0 22.8 1.0
O 0:HOH7339 2.0 27.7 1.0
O 0:HOH7256 2.1 30.5 1.0
OP1 0:A2465 2.1 40.3 1.0
OP1 0:C2464 2.1 29.5 1.0
O 0:HOH3138 2.2 9.9 1.0
P 0:U919 3.1 23.8 1.0
P 0:A2465 3.4 39.0 1.0
P 0:C2464 3.5 33.0 1.0
OP2 0:U919 3.7 23.3 1.0
O 0:HOH9857 3.7 59.2 1.0
O5' 0:U919 3.8 21.8 1.0
O5' 0:A2465 3.9 38.0 1.0
OP1 0:G2466 3.9 49.2 1.0
C5' 0:C2464 3.9 34.4 1.0
O5' 0:C2464 4.0 32.8 1.0
O 0:HOH8963 4.2 47.0 1.0
C3' 0:A2465 4.2 41.7 1.0
O 0:HOH5384 4.2 52.8 1.0
OP2 0:A2465 4.2 39.2 1.0
C5' 0:U919 4.3 25.1 1.0
O 0:HOH9058 4.4 31.3 1.0
O3' 0:G918 4.4 22.5 1.0
OP2 0:C2464 4.5 33.3 1.0
O3' 0:A2463 4.5 33.8 1.0
C2' 0:A2465 4.5 41.1 1.0
C5' 0:A2465 4.6 37.5 1.0
O 0:HOH9432 4.6 88.2 1.0
O3' 0:C2464 4.6 37.4 1.0
C5' 0:G2466 4.7 43.6 1.0
C4' 0:C2464 4.9 35.1 1.0
C3' 0:C2464 5.0 36.1 1.0
O2' 0:A2465 5.0 44.5 1.0

Magnesium binding site 9 out of 117 in 1kqs

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Magnesium binding site 9 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8009

b:18.2
occ:1.00
O 0:HOH6920 1.8 24.9 1.0
O 0:HOH7258 2.0 25.3 1.0
O 0:HOH7257 2.0 10.2 1.0
OP1 0:A2612 2.0 17.6 1.0
O 0:HOH3249 2.0 14.9 1.0
OP1 0:G2611 2.1 23.3 1.0
P 0:G2611 3.3 22.7 1.0
O3' 0:U2610 3.3 21.8 1.0
P 0:A2612 3.4 20.8 1.0
NA 0:NA8358 3.4 98.1 1.0
O 0:HOH8847 3.8 30.6 1.0
OP2 0:G2093 3.8 17.6 1.0
O 0:HOH8982 4.0 21.3 1.0
OP2 0:A2612 4.0 22.1 1.0
OP2 0:G2094 4.1 19.0 1.0
C5' 0:G2611 4.1 21.1 1.0
O5' 0:G2611 4.1 21.8 1.0
OP1 0:G2094 4.1 17.9 1.0
O5' 0:A2612 4.3 22.2 1.0
O3' 0:G2611 4.3 21.1 1.0
O 0:HOH8818 4.4 14.8 1.0
OP2 0:G2611 4.5 24.9 1.0
P 0:G2094 4.6 19.7 1.0
C3' 0:G2611 4.6 20.7 1.0
C3' 0:U2610 4.6 22.9 1.0
O 0:HOH7274 4.7 26.4 1.0
C4' 0:U2610 4.9 22.9 1.0
C4' 0:G2611 4.9 20.6 1.0

Magnesium binding site 10 out of 117 in 1kqs

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Magnesium binding site 10 out of 117 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8010

b:20.2
occ:1.00
O 0:HOH3347 1.8 20.0 1.0
OP1 0:G836 1.8 15.5 1.0
O B:HOH8524 1.9 24.9 1.0
O 0:HOH8873 2.0 26.0 1.0
OP1 0:U2615 2.2 21.3 1.0
OE1 B:GLN230 2.2 22.8 1.0
P 0:G836 3.3 18.1 1.0
CD B:GLN230 3.4 21.2 1.0
P 0:U2615 3.6 21.1 1.0
O 0:HOH4538 3.8 46.0 1.0
CG B:GLN230 4.0 21.6 1.0
C5' 0:G836 4.1 17.0 1.0
OP2 0:G836 4.1 18.4 1.0
CB B:GLN230 4.1 22.9 1.0
O5' 0:G836 4.1 15.8 1.0
O 0:HOH3497 4.1 17.7 1.0
OP2 0:U2615 4.2 23.2 1.0
O3' 0:U835 4.2 15.3 1.0
C3' 0:U835 4.2 15.8 1.0
O 0:HOH8723 4.3 27.5 1.0
NE2 B:GLN230 4.4 19.1 1.0
O5' 0:U2615 4.5 19.4 1.0
O3' 0:C2614 4.5 20.3 1.0
O 0:HOH6323 4.5 38.3 1.0
OP2 0:G2616 4.5 21.4 1.0
CA B:GLN230 4.6 24.9 1.0
C5' 0:U835 4.7 19.4 1.0
N2 0:G2616 4.8 27.1 1.0
O B:GLN230 4.8 24.4 1.0
O 0:HOH9060 4.9 29.4 1.0
C5' 0:U2615 5.0 18.3 1.0

Reference:

T.M.Schmeing, A.C.Seila, J.L.Hansen, B.Freeborn, J.K.Soukup, S.A.Scaringe, S.A.Strobel, P.B.Moore, T.A.Steitz. A Pre-Translocational Intermediate in Protein Synthesis Observed in Crystals of Enzymatically Active 50S Subunits. Nat.Struct.Biol. V. 9 225 2002.
ISSN: ISSN 1072-8368
PubMed: 11828326
Page generated: Mon Dec 14 06:22:19 2020

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