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Sodium 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:

Magnesium (Mg) 117 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms

Sodium 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 - 86;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 86 binding sites of Sodium where determined in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis, PDB code: 1kqs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 in 1kqs

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Sodium binding site 1 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8301

b:28.0
occ:1.00
O 0:HOH4468 2.3 35.6 1.0
OP2 0:C1069 2.4 13.1 1.0
N7 0:G1072 2.5 19.3 1.0
O6 0:G1072 3.0 23.4 1.0
O6 0:G1087 3.1 27.6 1.0
O 0:HOH9708 3.1 37.3 1.0
O 0:HOH9675 3.1 31.4 1.0
C5 0:G1072 3.2 20.4 1.0
C6 0:G1072 3.4 20.7 1.0
O 0:HOH8588 3.5 6.1 1.0
C8 0:G1072 3.6 18.8 1.0
P 0:C1069 3.8 14.1 1.0
C6 0:G1087 4.0 26.2 1.0
O 0:HOH3044 4.0 20.6 1.0
C4 0:G1072 4.4 19.4 1.0
C5' 0:C1068 4.4 23.4 1.0
O3' 0:C1068 4.5 15.3 1.0
OP1 0:C1069 4.5 12.1 1.0
C3' 0:C1068 4.5 19.0 1.0
N9 0:G1072 4.6 19.4 1.0
N1 0:G1087 4.6 25.2 1.0
N1 0:G1072 4.7 17.7 1.0
O 0:HOH3773 4.8 72.6 1.0
O5' 0:C1069 4.9 14.7 1.0
OP2 0:C1068 4.9 32.5 1.0
C5 0:G1087 4.9 26.0 1.0

Sodium binding site 2 out of 86 in 1kqs

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Sodium binding site 2 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8302

b:18.3
occ:1.00
O2' 0:G1119 2.8 24.1 1.0
O 0:HOH5185 2.9 54.1 1.0
OP2 0:U1120 2.9 27.9 1.0
O6 0:G1121 3.0 23.0 1.0
O3' 0:G1119 3.1 25.3 1.0
O 0:HOH7277 3.1 32.5 1.0
O 0:HOH3674 3.2 19.0 1.0
O 0:HOH4043 3.3 25.9 1.0
N7 0:G1121 3.4 25.2 1.0
P 0:U1120 3.6 26.6 1.0
O4 0:U1122 3.6 29.7 1.0
C6 0:G1121 3.8 23.6 1.0
C2' 0:G1119 3.8 24.1 1.0
C5 0:G1121 3.9 24.1 1.0
C3' 0:G1119 4.0 26.2 1.0
O 0:HOH6431 4.1 41.9 1.0
MG 0:MG8025 4.2 17.4 1.0
C1' 0:G1119 4.4 22.8 1.0
OP1 0:U1120 4.4 27.1 1.0
C4 0:U1122 4.4 28.6 1.0
C8 0:G1121 4.6 25.0 1.0
C5 0:U1122 4.8 27.6 1.0
O5' 0:U1120 4.8 25.9 1.0
N4 0:C1243 4.9 30.6 1.0
OP1 0:C1238 4.9 31.0 1.0
C5' 0:U1120 5.0 26.4 1.0

Sodium binding site 3 out of 86 in 1kqs

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Sodium binding site 3 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8303

b:33.7
occ:1.00
OP1 0:G644 2.9 18.4 1.0
O4 0:U904 2.9 21.5 1.0
OP2 0:A643 3.0 15.8 1.0
OP1 0:G1354 3.2 24.8 1.0
NH2 K:ARG8 3.3 31.5 1.0
O5' 0:A643 3.3 16.0 1.0
O 0:HOH9770 3.5 61.0 1.0
P 0:A643 3.5 17.8 1.0
OP1 0:C1353 3.9 43.2 1.0
C4 0:U904 3.9 18.7 1.0
OP1 0:A643 4.0 17.5 1.0
O 0:HOH4099 4.1 77.5 1.0
N3 0:U904 4.2 16.5 1.0
P 0:G644 4.2 18.8 1.0
O 0:HOH8944 4.2 15.4 1.0
C5' 0:A643 4.2 14.7 1.0
P 0:G1354 4.3 25.8 1.0
CZ K:ARG8 4.3 29.4 1.0
C3' 0:A643 4.5 17.4 1.0
OP2 0:G1354 4.5 25.7 1.0
O3' 0:A643 4.6 18.7 1.0
OP2 0:G644 4.7 16.8 1.0
O3' 0:C1353 4.8 27.3 1.0
NH1 K:ARG8 4.9 29.4 1.0
P 0:C1353 4.9 43.2 1.0
C4' 0:A643 5.0 16.6 1.0
NE K:ARG8 5.0 29.0 1.0

Sodium binding site 4 out of 86 in 1kqs

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Sodium binding site 4 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8305

b:19.4
occ:1.00
O 0:HOH4200 2.5 40.0 1.0
O 0:HOH3595 2.6 25.1 1.0
O2' 0:A630 2.7 24.5 1.0
O 0:HOH5286 2.7 39.2 1.0
N3 0:A630 2.7 27.5 1.0
O2' 0:A631 2.9 22.7 1.0
C1' 0:A630 3.5 24.1 1.0
C2 0:A630 3.6 26.6 1.0
C2' 0:A631 3.6 21.3 1.0
OP2 0:A2074 3.6 21.8 1.0
C2' 0:A630 3.6 23.6 1.0
C4 0:A630 3.7 25.4 1.0
N9 0:A630 4.0 24.6 1.0
O3' 0:A630 4.0 21.9 1.0
C3' 0:A631 4.0 21.1 1.0
OP1 0:A632 4.1 23.7 1.0
N2 0:G2070 4.1 19.9 1.0
O3' 0:A631 4.3 21.7 1.0
C3' 0:A630 4.5 21.9 1.0
O 0:HOH8921 4.5 19.1 1.0
N1 0:A629 4.6 23.2 1.0
O 0:HOH9592 4.6 65.5 1.0
P 0:A632 4.7 24.6 1.0
O4' 0:A630 4.7 25.4 1.0
OP2 0:G2072 4.7 37.3 1.0
C2 0:A629 4.8 22.8 1.0
C2 0:A628 4.8 21.4 1.0
C2 0:G2070 4.8 18.7 1.0
N1 0:A630 4.9 24.6 1.0
C5 0:A630 5.0 24.7 1.0

Sodium binding site 5 out of 86 in 1kqs

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Sodium binding site 5 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8306

b:21.6
occ:1.00
N7 0:G2094 2.8 23.1 1.0
N7 0:G2093 2.9 20.0 1.0
N1 0:A2649 3.0 31.5 1.0
O6 0:G2094 3.0 25.2 1.0
O 0:HOH8646 3.2 20.7 1.0
O2' 0:G2092 3.3 19.5 1.0
C5 0:G2093 3.3 21.5 1.0
N3 0:G2092 3.4 28.5 1.0
C2 0:A2649 3.4 31.3 1.0
O6 0:G2093 3.4 23.8 1.0
C5 0:G2094 3.5 23.8 1.0
C6 0:G2093 3.6 23.1 1.0
C6 0:G2094 3.6 24.2 1.0
N2 0:G2092 3.7 30.0 1.0
C8 0:G2093 3.7 19.7 1.0
C2 0:G2092 3.8 29.3 1.0
N6 0:A2612 3.9 23.5 1.0
C8 0:G2094 3.9 22.0 1.0
C6 0:A2649 4.1 30.9 1.0
C4 0:G2092 4.2 27.4 1.0
C6 0:A2612 4.3 24.4 1.0
C4 0:G2093 4.3 21.4 1.0
N6 0:A2649 4.4 32.0 1.0
C2' 0:G2092 4.5 21.0 1.0
C1' 0:G2092 4.5 23.8 1.0
N9 0:G2093 4.5 20.1 1.0
N3 0:A2649 4.6 31.9 1.0
N1 0:G2093 4.7 23.6 1.0
C5 0:A2612 4.7 23.5 1.0
N9 0:G2092 4.7 25.8 1.0
C4 0:G2094 4.8 23.1 1.0
N1 0:A2612 4.8 24.7 1.0
N1 0:G2092 4.8 27.9 1.0
O3' 0:G2092 4.9 19.6 1.0
N7 0:A2612 4.9 23.9 1.0
N1 0:G2094 5.0 24.1 1.0
N9 0:G2094 5.0 21.2 1.0

Sodium binding site 6 out of 86 in 1kqs

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Sodium binding site 6 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8307

b:40.5
occ:1.00
O2 0:C40 2.3 45.7 1.0
O2' 0:C40 2.7 44.8 1.0
O4' 0:G41 2.9 37.7 1.0
C2' 0:C40 3.0 42.7 1.0
N1 0:A442 3.1 44.8 1.0
O2 0:C443 3.1 46.4 1.0
C1' 0:C40 3.2 43.5 1.0
C2 0:C40 3.3 45.7 1.0
C1' 0:G41 3.6 37.7 1.0
C2 0:A442 3.7 44.2 1.0
N1 0:C40 3.7 45.4 1.0
N9 0:G41 3.9 39.4 1.0
C2 0:C443 3.9 46.2 1.0
C6 0:A442 4.0 43.6 1.0
C4' 0:G41 4.1 36.4 1.0
N6 0:A442 4.2 44.3 1.0
N2 0:G39 4.2 41.4 1.0
C8 0:G41 4.2 40.0 1.0
C5' 0:G41 4.3 36.8 1.0
N3 0:C443 4.4 46.3 1.0
N3 0:C40 4.5 44.9 1.0
O4' 0:C40 4.5 42.8 1.0
C4 0:G41 4.5 40.0 1.0
C3' 0:C40 4.5 41.4 1.0
O5' 0:G41 4.6 37.6 1.0
C2 0:G39 4.7 42.1 1.0
N1 0:C443 4.8 45.9 1.0
N1 0:G39 4.8 42.3 1.0
O 0:HOH5365 4.8 15.4 1.0
C1' 0:C443 4.9 44.0 1.0
O 0:HOH6475 4.9 28.7 1.0
N3 0:G41 4.9 40.0 1.0
N7 0:G41 5.0 39.4 1.0
N3 0:A442 5.0 43.1 1.0

Sodium binding site 7 out of 86 in 1kqs

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Sodium binding site 7 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8308

b:44.2
occ:1.00
O2 0:C1394 2.2 35.7 1.0
O2 0:U1724 2.3 29.8 1.0
O 0:HOH9919 2.6 25.5 1.0
O4 0:U1432 2.7 26.7 1.0
C2 0:C1394 3.4 35.0 1.0
C2 0:U1724 3.5 27.1 1.0
O6 0:G1433 3.7 36.6 1.0
O2' 0:C1394 3.8 30.6 1.0
C4 0:U1432 3.9 27.3 1.0
C2' 0:C1394 3.9 32.6 1.0
O 0:HOH8811 4.0 22.9 1.0
O 0:HOH6639 4.1 99.7 1.0
C1' 0:C1394 4.2 33.5 1.0
C6 0:G1433 4.2 35.2 1.0
N3 0:C1394 4.2 34.3 1.0
O2' 0:U1724 4.2 21.7 1.0
N1 0:C1394 4.3 35.2 1.0
C1' 0:U1724 4.3 26.4 1.0
N3 0:U1432 4.4 28.5 1.0
N3 0:U1724 4.4 26.8 1.0
N1 0:U1724 4.5 26.8 1.0
C2' 0:U1724 4.5 25.6 1.0
O 0:HOH4966 4.5 49.9 1.0
N1 0:G1433 4.6 35.4 1.0
O 0:HOH4329 4.7 42.3 1.0
O2' 0:C1725 4.7 30.7 1.0
OP2 0:U1722 4.9 36.0 1.0

Sodium binding site 8 out of 86 in 1kqs

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Sodium binding site 8 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8309

b:24.1
occ:1.00
O3' 0:A1133 2.6 29.7 1.0
O H:PRO155 2.7 42.1 1.0
OP1 0:G1134 2.7 31.6 1.0
O H:LYS150 2.8 48.0 1.0
O H:VAL153 3.0 35.8 1.0
O2' 0:A1133 3.1 30.8 1.0
P 0:G1134 3.3 31.5 1.0
C H:PRO155 3.6 42.7 1.0
O H:THR154 3.6 39.3 1.0
C3' 0:A1133 3.7 30.8 1.0
C2' 0:A1133 4.0 30.3 1.0
C H:LYS150 4.1 47.5 1.0
C H:THR154 4.1 38.1 1.0
C5' 0:G1134 4.1 31.6 1.0
O5' 0:G1134 4.2 29.8 1.0
C H:VAL153 4.2 35.6 1.0
N H:THR156 4.3 45.6 1.0
C4' 0:A1133 4.3 31.7 1.0
CA H:THR156 4.3 48.1 1.0
N H:PRO155 4.5 39.5 1.0
OP2 0:G1134 4.5 31.9 1.0
CA H:PRO155 4.5 40.7 1.0
O2' 0:G2520 4.6 33.7 1.0
CG H:LYS150 4.8 46.7 1.0
CA H:MET151 4.9 46.4 1.0
CA H:THR154 4.9 37.0 1.0
N H:MET151 4.9 47.5 1.0
O 0:HOH3501 5.0 17.1 1.0
N H:VAL153 5.0 36.2 1.0
C H:MET151 5.0 44.2 1.0

Sodium binding site 9 out of 86 in 1kqs

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Sodium binding site 9 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8310

b:16.9
occ:1.00
O6 0:G2579 2.7 29.0 1.0
N7 0:G2579 3.0 31.5 1.0
O 0:HOH4001 3.0 30.5 1.0
N3 0:A2577 3.0 25.6 1.0
O4' 0:A2577 3.1 30.7 1.0
N7 0:G2578 3.2 31.5 1.0
C6 0:G2579 3.4 29.1 1.0
C5 0:G2579 3.5 29.2 1.0
C1' 0:A2577 3.6 29.0 1.0
O6 0:G2578 3.6 33.7 1.0
C5 0:G2578 3.6 31.9 1.0
C6 0:G2578 3.8 32.3 1.0
C2 0:A2577 3.8 26.2 1.0
C4 0:A2577 3.9 26.5 1.0
O 0:HOH7223 3.9 98.0 1.0
C8 0:G2578 4.0 31.5 1.0
C4' 0:A2577 4.0 32.5 1.0
O 0:HOH5791 4.0 56.0 1.0
N9 0:A2577 4.1 26.5 1.0
C8 0:G2579 4.2 30.4 1.0
C4 0:G2578 4.6 32.0 1.0
O 0:HOH5469 4.6 53.3 1.0
N1 0:G2579 4.7 28.1 1.0
O3' 0:A2577 4.8 34.9 1.0
O6 0:G2580 4.8 26.4 1.0
N9 0:G2578 4.8 32.0 1.0
C4 0:G2579 4.8 28.8 1.0
N4 0:C2556 4.9 33.7 1.0
N1 0:G2578 4.9 32.8 1.0
C3' 0:A2577 4.9 32.4 1.0
C2' 0:A2577 4.9 31.4 1.0
N3 0:U2554 5.0 25.1 1.0

Sodium binding site 10 out of 86 in 1kqs

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Sodium binding site 10 out of 86 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na8311

b:38.0
occ:1.00
O6 0:G2525 2.2 33.5 1.0
O 0:HOH3083 2.4 2.7 1.0
O 0:HOH4153 2.6 20.4 1.0
O 0:HOH8701 2.7 24.9 1.0
N7 0:G2524 2.9 27.4 1.0
C6 0:G2525 3.3 34.1 1.0
O 0:HOH5868 3.5 45.2 1.0
O 0:HOH3127 3.6 20.0 1.0
C8 0:G2524 3.7 26.5 1.0
C5 0:G2524 4.0 25.8 1.0
C5 0:U2523 4.1 27.6 1.0
C5 0:G2525 4.1 33.0 1.0
O6 0:G2524 4.2 23.7 1.0
O2' 0:C2493 4.2 28.3 1.0
N1 0:G2525 4.3 33.7 1.0
N7 0:G2525 4.3 32.7 1.0
C4 0:U2523 4.3 28.8 1.0
OP2 0:G2524 4.4 31.1 1.0
C6 0:G2524 4.4 25.0 1.0
O4 0:U2523 4.6 32.2 1.0
C6 0:U2523 4.6 26.2 1.0
C2' 0:C2493 4.6 29.8 1.0
OP2 0:U2523 4.9 30.5 1.0
N3 0:U2523 4.9 28.5 1.0
N9 0:G2524 4.9 26.5 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: Tue Dec 15 05:28:48 2020

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