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

Protein crystallography data

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

Other elements in 2qex:

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:

Magnesium (Mg) 116 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 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 Sodium atom.
In total 86 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 in 2qex

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Sodium binding site 1 out of 86 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 Sodium with other atoms in the Na 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:Na8501

b:51.2
occ:1.00
OP2 0:C1069 2.0 24.1 1.0
O 0:HOH4826 2.0 61.6 1.0
O 0:HOH9998 2.7 30.5 1.0
N7 0:G1072 2.8 22.1 1.0
O 0:HOH4120 3.2 61.1 1.0
O 0:HOH3031 3.2 42.2 1.0
O6 0:G1087 3.2 29.9 1.0
P 0:C1069 3.4 26.0 1.0
C5 0:G1072 3.6 23.3 1.0
C8 0:G1072 3.7 23.4 1.0
O6 0:G1072 3.7 25.5 1.0
O 0:HOH8891 3.9 31.8 1.0
C6 0:G1072 4.0 22.7 1.0
O3' 0:C1068 4.0 24.8 1.0
C3' 0:C1068 4.0 27.3 1.0
OP1 0:C1069 4.1 25.4 1.0
C5' 0:C1068 4.2 30.3 1.0
C6 0:G1087 4.2 31.4 1.0
O5' 0:C1069 4.4 26.1 1.0
O 0:HOH3363 4.4 53.4 1.0
N1 0:G1087 4.7 31.1 1.0
C4' 0:C1068 4.7 29.6 1.0
C4 0:G1072 4.8 24.7 1.0
N9 0:G1072 4.8 24.6 1.0

Sodium binding site 2 out of 86 in 2qex

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Sodium binding site 2 out of 86 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 Sodium with other atoms in the Na 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:Na8502

b:51.8
occ:1.00
O 0:HOH7625 2.7 45.8 1.0
O2' 0:G1119 2.9 32.5 1.0
O6 0:G1121 3.0 25.8 1.0
OP2 0:U1120 3.2 36.3 1.0
O 0:HOH5539 3.2 64.8 1.0
O 0:HOH4402 3.2 41.1 1.0
O3' 0:G1119 3.2 36.4 1.0
N7 0:G1121 3.3 29.2 1.0
O4 0:U1122 3.3 39.7 1.0
O 0:HOH4014 3.6 29.1 1.0
C6 0:G1121 3.7 28.2 1.0
P 0:U1120 3.8 38.0 1.0
C5 0:G1121 3.8 27.6 1.0
C2' 0:G1119 3.9 32.6 1.0
C4 0:U1122 4.1 38.1 1.0
C3' 0:G1119 4.1 33.9 1.0
O 0:HOH6786 4.3 57.1 1.0
MG 0:MG8025 4.3 32.4 1.0
C1' 0:G1119 4.3 29.8 1.0
C8 0:G1121 4.5 27.6 1.0
C5 0:U1122 4.5 38.0 1.0
OP1 0:U1120 4.7 38.8 1.0
N4 0:C1243 4.9 34.4 1.0
O5' 0:U1120 5.0 35.4 1.0

Sodium binding site 3 out of 86 in 2qex

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Sodium binding site 3 out of 86 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 Sodium with other atoms in the Na 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:Na8503

b:1.0
occ:1.00
O 0:HOH9254 1.7 2.5 1.0
O 0:HOH7414 1.9 92.7 1.0
OP1 0:G1354 2.5 31.2 1.0
O 0:HOH6435 2.6 21.3 1.0
OP2 0:A643 3.0 30.0 1.0
OP1 0:C1353 3.1 42.4 1.0
OP1 0:A643 3.6 32.9 1.0
P 0:G1354 3.7 28.0 1.0
O 0:HOH4458 3.7 89.2 1.0
P 0:A643 3.7 30.8 1.0
O3' 0:C1353 3.9 31.8 1.0
O5' 0:C1353 4.2 44.5 1.0
P 0:C1353 4.3 47.4 1.0
OP2 0:G1354 4.3 26.1 1.0
O4 0:U904 4.3 32.5 1.0
C5' 0:C1353 4.4 38.9 1.0
O 0:HOH3091 4.4 45.4 1.0
O5' 0:A643 4.4 26.6 1.0
C3' 0:C1353 4.6 34.3 1.0
N3 0:U904 4.7 30.4 1.0
O2' 0:A1352 4.7 51.3 1.0
NH2 L:ARG8 4.8 35.5 1.0
OP1 0:G644 4.8 32.0 1.0
OP1 0:G642 4.8 29.4 1.0
O5' 0:G1354 4.9 27.6 1.0
C4 0:U904 5.0 30.4 1.0

Sodium binding site 4 out of 86 in 2qex

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Sodium binding site 4 out of 86 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 Sodium with other atoms in the Na 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:Na8505

b:36.9
occ:1.00
O 0:HOH5640 2.3 46.3 1.0
O2' 0:A630 2.4 32.9 1.0
N3 0:A630 2.6 35.0 1.0
O 0:HOH3932 2.8 29.4 1.0
O 0:HOH4559 3.0 41.2 1.0
O2' 0:A631 3.1 26.6 1.0
OP1 0:A632 3.4 28.0 1.0
C2' 0:A630 3.4 32.1 1.0
C1' 0:A630 3.5 33.1 1.0
C2 0:A630 3.5 32.7 1.0
C4 0:A630 3.5 33.9 1.0
C2' 0:A631 3.7 28.9 1.0
C3' 0:A631 3.8 29.0 1.0
N9 0:A630 3.8 34.6 1.0
O3' 0:A631 4.0 28.9 1.0
O 0:HOH9232 4.0 34.7 1.0
O3' 0:A630 4.0 30.6 1.0
P 0:A632 4.1 29.7 1.0
C2 0:1MA628 4.2 30.8 1.0
OP2 0:A2074 4.2 32.4 1.0
OP2 0:A632 4.4 29.3 1.0
C3' 0:A630 4.4 30.9 1.0
N1 0:A630 4.7 31.4 1.0
C5 0:A630 4.8 32.0 1.0
CM1 0:1MA628 4.8 29.6 1.0
O4' 0:A630 4.8 32.9 1.0
O 0:HOH9916 4.8 46.2 1.0
N3 0:1MA628 4.9 30.0 1.0
N1 0:1MA628 5.0 29.6 1.0
N2 0:G2070 5.0 26.7 1.0

Sodium binding site 5 out of 86 in 2qex

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Sodium binding site 5 out of 86 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 Sodium with other atoms in the Na 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:Na8506

b:52.0
occ:1.00
N7 0:G2094 2.5 29.6 1.0
N7 0:G2093 3.0 26.1 1.0
O6 0:G2094 3.2 36.9 1.0
N1 0:A2649 3.2 34.6 1.0
C5 0:G2093 3.3 28.2 1.0
O6 0:G2093 3.3 31.5 1.0
C5 0:G2094 3.3 32.0 1.0
O 0:HOH8947 3.4 24.5 1.0
C6 0:G2093 3.5 29.4 1.0
N3 0:G2092 3.5 29.4 1.0
C2 0:A2649 3.5 33.6 1.0
C6 0:G2094 3.6 34.1 1.0
C8 0:G2094 3.6 29.8 1.0
N2 0:G2092 3.6 30.3 1.0
O2' 0:G2092 3.7 28.0 1.0
C2 0:G2092 3.8 29.0 1.0
C8 0:G2093 3.8 27.3 1.0
N6 0:A2612 3.9 32.9 1.0
C4 0:G2093 4.3 28.2 1.0
C6 0:A2612 4.3 34.2 1.0
C6 0:A2649 4.3 34.4 1.0
C4 0:G2092 4.4 31.6 1.0
N1 0:G2093 4.5 29.0 1.0
N9 0:G2093 4.6 27.8 1.0
C4 0:G2094 4.6 31.4 1.0
N6 0:A2649 4.7 36.1 1.0
N9 0:G2094 4.7 29.8 1.0
N1 0:A2612 4.7 34.2 1.0
N3 0:A2649 4.7 33.8 1.0
C1' 0:G2092 4.8 28.2 1.0
C2' 0:G2092 4.9 27.7 1.0
N1 0:G2092 4.9 27.8 1.0
C5 0:A2612 4.9 34.6 1.0
N9 0:G2092 5.0 30.1 1.0
N1 0:G2094 5.0 34.4 1.0

Sodium binding site 6 out of 86 in 2qex

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Sodium binding site 6 out of 86 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 Sodium with other atoms in the Na 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:Na8507

b:54.9
occ:1.00
O2 0:C40 2.5 45.4 1.0
O2' 0:C40 2.8 46.0 1.0
O4' 0:G41 3.2 47.5 1.0
O2 0:C443 3.2 55.3 1.0
N1 0:A442 3.2 56.9 1.0
C2' 0:C40 3.3 46.4 1.0
C1' 0:C40 3.5 46.4 1.0
C2 0:C40 3.6 46.6 1.0
C2 0:A442 3.7 55.5 1.0
C2 0:C443 4.0 53.1 1.0
N1 0:C40 4.0 46.1 1.0
C1' 0:G41 4.1 47.8 1.0
C4' 0:G41 4.2 45.9 1.0
C6 0:A442 4.2 55.7 1.0
C5' 0:G41 4.2 45.3 1.0
N2 0:G39 4.3 47.0 1.0
O 0:HOH5721 4.4 54.3 1.0
N6 0:A442 4.4 55.7 1.0
N9 0:G41 4.5 49.3 1.0
O5' 0:G41 4.6 46.0 1.0
N3 0:C443 4.7 52.2 1.0
O4' 0:C40 4.7 47.3 1.0
N3 0:C40 4.8 47.1 1.0
C1' 0:C443 4.8 53.4 1.0
N1 0:C443 4.8 53.1 1.0
C3' 0:C40 4.8 47.1 1.0
N3 0:A442 4.8 54.7 1.0
C8 0:G41 4.9 50.3 1.0
C2 0:G39 4.9 48.0 1.0

Sodium binding site 7 out of 86 in 2qex

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Sodium binding site 7 out of 86 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 Sodium with other atoms in the Na 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:Na8508

b:36.9
occ:1.00
O2 0:C1394 2.3 36.6 1.0
O2 0:U1724 2.3 45.8 1.0
O4 0:U1432 2.4 37.6 1.0
O 0:HOH3237 2.9 32.2 1.0
O6 0:G1433 3.1 40.4 1.0
O 0:HOH9120 3.4 31.7 1.0
C2 0:C1394 3.4 34.7 1.0
C2 0:U1724 3.5 43.0 1.0
C4 0:U1432 3.6 37.7 1.0
O 0:HOH6995 3.7 65.8 1.0
C6 0:G1433 3.7 39.9 1.0
C2' 0:C1394 4.0 36.3 1.0
O2' 0:C1394 4.1 35.6 1.0
N3 0:C1394 4.1 34.4 1.0
N3 0:U1432 4.1 38.3 1.0
N3 0:U1724 4.2 43.3 1.0
N1 0:G1433 4.2 41.1 1.0
N1 0:C1394 4.3 35.4 1.0
C1' 0:C1394 4.4 36.2 1.0
O2' 0:U1724 4.5 39.5 1.0
N1 0:U1724 4.5 41.6 1.0
C1' 0:U1724 4.6 39.8 1.0
C2' 0:U1724 4.6 39.7 1.0
C5 0:G1433 4.7 38.1 1.0
O 0:HOH4690 4.7 80.7 1.0
C5 0:U1432 4.8 37.3 1.0
O2' 0:C1725 5.0 30.2 1.0

Sodium binding site 8 out of 86 in 2qex

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Sodium binding site 8 out of 86 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 Sodium with other atoms in the Na 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:Na8509

b:23.2
occ:1.00
O3' 0:A1133 2.6 40.8 1.0
O H:PRO159 2.8 48.0 1.0
O H:ILE157 2.8 48.7 1.0
O H:TYR154 3.0 55.5 1.0
O2' 0:A1133 3.0 39.0 1.0
OP1 0:G1134 3.1 40.4 1.0
O H:THR158 3.4 47.5 1.0
P 0:G1134 3.5 41.1 1.0
C3' 0:A1133 3.6 40.2 1.0
C H:PRO159 3.7 49.1 1.0
C2' 0:A1133 3.8 38.5 1.0
C H:THR158 3.9 47.2 1.0
C H:ILE157 4.0 47.9 1.0
C4' 0:A1133 4.1 39.3 1.0
C5' 0:G1134 4.2 42.8 1.0
C H:TYR154 4.2 54.8 1.0
O5' 0:G1134 4.3 41.5 1.0
N H:PRO159 4.4 47.6 1.0
O2' 0:G2520 4.5 42.7 1.0
CA H:PRO159 4.5 48.0 1.0
N H:SER160 4.5 50.9 1.0
CA H:THR158 4.6 46.9 1.0
CA H:SER160 4.7 53.1 1.0
OP2 0:G1134 4.7 40.1 1.0
N H:THR158 4.7 47.5 1.0
CA H:ASN155 4.9 53.7 1.0
O 0:HOH3834 4.9 50.2 1.0
N H:ILE157 4.9 48.5 1.0
O H:ASN155 5.0 54.0 1.0
C H:ASN155 5.0 53.0 1.0

Sodium binding site 9 out of 86 in 2qex

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Sodium binding site 9 out of 86 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 Sodium with other atoms in the Na 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:Na8510

b:22.0
occ:1.00
O6 0:G2579 2.7 31.7 1.0
N7 0:G2579 3.0 32.1 1.0
N7 0:G2578 3.1 34.2 1.0
O 0:HOH4360 3.1 44.5 1.0
O4' 0:A2577 3.2 37.5 1.0
N3 0:A2577 3.2 34.8 1.0
C6 0:G2579 3.3 31.2 1.0
O6 0:G2578 3.4 30.1 1.0
C5 0:G2579 3.5 31.9 1.0
C5 0:G2578 3.6 32.6 1.0
C6 0:G2578 3.7 32.2 1.0
O 0:HOH7569 3.7 74.1 1.0
C1' 0:A2577 3.9 36.8 1.0
O 0:HOH6141 3.9 55.6 1.0
C2 0:A2577 4.0 33.2 1.0
C4' 0:A2577 4.0 38.5 1.0
C8 0:G2578 4.0 34.0 1.0
C4 0:A2577 4.1 33.8 1.0
C8 0:G2579 4.3 32.8 1.0
N9 0:A2577 4.4 34.3 1.0
C4 0:G2578 4.6 34.3 1.0
N1 0:G2579 4.7 30.8 1.0
N4 0:C2556 4.8 33.7 1.0
N1 0:G2578 4.8 32.2 1.0
C4 0:G2579 4.8 31.9 1.0
N9 0:G2578 4.9 33.8 1.0
N3 0:U2554 4.9 25.8 1.0
C5' 0:A2577 4.9 38.3 1.0
O6 0:G2580 5.0 35.5 1.0

Sodium binding site 10 out of 86 in 2qex

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Sodium binding site 10 out of 86 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 Sodium with other atoms in the Na 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:Na8511

b:46.8
occ:1.00
O 0:HOH3401 2.3 24.5 1.0
O6 0:G2525 2.5 43.5 1.0
O 0:HOH9005 2.6 42.5 1.0
O 0:HOH4510 2.7 28.7 1.0
N7 0:G2524 2.8 33.5 1.0
C6 0:G2525 3.5 42.0 1.0
O 0:HOH3445 3.6 24.2 1.0
O 0:HOH6215 3.6 49.4 1.0
C8 0:G2524 3.8 32.9 1.0
C5 0:G2524 3.8 31.7 1.0
O6 0:G2524 3.9 28.1 1.0
C5 0:U2523 4.1 34.8 1.0
C4 0:U2523 4.2 34.8 1.0
C6 0:G2524 4.2 30.6 1.0
C5 0:G2525 4.2 40.9 1.0
N7 0:G2525 4.4 40.4 1.0
O4 0:U2523 4.4 34.4 1.0
N1 0:G2525 4.5 40.9 1.0
O2' 0:C2493 4.5 33.6 1.0
OP2 0:G2524 4.6 36.5 1.0
C6 0:U2523 4.6 34.1 1.0
N3 0:U2523 4.8 34.3 1.0
C2' 0:C2493 4.8 34.3 1.0
N9 0:G2524 5.0 33.1 1.0

Reference:

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
Page generated: Tue Dec 15 05:55:10 2020

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