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Sodium in PDB 3i55: Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit, PDB code: 3i55 was solved by G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.98 / 3.11
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.324, 299.649, 574.241, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26

Other elements in 3i55:

The structure of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Strontium (Sr) 108 atoms
Magnesium (Mg) 93 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 - 75;

Binding sites:

The binding sites of Sodium atom in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit (pdb code 3i55). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 75 binding sites of Sodium where determined in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit, PDB code: 3i55:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 3i55

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Sodium binding site 1 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8501

b:41.0
occ:1.00
OP2 0:C1069 2.7 35.7 1.0
O 0:HOH6913 2.8 45.7 1.0
O 0:HOH7057 3.0 92.2 1.0
O 0:HOH3877 3.0 63.3 1.0
O6 0:G1072 3.2 42.0 1.0
N7 0:G1072 3.2 39.9 1.0
O6 0:G1087 3.4 51.7 1.0
C6 0:G1072 3.8 40.4 1.0
C5 0:G1072 3.8 40.0 1.0
C5' 0:C1068 4.0 48.8 1.0
P 0:C1069 4.1 37.7 1.0
O 0:HOH3126 4.2 32.0 1.0
OP2 0:C1068 4.3 56.4 1.0
C8 0:G1072 4.3 39.5 1.0
C3' 0:C1068 4.4 42.2 1.0
C6 0:G1087 4.4 49.5 1.0
O3' 0:C1068 4.5 38.8 1.0
O 0:HOH8095 4.8 25.9 1.0
C4' 0:C1068 4.8 45.2 1.0
OP1 0:C1069 4.9 34.3 1.0
N6 0:A1070 5.0 45.0 1.0
O 0:HOH4369 5.0 92.7 1.0
O 0:HOH8952 5.0 0.4 1.0

Sodium binding site 2 out of 75 in 3i55

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Sodium binding site 2 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8502

b:53.2
occ:1.00
OP2 0:U1120 3.0 51.2 1.0
N7 0:G1121 3.0 49.8 1.0
O2' 0:G1119 3.1 46.6 1.0
O3' 0:G1119 3.2 49.2 1.0
O 0:HOH7759 3.2 87.5 1.0
O 0:HOH8797 3.3 58.6 1.0
O 0:HOH4850 3.4 42.3 1.0
O6 0:G1121 3.4 48.5 1.0
O 0:HOH3297 3.5 71.4 1.0
O4 0:U1122 3.6 53.9 1.0
P 0:U1120 3.7 52.0 1.0
O 0:HOH6604 3.7 44.7 1.0
MG 0:MG8018 3.8 32.1 1.0
C5 0:G1121 3.8 48.6 1.0
C6 0:G1121 4.0 48.2 1.0
C8 0:G1121 4.0 49.2 1.0
C2' 0:G1119 4.1 46.3 1.0
C3' 0:G1119 4.2 47.7 1.0
C4 0:U1122 4.2 51.8 1.0
C5 0:U1122 4.4 52.2 1.0
C1' 0:G1119 4.5 44.8 1.0
OP1 0:U1120 4.7 51.5 1.0
OP2 0:G1121 4.8 52.0 1.0
O5' 0:U1120 4.8 49.9 1.0
C5' 0:U1120 4.9 50.1 1.0

Sodium binding site 3 out of 75 in 3i55

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Sodium binding site 3 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8504

b:32.0
occ:1.00
O 0:HOH8718 2.8 48.3 1.0
N3 0:A630 2.8 44.2 1.0
O2' 0:A630 2.8 43.7 1.0
O 0:HOH3514 2.9 34.0 1.0
O2' 0:A631 2.9 40.5 1.0
O 0:HOH4986 3.1 36.2 1.0
C1' 0:A630 3.2 44.5 1.0
C2' 0:A631 3.4 38.7 1.0
O3' 0:A630 3.5 41.1 1.0
C2' 0:A630 3.5 43.9 1.0
OP2 0:A2074 3.5 48.6 1.0
C4 0:A630 3.7 43.9 1.0
C2 0:A630 3.8 45.5 1.0
N9 0:A630 3.8 44.2 1.0
N2 0:G2070 3.9 46.6 1.0
C3' 0:A631 3.9 38.3 1.0
N1 0:A629 4.0 44.7 1.0
C2 0:A629 4.1 44.1 1.0
C3' 0:A630 4.1 43.1 1.0
O4' 0:A630 4.2 47.2 1.0
OP1 0:A632 4.4 41.8 1.0
O3' 0:A631 4.5 39.5 1.0
P 0:A631 4.7 43.0 1.0
O5' 0:A631 4.8 42.2 1.0
OP1 0:A631 4.8 43.3 1.0
C4' 0:A630 4.8 46.0 1.0
C2 0:G2070 4.8 45.0 1.0
C6 0:A629 4.9 45.4 1.0
O 0:HOH4327 4.9 49.5 1.0
C1' 0:A631 4.9 38.6 1.0
N3 0:A629 4.9 43.7 1.0
P 0:A632 4.9 42.2 1.0
P 0:A2074 5.0 49.3 1.0

Sodium binding site 4 out of 75 in 3i55

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Sodium binding site 4 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8505

b:58.4
occ:1.00
N7 0:G2094 2.9 42.7 1.0
N1 0:A2649 3.0 47.0 1.0
N7 0:G2093 3.0 41.9 1.0
O6 0:G2094 3.1 43.8 1.0
N3 0:G2092 3.2 44.5 1.0
O6 0:G2093 3.2 40.4 1.0
O2' 0:G2092 3.3 37.6 1.0
C2 0:A2649 3.4 48.2 1.0
C5 0:G2093 3.4 41.9 1.0
N2 0:G2092 3.5 46.5 1.0
C6 0:G2093 3.5 41.2 1.0
O 0:HOH3317 3.6 57.2 1.0
C5 0:G2094 3.6 43.5 1.0
C2 0:G2092 3.6 45.5 1.0
C6 0:G2094 3.7 43.6 1.0
C8 0:G2093 4.0 40.6 1.0
N6 0:A2612 4.0 38.3 1.0
C8 0:G2094 4.0 43.0 1.0
C6 0:A2649 4.1 47.4 1.0
C4 0:G2092 4.1 43.1 1.0
N6 0:A2649 4.4 48.8 1.0
C6 0:A2612 4.4 41.0 1.0
C2' 0:G2092 4.4 38.8 1.0
C1' 0:G2092 4.4 39.5 1.0
C4 0:G2093 4.5 42.2 1.0
N9 0:G2092 4.6 40.8 1.0
N3 0:A2649 4.7 49.6 1.0
N1 0:G2092 4.7 44.4 1.0
N1 0:G2093 4.7 42.0 1.0
N9 0:G2093 4.8 40.3 1.0
N1 0:A2612 4.9 41.1 1.0
C4 0:G2094 4.9 43.5 1.0
C5 0:A2612 4.9 40.8 1.0

Sodium binding site 5 out of 75 in 3i55

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Sodium binding site 5 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8506

b:65.7
occ:1.00
O2 0:C40 2.9 69.5 1.0
O2' 0:C40 2.9 69.7 1.0
O4' 0:G41 3.0 63.0 1.0
O2 0:C443 3.0 74.2 1.0
N1 0:A442 3.1 68.1 1.0
C2 0:A442 3.4 67.7 1.0
C2' 0:C40 3.4 69.0 1.0
C1' 0:C40 3.6 69.4 1.0
C1' 0:G41 3.7 63.2 1.0
C2 0:C443 3.9 73.5 1.0
C2 0:C40 3.9 69.9 1.0
C4' 0:G41 4.1 62.1 1.0
C6 0:A442 4.2 68.0 1.0
N9 0:G41 4.2 63.8 1.0
N2 0:G39 4.2 73.3 1.0
N1 0:C40 4.2 70.5 1.0
C1' 0:C443 4.4 70.2 1.0
C5' 0:G41 4.5 61.7 1.0
N1 0:C443 4.5 72.6 1.0
N6 0:A442 4.6 69.5 1.0
N3 0:A442 4.6 67.3 1.0
N3 0:C443 4.7 73.1 1.0
C8 0:G41 4.7 64.0 1.0
O4' 0:C40 4.8 68.7 1.0
C4 0:G41 4.9 65.2 1.0
C2 0:G39 4.9 72.5 1.0
O5' 0:G41 4.9 63.2 1.0
C3' 0:C40 4.9 67.5 1.0
O 0:HOH5107 4.9 58.2 1.0
N1 0:G39 5.0 72.1 1.0

Sodium binding site 6 out of 75 in 3i55

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Sodium binding site 6 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8507

b:27.1
occ:1.00
O2 0:C1394 2.6 52.9 1.0
O2 0:U1724 2.6 51.7 1.0
O 0:HOH7854 2.8 57.1 1.0
O4 0:U1432 2.9 53.6 1.0
O6 0:G1433 3.4 58.4 1.0
O 0:HOH6898 3.4 77.0 1.0
O2' 0:C1394 3.4 48.4 1.0
C2 0:C1394 3.6 51.8 1.0
C2' 0:C1394 3.6 50.1 1.0
C2 0:U1724 3.8 52.7 1.0
SR 0:SR8962 3.9 0.0 1.0
C6 0:G1433 3.9 57.0 1.0
C1' 0:C1394 4.1 50.5 1.0
C4 0:U1432 4.1 52.2 1.0
N1 0:G1433 4.2 56.8 1.0
N1 0:C1394 4.2 51.6 1.0
N3 0:C1394 4.5 49.6 1.0
O 0:HOH3689 4.5 74.8 1.0
O2' 0:U1724 4.5 50.5 1.0
O 0:HOH4537 4.5 39.5 1.0
N3 0:U1724 4.6 53.8 1.0
N3 0:U1432 4.7 52.4 1.0
C1' 0:U1724 4.7 51.4 1.0
C2' 0:U1724 4.8 51.0 1.0
N1 0:U1724 4.8 52.1 1.0
C5 0:G1433 4.8 55.1 1.0
OP2 0:U1722 4.8 53.7 1.0
O2' 0:C1725 5.0 48.4 1.0
OP2 0:C1395 5.0 52.0 1.0

Sodium binding site 7 out of 75 in 3i55

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Sodium binding site 7 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8508

b:68.4
occ:1.00
N7 0:G2579 2.9 51.3 1.0
O4' 0:A2577 2.9 55.7 1.0
O6 0:G2579 3.0 52.5 1.0
N3 0:A2577 3.2 52.6 1.0
N7 0:G2578 3.3 48.0 1.0
O 0:HOH3242 3.3 47.1 1.0
O 0:HOH5700 3.3 91.1 1.0
C1' 0:A2577 3.5 55.7 1.0
C5 0:G2579 3.6 50.2 1.0
C6 0:G2579 3.6 51.2 1.0
C5 0:G2578 3.7 47.7 1.0
C4' 0:A2577 3.8 55.7 1.0
O6 0:G2578 3.8 49.3 1.0
C6 0:G2578 3.9 47.9 1.0
C4 0:A2577 4.0 54.0 1.0
C8 0:G2578 4.0 47.4 1.0
C8 0:G2579 4.0 51.1 1.0
C2 0:A2577 4.1 52.9 1.0
N9 0:A2577 4.1 54.7 1.0
O 0:HOH7700 4.2 0.4 1.0
O3' 0:A2577 4.4 56.4 1.0
O 0:HOH5252 4.5 0.7 1.0
C3' 0:A2577 4.6 55.8 1.0
C4 0:G2578 4.6 48.3 1.0
C2' 0:A2577 4.7 56.1 1.0
N9 0:G2578 4.8 47.9 1.0
O 0:HOH3510 4.9 41.1 1.0
C5' 0:A2577 4.9 54.7 1.0
C4 0:G2579 4.9 49.1 1.0
N1 0:G2578 5.0 48.7 1.0

Sodium binding site 8 out of 75 in 3i55

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Sodium binding site 8 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8509

b:90.8
occ:1.00
O6 0:G2525 2.9 59.9 1.0
O 0:HOH3502 3.1 60.2 1.0
O 0:HOH8135 3.2 42.8 1.0
N7 0:G2524 3.2 49.3 1.0
O 0:HOH3440 3.2 55.9 1.0
OP2 0:G2524 3.4 51.4 1.0
O 0:HOH5803 3.5 0.1 1.0
C8 0:G2524 3.7 49.2 1.0
C5 0:U2523 3.8 53.3 1.0
C6 0:G2525 4.0 60.6 1.0
C6 0:U2523 4.1 52.2 1.0
OP2 0:U2523 4.1 55.0 1.0
O 0:HOH8178 4.1 33.8 1.0
C4 0:U2523 4.4 52.9 1.0
C5 0:G2524 4.4 48.4 1.0
O5' 0:U2523 4.5 54.4 1.0
N7 0:G2525 4.5 59.5 1.0
C5 0:G2525 4.6 59.4 1.0
N1 0:U2523 4.8 51.2 1.0
P 0:G2524 4.8 51.7 1.0
C3' 0:U2523 4.8 52.8 1.0
O6 0:G2524 4.8 48.5 1.0
O4 0:U2523 4.8 52.2 1.0
P 0:U2523 4.9 55.3 1.0
N3 0:U2523 5.0 51.7 1.0
C6 0:G2524 5.0 47.2 1.0

Sodium binding site 9 out of 75 in 3i55

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Sodium binding site 9 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8511

b:54.0
occ:1.00
OP2 0:A2398 2.7 65.0 1.0
N7 0:G2399 2.9 64.1 1.0
O 0:HOH4019 3.0 28.4 1.0
O 0:HOH4089 3.0 36.6 1.0
O 0:HOH8397 3.0 71.6 1.0
O 0:HOH6201 3.1 49.8 1.0
O6 0:G2399 3.5 65.3 1.0
O5' 0:A2398 3.6 63.0 1.0
O 0:HOH6003 3.6 65.6 1.0
P 0:A2398 3.6 64.0 1.0
C5 0:G2399 3.7 65.3 1.0
C8 0:G2399 3.9 63.2 1.0
OP2 0:G2399 4.0 61.7 1.0
C6 0:G2399 4.0 65.2 1.0
C8 0:A2398 4.0 63.6 1.0
N7 0:A2398 4.1 63.5 1.0
OP1 0:A2398 4.4 64.6 1.0
O 0:HOH5380 4.8 51.2 1.0
C3' 0:A2398 4.9 61.9 1.0
C5' 0:A2398 4.9 62.6 1.0
O3' 0:G2397 4.9 63.3 1.0
O 0:HOH5496 4.9 68.5 1.0
C4 0:G2399 5.0 65.0 1.0

Sodium binding site 10 out of 75 in 3i55

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Sodium binding site 10 out of 75 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8512

b:54.5
occ:1.00
O2' 0:U2607 2.8 43.0 1.0
OP1 0:U2541 2.8 54.8 1.0
O 0:HOH4041 2.8 39.9 1.0
O2 0:U2607 3.0 48.2 1.0
O 0:HOH4610 3.2 43.2 1.0
CZ3 B:TRP242 3.2 47.3 1.0
O 0:HOH3493 3.4 29.7 1.0
O 0:HOH6783 3.6 64.8 1.0
P 0:U2541 3.8 53.4 1.0
OP2 0:U2541 3.8 52.1 1.0
O 0:HOH7760 3.8 58.8 1.0
C2 0:U2607 3.8 48.2 1.0
CH2 B:TRP242 3.9 47.0 1.0
C2' 0:U2607 4.0 43.2 1.0
OP1 0:U2610 4.1 44.7 1.0
OP2 0:C2608 4.1 39.4 1.0
CE3 B:TRP242 4.1 46.1 1.0
O 0:HOH3421 4.3 70.2 1.0
C1' 0:U2607 4.3 44.5 1.0
N1 0:U2607 4.4 47.2 1.0
N3 0:U2607 4.7 49.8 1.0
O5' 0:U2541 4.8 52.4 1.0
O 0:HOH3183 4.8 53.2 1.0
O3' 0:U2607 4.8 39.7 1.0
O3' 0:G2540 4.9 54.9 1.0
O2 0:U2539 5.0 57.8 1.0
O 0:HOH4280 5.0 35.6 1.0

Reference:

G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore. Structures of Triacetyloleandomycin and Mycalamide A Bind to the Large Ribosomal Subunit of Haloarcula Marismortui. Antimicrob.Agents Chemother. V. 53 5010 2009.
ISSN: ISSN 0066-4804
PubMed: 19738021
DOI: 10.1128/AAC.00817-09
Page generated: Tue Dec 15 06:14:20 2020

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