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Sodium in PDB 3cc4: Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4 was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.85 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.780, 299.084, 573.837, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.4

Other elements in 3cc4:

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S 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 Anisomycin Bound to the 50S Ribosomal Subunit (pdb code 3cc4). 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 Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 3cc4

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Sodium binding site 1 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na8552

b:56.8
occ:1.00
 O 0:HOH4963 3.0 55.0 1.0
O B:GLN230 3.1 34.6 1.0
O 0:HOH7421 3.2 67.6 1.0
O 0:HOH6902 3.2 46.3 1.0
O 0:HOH4647 3.2 46.4 1.0
O 0:HOH5158 3.3 40.5 1.0
O B:HOH8994 3.4 78.6 1.0
OP1 0:U837 3.7 30.5 1.0
CZ3 B:TRP232 3.8 34.2 1.0
CH2 B:TRP232 4.0 34.8 1.0
CA B:GLY231 4.1 35.2 1.0
OP2 0:U837 4.2 31.7 1.0
C B:GLN230 4.2 34.1 1.0
P 0:U837 4.4 29.4 1.0
CE3 B:TRP232 4.6 34.5 1.0
OP2 0:C838 4.7 24.6 1.0
N B:GLY231 4.7 35.2 1.0
N4 0:C839 4.8 22.6 1.0
O 0:HOH4516 4.8 47.9 1.0
CZ2 B:TRP232 4.9 34.1 1.0
O 0:HOH9576 4.9 37.4 1.0

Sodium binding site 2 out of 75 in 3cc4

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Sodium binding site 2 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na8503

b:37.9
occ:1.00
 OD1 C:ASP45 2.9 41.0 1.0
O C:LYS96 2.9 40.5 1.0
O C:THR94 3.1 36.2 1.0
OD2 C:ASP45 3.3 39.9 1.0
O C:HOH8507 3.3 36.1 1.0
CG C:ASP45 3.3 38.7 1.0
C C:LYS96 3.6 38.9 1.0
O C:GLU95 3.7 39.1 1.0
C C:GLU95 3.8 39.3 1.0
N C:LYS96 4.1 39.0 1.0
C C:THR94 4.2 35.9 1.0
N C:ASP97 4.2 37.0 1.0
CA C:GLU95 4.3 39.8 1.0
CA C:ASP97 4.3 33.6 1.0
O C:HOH8620 4.4 47.6 1.0
CA C:LYS96 4.5 39.1 1.0
CB C:ASP45 4.5 35.7 1.0
O C:HOH8588 4.6 45.0 1.0
N C:GLU95 4.7 38.0 1.0

Sodium binding site 3 out of 75 in 3cc4

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Sodium binding site 3 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na8538

b:56.3
occ:1.00
 O J:TYR69 2.6 57.5 1.0
O J:ILE63 2.9 47.5 1.0
O J:VAL61 2.9 46.4 1.0
O 0:HOH9512 2.9 51.8 1.0
O J:ARG60 2.9 40.9 1.0
O 0:HOH5825 3.0 43.1 1.0
C J:VAL61 3.5 45.0 1.0
CA J:VAL61 3.6 43.0 1.0
OP1 0:A2677 3.7 58.9 1.0
C J:TYR69 3.8 56.7 1.0
N J:TYR71 3.9 54.8 1.0
C J:ARG60 3.9 40.3 1.0
CB J:TYR71 4.0 50.7 1.0
C J:ILE63 4.0 46.6 1.0
CD2 J:TYR69 4.1 53.1 1.0
N J:VAL61 4.3 41.0 1.0
CB J:TYR69 4.3 52.8 1.0
N J:ILE63 4.4 47.7 1.0
CA J:TYR71 4.5 52.3 1.0
N J:ASP62 4.5 46.7 1.0
CA J:TYR69 4.7 54.8 1.0
C J:PHE70 4.7 57.5 1.0
CG J:TYR69 4.7 52.5 1.0
CA J:ILE63 4.8 47.1 1.0
N J:PHE70 4.8 58.9 1.0
CA J:PHE70 4.8 59.9 1.0
CL J:CL8821 4.9 56.6 1.0
CB J:VAL61 4.9 42.8 1.0
C J:ASP62 4.9 48.3 1.0

Sodium binding site 4 out of 75 in 3cc4

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Sodium binding site 4 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na8539

b:41.9
occ:1.00
 O M:LEU112 2.8 35.8 1.0
OG M:SER106 2.8 36.8 1.0
O M:SER106 2.9 38.6 1.0
O M:HOH8924 3.0 55.2 1.0
O M:PHE109 3.2 37.6 1.0
O M:PRO110 3.4 41.6 1.0
C M:PRO110 3.7 38.5 1.0
CA M:PRO110 3.8 37.4 1.0
C M:SER106 3.8 38.3 1.0
CB M:SER106 3.9 36.4 1.0
C M:LEU112 4.0 33.8 1.0
C M:PHE109 4.1 37.5 1.0
CA M:SER106 4.1 36.7 1.0
CL M:CL8818 4.3 37.1 1.0
N M:PRO110 4.3 37.4 1.0
OD1 M:ASP157 4.4 39.9 1.0
N M:LEU112 4.5 33.5 1.0
CE1 M:PHE160 4.5 33.2 1.0
N M:ASN111 4.5 38.1 1.0
CA M:LEU112 4.8 32.4 1.0
N M:ARG113 4.9 33.8 1.0
C M:ASN111 4.9 35.7 1.0
N M:ARG107 4.9 39.2 1.0
CA M:ARG113 5.0 32.0 1.0

Sodium binding site 5 out of 75 in 3cc4

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Sodium binding site 5 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Na8540

b:60.2
occ:1.00
 O Q:ASP20 2.8 60.1 1.0
O Q:GLY22 2.9 51.5 1.0
O Q:HOH1795 2.9 40.2 1.0
OG Q:SER46 2.9 41.4 1.0
OG Q:SER24 3.0 48.6 1.0
O Q:HOH5427 3.6 54.1 1.0
CB Q:SER46 3.7 42.2 1.0
CA Q:SER24 3.8 49.3 1.0
O Q:HOH7505 3.8 64.8 1.0
N Q:SER24 3.9 50.5 1.0
C Q:ASP20 3.9 61.1 1.0
CB Q:SER24 3.9 49.1 1.0
O Q:THR23 4.0 52.0 1.0
C Q:THR23 4.0 51.3 1.0
C Q:GLY22 4.0 51.8 1.0
O Q:ARG21 4.0 56.9 1.0
OD1 Q:ASN16 4.1 46.9 1.0
C Q:ARG21 4.3 55.7 1.0
OD1 Q:ASP44 4.3 48.9 1.0
NH2 Q:ARG28 4.5 47.5 1.0
N Q:GLY22 4.7 53.9 1.0
N Q:ARG21 4.8 59.3 1.0
CA Q:ASP20 4.8 63.4 1.0
N Q:THR23 4.8 51.1 1.0
CA Q:THR23 4.8 51.5 1.0
O 0:HOH7010 4.9 52.5 1.0
CA Q:GLY22 4.9 52.7 1.0
CA Q:ARG21 4.9 56.8 1.0
OD2 Q:ASP44 4.9 51.7 1.0
CG Q:ASN16 4.9 48.7 1.0

Sodium binding site 6 out of 75 in 3cc4

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Sodium binding site 6 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na8532

b:53.1
occ:1.00
 O R:SER70 2.9 42.2 1.0
O 0:HOH3790 2.9 50.1 1.0
O 0:HOH5987 3.0 65.8 1.0
NA 0:NA8533 3.1 63.2 1.0
O R:VAL72 3.2 48.0 1.0
O 0:HOH7070 3.5 33.5 1.0
C R:VAL72 3.7 47.8 1.0
CA R:ASP73 3.9 49.8 1.0
N R:ASP73 4.0 49.1 1.0
OD1 R:ASP73 4.0 58.0 1.0
O 0:HOH3802 4.0 65.5 1.0
C R:SER70 4.1 42.0 1.0
O 0:HOH3116 4.1 66.0 1.0
OP1 0:G2660 4.1 38.8 1.0
C R:LYS71 4.2 46.1 1.0
N R:VAL72 4.2 45.9 1.0
CB R:ASP73 4.3 52.5 1.0
O R:LYS71 4.4 47.7 1.0
CA R:LYS71 4.5 45.2 1.0
CG R:ASP73 4.6 56.6 1.0
CA R:VAL72 4.6 47.1 1.0
N R:LYS71 4.8 42.6 1.0

Sodium binding site 7 out of 75 in 3cc4

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Sodium binding site 7 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na8510

b:80.0
occ:1.00
 OE2 S:GLU61 3.0 65.7 1.0
NE2 S:HIS7 3.1 55.8 1.0
O S:HOH2519 3.3 48.8 1.0
OE1 S:GLU61 3.5 65.4 1.0
CD S:GLU61 3.6 63.4 1.0
CE1 S:HIS7 3.8 55.7 1.0
CD2 S:HIS7 4.2 56.7 1.0
ND1 S:HIS7 4.9 56.6 1.0

Sodium binding site 8 out of 75 in 3cc4

Go back to Sodium Binding Sites List in 3cc4
Sodium binding site 8 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8501

b:39.2
occ:1.00
 OP2 0:C1069 2.7 22.7 1.0
N7 0:G1072 2.9 27.0 1.0
O 0:HOH3208 2.9 39.8 1.0
O6 0:G1072 3.0 29.5 1.0
O 0:HOH5029 3.1 62.1 1.0
O 0:HOH3240 3.1 54.4 1.0
O6 0:G1087 3.3 30.9 1.0
O 0:HOH9076 3.4 24.5 1.0
C5 0:G1072 3.5 27.0 1.0
C6 0:G1072 3.5 26.4 1.0
C8 0:G1072 4.0 25.8 1.0
P 0:C1069 4.1 27.1 1.0
C6 0:G1087 4.2 28.1 1.0
C5' 0:C1068 4.3 32.8 1.0
O 0:HOH3578 4.5 35.0 1.0
C3' 0:C1068 4.5 28.8 1.0
O3' 0:C1068 4.6 26.9 1.0
C4 0:G1072 4.7 27.2 1.0
OP2 0:C1068 4.7 36.0 1.0
OP1 0:C1069 4.8 22.5 1.0
N1 0:G1072 4.8 24.9 1.0
N1 0:G1087 4.9 27.3 1.0
O 0:HOH5390 4.9 51.2 1.0
N9 0:G1072 5.0 25.3 1.0

Sodium binding site 9 out of 75 in 3cc4

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Sodium binding site 9 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8502

b:67.2
occ:1.00
 OP2 0:U1120 3.0 39.4 1.0
O6 0:G1121 3.1 32.4 1.0
O 0:HOH4604 3.2 49.1 1.0
O2' 0:G1119 3.2 32.6 1.0
N7 0:G1121 3.3 34.2 1.0
O 0:HOH4225 3.3 34.6 1.0
MG 0:MG8018 3.4 38.8 1.0
O4 0:U1122 3.5 37.8 1.0
O3' 0:G1119 3.5 35.9 1.0
O 0:HOH5750 3.5 49.8 1.0
C6 0:G1121 3.8 31.2 1.0
P 0:U1120 3.9 39.2 1.0
C5 0:G1121 3.9 31.6 1.0
O 0:HOH7015 4.0 55.6 1.0
O 0:HOH7864 4.0 55.9 1.0
C4 0:U1122 4.1 37.0 1.0
C2' 0:G1119 4.2 31.9 1.0
C5 0:U1122 4.3 35.8 1.0
C3' 0:G1119 4.4 33.4 1.0
C8 0:G1121 4.5 33.2 1.0
C1' 0:G1119 4.7 30.4 1.0
OP1 0:U1120 4.8 41.6 1.0
N6 0:A1242 4.9 35.8 1.0

Sodium binding site 10 out of 75 in 3cc4

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Sodium binding site 10 out of 75 in the Co-Crystal Structure of Anisomycin Bound to 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8504

b:26.5
occ:1.00
 O2' 0:A631 2.8 27.1 1.0
O 0:HOH4757 2.8 33.1 1.0
N3 0:A630 2.8 30.8 1.0
O2' 0:A630 2.9 31.3 1.0
O 0:HOH4143 2.9 39.9 1.0
O 0:HOH5852 3.0 49.6 1.0
OP2 0:A2074 3.3 31.3 1.0
C2' 0:A631 3.5 27.6 1.0
C1' 0:A630 3.7 29.9 1.0
C2 0:A630 3.7 30.5 1.0
C2' 0:A630 3.8 30.2 1.0
C4 0:A630 3.8 29.6 1.0
N2 0:G2070 3.9 31.2 1.0
C3' 0:A631 3.9 25.3 1.0
O3' 0:A630 4.0 26.3 1.0
N9 0:A630 4.2 30.2 1.0
OP1 0:A632 4.2 30.9 1.0
O3' 0:A631 4.3 27.1 1.0
O 0:HOH9434 4.3 23.2 1.0
N1 0:A629 4.4 31.0 1.0
C3' 0:A630 4.6 26.9 1.0
C2 0:A629 4.6 31.5 1.0
C2 0:G2070 4.6 30.9 1.0
OP2 0:G2072 4.7 44.0 1.0
P 0:A2074 4.7 30.2 1.0
P 0:A632 4.7 30.4 1.0
O4' 0:A630 4.8 29.9 1.0
C1' 0:A631 4.9 26.4 1.0
N1 0:A630 5.0 31.9 1.0

Reference:

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075
Page generated: Mon Oct 7 06:14:17 2024

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