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Sodium in PDB 3ccj: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U, PDB code: 3ccj 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) 50.00 / 3.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.010, 299.254, 573.808, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 28.7

Other elements in 3ccj:

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U 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 Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U (pdb code 3ccj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 75 binding sites of Sodium where determined in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U, PDB code: 3ccj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 3ccj

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Sodium binding site 1 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na8552

b:70.4
occ:1.00
 O B:HOH9061 2.7 89.3 1.0
OP1 0:U837 3.0 44.1 1.0
O 0:HOH4573 3.0 97.0 1.0
CA B:GLY231 3.3 48.1 1.0
O B:GLN230 3.3 47.5 1.0
O 0:HOH4883 3.5 0.8 1.0
O B:HOH9136 3.6 63.0 1.0
O B:HOH8994 3.8 39.0 1.0
OP2 0:C838 3.9 42.9 1.0
C B:GLN230 4.0 47.5 1.0
N B:GLY231 4.1 48.6 1.0
P 0:U837 4.2 44.1 1.0
C B:GLY231 4.3 48.4 1.0
O B:GLY231 4.3 47.0 1.0
OP2 0:U837 4.5 43.3 1.0
O B:HOH9042 4.7 65.9 1.0
CZ3 B:TRP232 4.9 52.0 1.0
O5' 0:U837 4.9 43.1 1.0
C5' 0:A1736 4.9 46.0 1.0
O2' 0:C1735 5.0 51.9 1.0
OP1 0:A1736 5.0 44.8 1.0

Sodium binding site 2 out of 75 in 3ccj

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Sodium binding site 2 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na8503

b:36.3
occ:1.00
 O C:LYS96 2.5 59.4 1.0
OD2 C:ASP45 2.7 48.2 1.0
OD1 C:ASP45 2.9 51.8 1.0
CG C:ASP45 3.0 49.5 1.0
O C:HOH8508 3.1 52.6 1.0
O C:THR94 3.4 59.7 1.0
O C:HOH8624 3.6 54.2 1.0
C C:LYS96 3.7 58.3 1.0
CB C:ASP45 4.2 48.3 1.0
O C:GLU95 4.3 57.2 1.0
O C:HOH8590 4.3 85.5 1.0
C C:GLU95 4.4 58.5 1.0
CA C:ASP97 4.4 56.8 1.0
N C:ASP97 4.4 58.1 1.0
N C:LYS96 4.5 57.4 1.0
C C:THR94 4.6 57.7 1.0
CA C:LYS96 4.7 58.0 1.0
CA C:GLU95 4.9 60.3 1.0

Sodium binding site 3 out of 75 in 3ccj

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Sodium binding site 3 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na8538

b:84.4
occ:1.00
 O J:HOH4949 2.6 64.6 1.0
O 0:HOH9502 2.7 67.3 1.0
O J:VAL61 2.7 66.1 1.0
O J:TYR69 2.8 76.2 1.0
O J:ARG60 3.0 61.9 1.0
CA J:VAL61 3.3 63.7 1.0
C J:VAL61 3.4 65.6 1.0
O J:ILE63 3.4 68.3 1.0
OP1 0:A2677 3.4 68.9 1.0
N J:TYR71 3.8 72.0 1.0
C J:ARG60 3.9 61.5 1.0
CB J:TYR71 4.0 67.9 1.0
C J:TYR69 4.0 75.9 1.0
N J:VAL61 4.1 61.8 1.0
C J:PHE70 4.4 74.1 1.0
CB J:VAL61 4.4 63.5 1.0
CG1 J:VAL61 4.4 64.8 1.0
CA J:PHE70 4.4 76.6 1.0
CA J:TYR71 4.5 69.5 1.0
C J:ILE63 4.6 68.5 1.0
N J:ASP62 4.6 67.8 1.0
CD2 J:TYR69 4.6 75.3 1.0
N J:PHE70 4.7 76.2 1.0
N J:ILE63 4.8 68.1 1.0
O J:TYR71 4.9 67.7 1.0
P 0:A2677 4.9 68.0 1.0
CG2 J:VAL61 4.9 62.7 1.0
CB J:TYR69 5.0 75.6 1.0

Sodium binding site 4 out of 75 in 3ccj

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Sodium binding site 4 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na8568

b:59.9
occ:1.00
 O L:HOH8855 2.5 39.4 1.0
O L:HIS18 2.6 55.4 1.0
O L:HOH8832 2.7 68.1 1.0
N4 0:C762 2.7 38.4 1.0
O6 0:G902 3.1 35.9 1.0
N L:ARG21 3.1 60.8 1.0
O 0:HOH3206 3.3 39.5 1.0
CB L:ARG21 3.5 61.2 1.0
CA L:ARG21 3.5 61.0 1.0
C L:HIS18 3.6 54.4 1.0
O L:ARG21 3.6 59.6 1.0
C L:ARG21 3.7 61.2 1.0
O4 0:U903 3.9 29.2 1.0
C4 0:C762 3.9 38.9 1.0
C L:ASN20 3.9 61.2 1.0
N L:ASN20 4.0 57.3 1.0
CA L:HIS18 4.1 55.1 1.0
C6 0:G902 4.3 34.9 1.0
CA L:ASN20 4.3 61.0 1.0
CG L:ARG21 4.4 61.1 1.0
O L:SER17 4.5 57.3 1.0
C5 0:C762 4.6 38.9 1.0
N L:LYS19 4.6 54.0 1.0
C L:LYS19 4.6 54.7 1.0
C4 0:U903 4.6 28.6 1.0
N L:ARG22 4.7 61.2 1.0
N3 0:C762 4.7 39.1 1.0
N3 0:U903 4.8 30.1 1.0
O L:ASN20 4.8 62.5 1.0
O L:HOH8815 4.9 46.7 1.0
N1 0:G902 4.9 34.2 1.0
CB L:HIS18 4.9 55.5 1.0
CD L:ARG21 4.9 61.0 1.0
CB L:ASN20 4.9 63.9 1.0
CA L:LYS19 4.9 54.3 1.0

Sodium binding site 5 out of 75 in 3ccj

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Sodium binding site 5 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na8539

b:38.9
occ:1.00
 O M:SER106 2.7 53.7 1.0
O M:PHE109 2.9 48.9 1.0
O M:LEU112 3.0 44.9 1.0
OG M:SER106 3.0 47.9 1.0
CA M:PRO110 3.3 46.6 1.0
C M:PRO110 3.4 47.3 1.0
O M:HOH8946 3.5 75.4 1.0
C M:PHE109 3.6 48.3 1.0
N M:PRO110 3.7 47.5 1.0
O M:PRO110 3.8 47.3 1.0
N M:ASN111 3.8 47.0 1.0
C M:SER106 3.8 52.7 1.0
C M:LEU112 4.1 44.7 1.0
CB M:SER106 4.2 50.6 1.0
N M:LEU112 4.3 46.2 1.0
OD1 M:ASP157 4.4 56.9 1.0
CA M:SER106 4.4 52.1 1.0
CB M:PRO110 4.6 47.3 1.0
C M:ASN111 4.6 47.6 1.0
CA M:ASN111 4.7 48.0 1.0
CE1 M:PHE160 4.8 44.4 1.0
O M:HOH8860 4.8 47.2 1.0
CL M:CL8818 4.8 58.7 1.0
CA M:LEU112 4.8 44.8 1.0
N M:ARG107 4.9 53.1 1.0
CA M:PHE109 5.0 49.1 1.0

Sodium binding site 6 out of 75 in 3ccj

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Sodium binding site 6 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Na8540

b:74.3
occ:1.00
 OG Q:SER46 2.7 68.5 1.0
O Q:HOH1795 2.7 60.3 1.0
O Q:ASP20 2.8 84.1 1.0
OG Q:SER24 2.8 72.2 1.0
OD1 Q:ASN16 3.2 84.7 1.0
O Q:GLY22 3.6 75.2 1.0
OD1 Q:ASP44 3.7 74.0 1.0
CB Q:SER46 3.8 69.0 1.0
C Q:ASP20 3.9 85.0 1.0
CB Q:SER24 4.0 71.5 1.0
O Q:HOH6597 4.0 58.3 1.0
O Q:HOH5427 4.2 62.0 1.0
CG Q:ASN16 4.3 84.0 1.0
CB Q:ASP20 4.3 89.2 1.0
CA Q:SER24 4.4 72.2 1.0
NH2 Q:ARG28 4.5 84.5 1.0
N Q:SER24 4.6 71.5 1.0
CA Q:ASP20 4.6 86.4 1.0
CG Q:ASP44 4.6 73.6 1.0
O Q:HOH7505 4.6 53.9 1.0
OD2 Q:ASP44 4.6 73.8 1.0
C Q:GLY22 4.7 75.3 1.0
ND2 Q:ASN16 4.7 85.3 1.0
N Q:GLY22 4.9 78.6 1.0
C Q:THR23 4.9 72.3 1.0

Sodium binding site 7 out of 75 in 3ccj

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Sodium binding site 7 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na8532

b:68.5
occ:1.00
 O R:HOH8928 2.7 80.5 1.0
O R:HOH8929 3.0 50.5 1.0
O R:SER70 3.3 59.6 1.0
OD1 R:ASP73 3.4 71.8 1.0
O R:VAL72 3.5 62.0 1.0
O 0:HOH5869 4.2 0.5 1.0
O2' 0:U2830 4.2 95.2 1.0
CG R:ASP73 4.4 69.2 1.0
C R:SER70 4.4 60.1 1.0
C R:VAL72 4.5 62.7 1.0
O R:HOH8978 4.6 60.0 1.0
CB R:ASP73 4.7 66.6 1.0
C R:LYS71 4.7 65.0 1.0
CA R:ASP73 4.7 64.9 1.0
O R:LYS71 4.8 66.3 1.0
CA R:LYS71 4.8 64.6 1.0
NA R:NA8533 4.9 94.7 1.0

Sodium binding site 8 out of 75 in 3ccj

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Sodium binding site 8 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na8533

b:94.7
occ:1.00
 OP1 0:G2660 2.4 61.9 1.0
O R:HOH8929 2.5 50.5 1.0
O R:TRP75 2.6 58.3 1.0
O R:VAL72 2.6 62.0 1.0
O R:HOH8919 2.7 1.0 1.0
N R:GLY74 2.8 65.2 1.0
CA R:ASP73 2.9 64.9 1.0
C R:VAL72 3.0 62.7 1.0
N R:TRP75 3.1 60.5 1.0
C R:ASP73 3.1 65.6 1.0
O3' 0:U2659 3.1 62.0 1.0
N R:ASP73 3.2 63.5 1.0
P 0:G2660 3.3 62.9 1.0
C R:TRP75 3.6 57.4 1.0
CA R:GLY74 3.8 63.4 1.0
C R:GLY74 3.9 62.1 1.0
CA R:TRP75 3.9 59.2 1.0
O5' 0:G2660 4.0 60.3 1.0
CG1 R:VAL72 4.0 63.1 1.0
CB R:VAL72 4.0 63.4 1.0
O R:ASP73 4.1 66.8 1.0
CA R:VAL72 4.1 62.9 1.0
CB R:ASP73 4.3 66.6 1.0
C3' 0:U2659 4.5 61.4 1.0
OP2 0:G2660 4.6 62.2 1.0
CG R:ASP73 4.7 69.2 1.0
O2' 0:U2659 4.8 60.4 1.0
N R:ASP76 4.8 54.5 1.0
O R:SER70 4.8 59.6 1.0
N R:VAL72 4.8 63.3 1.0
CB R:TRP75 4.9 59.3 1.0
OD1 R:ASP73 4.9 71.8 1.0
O R:HOH8928 4.9 80.5 1.0
NA R:NA8532 4.9 68.5 1.0
C4' 0:U2659 5.0 61.2 1.0

Sodium binding site 9 out of 75 in 3ccj

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Sodium binding site 9 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na8575

b:97.5
occ:1.00
 O2' 0:U12 3.0 71.3 1.0
ND2 R:ASN63 3.3 49.8 1.0
OD1 R:ASN63 3.5 51.0 1.0
O3' 0:C2086 3.6 52.7 1.0
SR R:SR8912 3.6 0.8 1.0
OP1 0:C2087 3.7 54.2 1.0
C5' 0:C2087 3.7 51.0 1.0
O R:LYS60 3.8 58.4 1.0
CG R:ASN63 3.8 49.7 1.0
O3' 0:U12 3.8 67.9 1.0
O2' 0:C2086 3.8 46.6 1.0
C4' 0:U12 4.1 71.7 1.0
C2' 0:U12 4.2 71.5 1.0
C3' 0:U12 4.2 70.5 1.0
P 0:C2087 4.2 53.4 1.0
CH2 R:TRP75 4.3 58.1 1.0
CZ2 R:TRP75 4.4 58.5 1.0
O5' 0:C2087 4.5 53.0 1.0
C3' 0:C2086 4.6 49.2 1.0
C2' 0:C2086 4.8 47.9 1.0
O R:GLN61 4.8 58.2 1.0
O4' 0:U12 4.8 70.2 1.0
C4' 0:C2087 4.9 50.3 1.0
C1' 0:U12 4.9 71.3 1.0
C R:LYS60 5.0 58.3 1.0

Sodium binding site 10 out of 75 in 3ccj

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Sodium binding site 10 out of 75 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na8510

b:41.4
occ:1.00
 OE2 S:GLU61 2.8 82.7 1.0
NE2 S:HIS7 2.8 82.0 1.0
OE1 S:GLU61 2.8 82.2 1.0
O S:HOH8977 3.0 46.0 1.0
CE1 S:HIS7 3.1 83.5 1.0
CD S:GLU61 3.2 81.2 1.0
CD2 S:HIS7 4.0 82.5 1.0
ND1 S:HIS7 4.3 83.0 1.0
CG S:GLU61 4.7 79.0 1.0
CB S:ALA27 4.7 71.9 1.0
CG S:HIS7 4.8 82.5 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 06:15:01 2024

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