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Chlorine 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
Sodium (Na) 75 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 3cc4

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Chlorine binding site 1 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl8809

b:57.5
occ:1.00
 NZ A:LYS178 3.1 36.0 1.0
O 0:HOH6467 3.3 26.0 1.0
O 0:HOH5287 3.5 39.5 1.0
CE A:LYS175 3.7 33.0 1.0
CD A:LYS178 3.9 36.9 1.0
CE A:LYS178 4.0 34.7 1.0
CE A:MET179 4.0 45.0 1.0
O A:HOH9041 4.3 51.9 1.0
CZ A:PHE169 4.3 32.1 1.0
SD A:MET179 4.5 42.6 1.0
CE1 A:PHE169 4.5 33.3 1.0
CD A:LYS175 4.7 30.2 1.0
O 0:HOH6728 4.7 44.6 1.0
OP2 0:G1878 4.7 33.7 1.0
NZ A:LYS175 4.8 32.7 1.0
O 0:HOH3280 4.9 39.2 1.0
O 0:HOH5443 4.9 66.0 1.0

Chlorine binding site 2 out of 22 in 3cc4

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Chlorine binding site 2 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl8819

b:46.3
occ:1.00
 O 0:HOH9674 3.1 26.6 1.0
O 0:HOH9608 3.2 35.2 1.0
N B:LYS224 3.3 31.6 1.0
O B:HOH9049 3.4 29.0 1.0
CA B:ARG223 3.6 33.6 1.0
CD2 B:HIS227 3.6 28.1 1.0
CB B:HIS227 3.6 29.3 1.0
CG B:HIS227 3.8 29.0 1.0
O2' 0:U2545 3.8 32.0 1.0
C B:ARG223 4.0 32.7 1.0
CB B:ARG223 4.0 35.7 1.0
O 0:HOH6226 4.0 37.4 1.0
CD B:ARG223 4.1 38.4 1.0
O B:LYS224 4.2 33.1 1.0
CA B:LYS224 4.3 30.6 1.0
C4' 0:U2546 4.4 27.7 1.0
O4' 0:U2546 4.4 27.5 1.0
CG B:ARG223 4.5 36.9 1.0
C5' 0:U2546 4.5 27.2 1.0
CB B:LYS224 4.6 31.1 1.0
NE2 B:HIS227 4.7 29.4 1.0
O B:LYS222 4.7 35.0 1.0
C B:LYS224 4.8 31.5 1.0
ND1 B:HIS227 4.8 28.8 1.0
N2 0:G2613 4.9 31.8 1.0
N B:ARG223 4.9 33.9 1.0

Chlorine binding site 3 out of 22 in 3cc4

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Chlorine binding site 3 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8801

b:62.9
occ:1.00
 O J:HOH4193 3.0 55.4 1.0
N J:ILE127 3.0 50.2 1.0
N J:LYS128 3.2 44.6 1.0
CG2 J:ILE127 3.4 52.1 1.0
O J:HOH4038 3.6 70.8 1.0
CA J:ASN126 3.8 52.0 1.0
CB J:LYS128 3.8 40.9 1.0
CA J:ILE127 3.8 49.6 1.0
C J:ASN126 3.9 51.0 1.0
CG J:LYS128 3.9 40.7 1.0
CG E:PRO36 3.9 52.7 1.0
OD1 J:ASN126 3.9 54.8 1.0
C J:ILE127 4.0 47.5 1.0
CA J:LYS128 4.0 42.0 1.0
CB J:ILE127 4.1 52.0 1.0
O 0:HOH3943 4.3 92.9 1.0
CB J:ASN126 4.3 53.1 1.0
O J:SER125 4.5 53.6 1.0
CG J:ASN126 4.5 54.4 1.0
CD J:LYS128 4.6 40.4 1.0
O J:LYS128 4.8 42.0 1.0
C J:LYS128 4.8 42.2 1.0
O 0:HOH6575 4.9 43.9 1.0
N J:ASN126 4.9 52.7 1.0
CD E:PRO36 4.9 52.9 1.0
CB E:PRO36 5.0 53.2 1.0

Chlorine binding site 4 out of 22 in 3cc4

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Chlorine binding site 4 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
J:Cl8802

b:60.6
occ:1.00
 N J:LYS90 3.4 48.6 1.0
C J:PRO88 3.4 43.6 1.0
O J:PRO88 3.5 43.9 1.0
CA J:PRO88 3.5 44.0 1.0
CB J:LYS90 3.6 50.5 1.0
CB J:PRO88 3.8 44.2 1.0
CA J:LYS90 3.8 51.3 1.0
N J:LYS91 3.9 54.8 1.0
N J:HIS89 4.0 44.2 1.0
C J:LYS90 4.2 53.1 1.0
CG J:LYS91 4.2 61.0 1.0
C J:HIS89 4.5 46.5 1.0
CB J:LYS91 4.6 58.2 1.0
CG J:LYS90 4.7 48.4 1.0
CA J:HIS89 4.8 44.9 1.0
CA J:LYS91 4.8 57.7 1.0
ND1 J:HIS89 5.0 42.7 1.0
N J:PRO88 5.0 44.9 1.0
CD J:LYS90 5.0 45.8 1.0

Chlorine binding site 5 out of 22 in 3cc4

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Chlorine binding site 5 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
J:Cl8821

b:56.6
occ:1.00
 O 0:HOH5825 3.1 43.1 1.0
O J:ASN65 3.5 48.4 1.0
N J:TYR69 3.5 53.4 1.0
CA J:GLY68 3.7 51.3 1.0
CA J:GLY64 3.7 46.2 1.0
N J:ASN65 3.7 46.5 1.0
C J:GLY64 4.1 46.5 1.0
C J:GLY68 4.1 52.3 1.0
O J:TYR69 4.3 57.5 1.0
OP1 0:A2678 4.3 46.2 1.0
O3' 0:A2677 4.3 45.1 1.0
O J:ILE63 4.4 47.5 1.0
C J:ASN65 4.4 47.1 1.0
C J:TYR69 4.5 56.7 1.0
CA J:TYR69 4.5 54.8 1.0
O J:HOH6706 4.6 67.5 1.0
N J:GLY68 4.6 48.8 1.0
CA J:ASN65 4.7 47.4 1.0
C5' 0:A2677 4.7 51.3 1.0
CB J:TYR69 4.8 52.8 1.0
N J:GLY64 4.8 46.1 1.0
NA J:NA8538 4.9 56.3 1.0
P 0:A2678 5.0 44.3 1.0
C4' 0:A2677 5.0 49.1 1.0

Chlorine binding site 6 out of 22 in 3cc4

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Chlorine binding site 6 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
L:Cl8810

b:49.0
occ:1.00
 N L:ARG53 3.2 44.4 1.0
NE2 L:GLN58 3.7 79.4 1.0
C5' 0:A693 3.7 41.7 1.0
CB L:ARG53 3.8 45.3 1.0
CA L:LYS52 3.9 41.5 1.0
C L:LYS52 4.0 42.8 1.0
CA L:ARG53 4.0 45.9 1.0
O L:ARG53 4.2 48.4 1.0
CG L:ARG53 4.2 43.8 1.0
CD L:GLN58 4.3 79.4 1.0
C4' 0:A693 4.4 43.6 1.0
CB L:LYS52 4.4 40.9 1.0
O3' 0:A693 4.4 45.5 1.0
OP1 0:A693 4.6 42.3 1.0
O L:PHE51 4.6 40.8 1.0
C L:ARG53 4.6 47.7 1.0
CG L:LYS52 4.8 42.8 1.0
O5' 0:A693 4.8 41.8 1.0
CD L:ARG53 4.8 42.6 1.0
OE1 L:GLN58 4.8 79.6 1.0
CG L:GLN58 4.9 79.3 1.0

Chlorine binding site 7 out of 22 in 3cc4

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Chlorine binding site 7 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
M:Cl8818

b:37.1
occ:1.00
 OG M:SER106 3.1 36.8 1.0
N M:VAL114 3.3 32.7 1.0
CG1 M:VAL159 3.4 28.7 1.0
O M:HOH8924 3.5 55.2 1.0
CA M:ARG113 3.6 32.0 1.0
N M:VAL159 3.6 31.6 1.0
N M:ARG158 3.8 36.4 1.0
CB M:VAL159 3.8 29.8 1.0
CA M:ASP157 3.9 39.1 1.0
CG2 M:VAL114 3.9 33.7 1.0
CG M:ARG158 3.9 31.9 1.0
C M:ASP157 3.9 38.2 1.0
C M:ARG113 4.0 32.6 1.0
CB M:VAL114 4.1 32.7 1.0
CB M:ARG113 4.2 29.5 1.0
CB M:SER106 4.2 36.4 1.0
NA M:NA8539 4.3 41.9 1.0
O M:LEU112 4.3 35.8 1.0
CA M:VAL114 4.3 33.5 1.0
CA M:VAL159 4.4 30.7 1.0
N M:ASP157 4.4 38.7 1.0
CG M:ARG113 4.5 28.8 1.0
CA M:ARG158 4.5 35.3 1.0
C M:ARG158 4.6 35.0 1.0
O M:ASP157 4.6 39.3 1.0
N M:ARG113 4.8 33.8 1.0
CB M:ARG158 4.8 33.2 1.0
CE1 M:PHE160 4.8 33.2 1.0
CD M:ARG158 4.9 32.2 1.0
C M:LEU112 5.0 33.8 1.0
CD1 M:PHE160 5.0 34.7 1.0

Chlorine binding site 8 out of 22 in 3cc4

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Chlorine binding site 8 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
N:Cl8807

b:61.7
occ:1.00
 OD1 N:ASN107 3.2 54.2 1.0
N N:LYS38 3.2 63.3 1.0
O N:LYS38 3.3 68.9 1.0
NZ D:LYS146 3.4 71.1 1.0
CD N:ARG37 3.5 60.7 1.0
CA N:ARG37 3.7 60.5 1.0
CB N:ARG37 3.8 60.4 1.0
CD D:LYS146 3.9 66.8 1.0
C N:ARG37 4.0 61.7 1.0
O 9:HOH9026 4.1 54.7 1.0
C N:LYS38 4.1 67.8 1.0
CG N:ASN107 4.1 54.1 1.0
CA N:LYS38 4.2 66.0 1.0
CG N:ARG37 4.2 60.7 1.0
CE D:LYS146 4.3 69.7 1.0
ND2 N:ASN107 4.4 53.5 1.0
CG N:LYS38 4.4 68.6 1.0
NE N:ARG37 4.6 61.2 1.0
CB N:LYS38 4.8 66.5 1.0

Chlorine binding site 9 out of 22 in 3cc4

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Chlorine binding site 9 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
O:Cl8808

b:61.2
occ:1.00
 O 0:HOH7113 3.0 63.3 1.0
ND2 O:ASN44 3.2 44.6 1.0
N O:ASN44 3.2 43.2 1.0
O 0:HOH6898 3.4 63.0 1.0
CB O:ASN44 3.5 45.4 1.0
NH2 O:ARG47 3.6 60.8 1.0
NE O:ARG47 3.7 60.9 1.0
CG O:ASN44 3.8 46.3 1.0
C8 0:G745 3.8 52.8 1.0
CA O:ASN44 4.0 45.1 1.0
O O:HOH6754 4.0 70.8 1.0
O O:GLU42 4.0 47.9 1.0
CA O:VAL43 4.1 44.5 1.0
C O:VAL43 4.1 43.8 1.0
N7 0:G745 4.1 53.8 1.0
CZ O:ARG47 4.2 61.0 1.0
OP2 0:A746 4.3 39.0 1.0
CG1 O:VAL43 4.6 46.3 1.0
O O:HOH510 4.6 57.2 1.0
O O:ASN44 4.7 49.1 1.0
C O:ASN44 4.7 47.1 1.0
OP2 0:G745 4.8 47.1 1.0
CB O:ARG47 4.8 55.9 1.0
C3' 0:G745 4.8 45.1 1.0
CD O:ARG47 4.8 59.1 1.0
OD1 O:ASN44 4.9 48.0 1.0
C O:GLU42 4.9 47.5 1.0
O5' 0:G745 4.9 47.2 1.0
N O:VAL43 5.0 46.0 1.0

Chlorine binding site 10 out of 22 in 3cc4

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Chlorine binding site 10 out of 22 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
R:Cl8806

b:43.2
occ:1.00
 O R:HOH8914 2.9 32.3 1.0
NZ R:LYS118 3.4 42.5 1.0
CE R:LYS118 4.0 42.5 1.0
CB R:PHE25 4.0 35.4 1.0
CG R:LYS26 4.0 28.9 1.0
CE R:LYS26 4.1 27.5 1.0
CD2 R:PHE25 4.1 38.2 1.0
CD R:LYS118 4.1 40.6 1.0
CD R:LYS26 4.5 27.6 1.0
CG R:PHE25 4.6 36.6 1.0
CG R:PRO139 4.7 38.2 1.0
N R:LYS26 4.8 33.1 1.0
CB R:PRO139 5.0 38.5 1.0
CA R:PHE25 5.0 33.7 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: Sat Jul 20 17:00:48 2024

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