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Chlorine in PDB 3cd6: Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin

Protein crystallography data

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6 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) 49.95 / 2.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.805, 299.997, 576.002, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Other elements in 3cd6:

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin also contains other interesting chemical elements:

Strontium (Sr) 107 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-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin (pdb code 3cd6). 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-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 3cd6

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Chlorine binding site 1 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8809

b:88.8
occ:1.00
 NZ A:LYS178 3.2 51.0 1.0
O A:HOH9021 3.2 50.3 1.0
CE A:LYS175 3.5 42.1 1.0
CE A:MET179 3.9 48.6 1.0
O A:HOH8992 4.0 51.2 1.0
O 0:HOH5281 4.0 48.7 1.0
CD A:LYS178 4.1 47.3 1.0
CE A:LYS178 4.2 48.6 1.0
SD A:MET179 4.4 47.5 1.0
NZ A:LYS175 4.4 45.2 1.0
CZ A:PHE169 4.5 37.4 1.0
CD A:LYS175 4.6 39.9 1.0
OP2 0:G1878 4.6 51.7 1.0
O 0:HOH3952 4.7 67.5 1.0
CE1 A:PHE169 4.7 38.2 1.0
O 0:HOH3268 4.7 80.5 1.0

Chlorine binding site 2 out of 22 in 3cd6

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Chlorine binding site 2 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl8819

b:54.0
occ:1.00
 O 0:HOH9671 3.0 38.5 1.0
O 0:HOH9602 3.0 29.0 1.0
N B:LYS224 3.1 39.0 1.0
O B:HOH9009 3.2 36.7 1.0
CA B:ARG223 3.5 40.2 1.0
O2' 0:U2545 3.8 40.1 1.0
C B:ARG223 3.8 40.0 1.0
CB B:HIS227 3.8 33.1 1.0
CD2 B:HIS227 3.8 33.4 1.0
CB B:ARG223 3.9 42.8 1.0
CG B:HIS227 4.0 32.5 1.0
O B:LYS224 4.1 38.7 1.0
CA B:LYS224 4.1 36.5 1.0
O 0:HOH6202 4.3 38.1 1.0
CB B:LYS224 4.3 35.6 1.0
C4' 0:U2546 4.4 32.5 1.0
C5' 0:U2546 4.4 31.2 1.0
CD B:ARG223 4.4 47.0 1.0
O4' 0:U2546 4.5 32.5 1.0
CG B:ARG223 4.5 45.5 1.0
O B:LYS222 4.5 41.7 1.0
C B:LYS224 4.6 36.3 1.0
CG B:LYS224 4.7 34.6 1.0
N B:ARG223 4.8 39.4 1.0
NE2 B:HIS227 4.9 34.2 1.0

Chlorine binding site 3 out of 22 in 3cd6

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Chlorine binding site 3 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl8801

b:68.7
occ:1.00
 N J:ILE127 2.8 49.4 1.0
N J:LYS128 3.1 46.4 1.0
O J:HOH9009 3.4 47.4 1.0
CA J:ASN126 3.7 52.1 1.0
CA J:ILE127 3.7 49.1 1.0
CG2 J:ILE127 3.7 48.3 1.0
C J:ASN126 3.7 50.4 1.0
CB J:LYS128 3.7 46.0 1.0
CG E:PRO36 3.8 56.4 1.0
O J:HOH9008 3.8 84.0 1.0
C J:ILE127 3.8 48.1 1.0
OD1 J:ASN126 3.9 56.5 1.0
CA J:LYS128 4.0 45.2 1.0
O 0:HOH3932 4.0 76.2 1.0
CG J:LYS128 4.0 46.2 1.0
CB J:ILE127 4.2 50.6 1.0
CB J:ASN126 4.2 54.2 1.0
CG J:ASN126 4.5 56.0 1.0
O J:SER125 4.5 53.9 1.0
CD J:LYS128 4.6 47.9 1.0
C J:LYS128 4.8 45.3 1.0
N J:ASN126 4.8 52.1 1.0
CD E:PRO36 4.9 55.2 1.0
O J:LYS128 4.9 44.3 1.0
CB E:PRO36 4.9 56.5 1.0
O J:ASN126 4.9 49.9 1.0

Chlorine binding site 4 out of 22 in 3cd6

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Chlorine binding site 4 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl8802

b:68.0
occ:1.00
 N J:LYS90 3.3 52.9 1.0
C J:PRO88 3.3 46.3 1.0
O J:PRO88 3.5 45.8 1.0
CA J:PRO88 3.5 45.5 1.0
CB J:LYS90 3.6 55.0 1.0
CA J:LYS90 3.8 55.5 1.0
N J:HIS89 3.8 47.2 1.0
N J:LYS91 3.9 58.3 1.0
CB J:PRO88 4.0 46.0 1.0
C J:LYS90 4.2 57.5 1.0
CG J:LYS91 4.3 64.4 1.0
C J:HIS89 4.4 50.9 1.0
CG J:LYS90 4.5 53.3 1.0
CA J:HIS89 4.6 49.0 1.0
CB J:LYS91 4.7 61.1 1.0
CA J:LYS91 4.9 59.7 1.0
CD J:LYS90 4.9 51.1 1.0
N J:PRO88 4.9 46.1 1.0
ND1 J:HIS89 5.0 47.2 1.0

Chlorine binding site 5 out of 22 in 3cd6

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Chlorine binding site 5 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl8821

b:56.6
occ:1.00
 O 0:HOH5802 3.0 50.7 1.0
O J:ASN65 3.2 55.6 1.0
N J:ASN65 3.4 54.2 1.0
CA J:GLY64 3.6 54.0 1.0
N J:TYR69 3.6 57.5 1.0
CA J:GLY68 3.7 57.5 1.0
C J:GLY64 3.9 55.1 1.0
C J:ASN65 4.2 55.2 1.0
C J:GLY68 4.2 58.1 1.0
OP1 0:A2678 4.2 46.2 1.0
O3' 0:A2677 4.3 46.7 1.0
CA J:ASN65 4.4 54.4 1.0
O J:TYR69 4.5 59.6 1.0
N J:GLY68 4.5 56.0 1.0
O J:ILE63 4.6 54.0 1.0
C J:TYR69 4.7 59.3 1.0
CA J:TYR69 4.7 57.9 1.0
C5' 0:A2677 4.8 51.8 1.0
N J:GLY64 4.8 52.8 1.0
P 0:A2678 4.9 46.8 1.0
C4' 0:A2677 4.9 48.9 1.0
CB J:TYR69 5.0 56.8 1.0
O J:GLY64 5.0 57.0 1.0

Chlorine binding site 6 out of 22 in 3cd6

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Chlorine binding site 6 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl8810

b:70.7
occ:1.00
 N L:ARG53 3.0 61.7 1.0
NE2 L:GLN58 3.1 96.0 1.0
CA L:LYS52 3.7 58.5 1.0
CB L:ARG53 3.8 62.4 1.0
C L:LYS52 3.9 60.2 1.0
C5' 0:A693 3.9 57.1 1.0
CA L:ARG53 3.9 63.9 1.0
O L:ARG53 4.0 66.2 1.0
CD L:GLN58 4.1 95.6 1.0
CG L:ARG53 4.2 61.3 1.0
CB L:LYS52 4.3 57.7 1.0
C L:ARG53 4.5 66.1 1.0
O L:PHE51 4.5 57.6 1.0
OP1 0:A693 4.6 57.8 1.0
C4' 0:A693 4.6 58.2 1.0
O3' 0:A693 4.7 59.7 1.0
CG L:GLN58 4.8 95.0 1.0
CD L:ARG53 4.8 59.1 1.0
CG L:LYS52 4.9 57.6 1.0
N L:LYS52 4.9 57.5 1.0
O5' 0:A693 5.0 57.5 1.0
OE1 L:GLN58 5.0 96.2 1.0

Chlorine binding site 7 out of 22 in 3cd6

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Chlorine binding site 7 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl8818

b:40.5
occ:1.00
 O M:HOH8924 3.0 51.8 1.0
OG M:SER106 3.0 38.2 1.0
N M:VAL114 3.4 33.7 1.0
CG1 M:VAL159 3.4 38.8 1.0
N M:VAL159 3.6 39.2 1.0
N M:ARG158 3.7 43.2 1.0
CA M:ASP157 3.8 46.5 1.0
CA M:ARG113 3.8 34.6 1.0
C M:ASP157 3.8 45.1 1.0
CB M:VAL159 3.8 39.0 1.0
CG M:ARG158 4.0 40.2 1.0
CB M:SER106 4.1 39.4 1.0
C M:ARG113 4.1 34.6 1.0
CG2 M:VAL114 4.1 29.9 1.0
CB M:VAL114 4.2 30.6 1.0
N M:ASP157 4.3 45.8 1.0
CA M:VAL159 4.3 38.7 1.0
CB M:ARG113 4.3 33.2 1.0
O M:LEU112 4.3 38.6 1.0
NA M:NA8539 4.4 38.1 1.0
CA M:VAL114 4.4 32.3 1.0
CA M:ARG158 4.5 41.5 1.0
C M:ARG158 4.5 41.8 1.0
O M:ASP157 4.5 45.4 1.0
CG M:ARG113 4.5 32.4 1.0
CE1 M:PHE160 4.7 33.9 1.0
OD1 M:ASP157 4.8 52.7 1.0
CB M:ARG158 4.8 40.7 1.0
CD1 M:PHE160 4.8 36.9 1.0
N M:ARG113 4.9 36.9 1.0
CD M:ARG158 4.9 39.5 1.0

Chlorine binding site 8 out of 22 in 3cd6

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Chlorine binding site 8 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl8807

b:71.9
occ:1.00
 N N:LYS38 3.1 83.0 1.0
O N:HOH8815 3.3 88.4 1.0
CD D:LYS146 3.4 94.4 1.0
OD1 N:ASN107 3.5 71.1 1.0
CD N:ARG37 3.5 77.0 1.0
O N:LYS38 3.6 89.2 1.0
CA N:ARG37 3.8 79.1 1.0
CB N:ARG37 3.8 78.1 1.0
ND2 N:ASN107 3.9 71.1 1.0
C N:ARG37 4.0 81.1 1.0
CA N:LYS38 4.0 85.6 1.0
CG N:ASN107 4.1 72.0 1.0
NZ D:LYS146 4.2 95.6 1.0
C N:LYS38 4.2 88.0 1.0
CG N:ARG37 4.2 77.8 1.0
CB N:LYS38 4.3 85.8 1.0
CE D:LYS146 4.4 95.3 1.0
CG D:LYS146 4.5 93.3 1.0
NE N:ARG37 4.7 76.4 1.0

Chlorine binding site 9 out of 22 in 3cd6

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Chlorine binding site 9 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cl8808

b:62.4
occ:1.00
 O 0:HOH7090 2.9 56.7 1.0
N O:ASN44 3.3 53.1 1.0
ND2 O:ASN44 3.3 56.8 1.0
O 0:HOH6873 3.4 70.3 1.0
CB O:ASN44 3.6 54.8 1.0
NE O:ARG47 3.7 68.5 1.0
O O:HOH6754 3.8 77.2 1.0
O O:GLU42 3.9 58.2 1.0
CG O:ASN44 3.9 56.7 1.0
C8 0:G745 4.0 60.7 1.0
NH2 O:ARG47 4.0 70.0 1.0
CA O:ASN44 4.0 53.3 1.0
CA O:VAL43 4.1 55.4 1.0
C O:VAL43 4.2 54.3 1.0
N7 0:G745 4.3 61.3 1.0
CZ O:ARG47 4.3 69.1 1.0
OP2 0:A746 4.6 51.5 1.0
CD O:ARG47 4.6 65.1 1.0
CB O:ARG47 4.6 61.6 1.0
O O:ASN44 4.7 53.3 1.0
O 0:HOH9423 4.7 69.8 1.0
C O:GLU42 4.8 56.9 1.0
C O:ASN44 4.8 53.4 1.0
CG1 O:VAL43 4.8 58.3 1.0
C3' 0:G745 4.9 55.8 1.0
N O:VAL43 4.9 56.0 1.0
OP2 0:G745 4.9 56.4 1.0

Chlorine binding site 10 out of 22 in 3cd6

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Chlorine binding site 10 out of 22 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl8806

b:47.6
occ:1.00
 O R:HOH8914 3.0 27.2 1.0
NZ R:LYS118 3.6 47.3 1.0
CE R:LYS26 3.9 25.4 1.0
CG R:LYS26 4.0 26.8 1.0
CB R:PHE25 4.0 34.2 1.0
CE R:LYS118 4.0 45.8 1.0
CD2 R:PHE25 4.0 36.7 1.0
CD R:LYS118 4.2 44.7 1.0
CD R:LYS26 4.4 26.0 1.0
CG R:PHE25 4.5 34.7 1.0
N R:LYS26 4.7 32.4 1.0
CG R:PRO139 4.7 42.6 1.0
CA R:PHE25 5.0 33.3 1.0
N R:PHE25 5.0 34.5 1.0
CB R:PRO139 5.0 42.6 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 17:20:03 2024

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