Chlorine in PDB 3cma: The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma was solved by M.Simonovic, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.79 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.316, 297.905, 573.138, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.5

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui 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

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 The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cma). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8809 b:57.9 occ:1.00 O 0:HOH7232 3.1 32.3 1.0 NZ A:LYS178 3.3 33.9 1.0 CE A:LYS175 3.5 23.7 1.0 O 0:HOH6094 3.8 17.3 1.0 CE A:LYS178 3.9 32.0 1.0 CD A:LYS178 3.9 32.4 1.0 CE1 A:PHE169 4.2 33.4 1.0 CZ A:PHE169 4.2 33.7 1.0 CE A:MET179 4.4 38.2 1.0 O 0:HOH4143 4.4 71.6 1.0 SD A:MET179 4.5 38.7 1.0 O A:HOH9052 4.5 24.5 1.0 O 0:HOH7472 4.5 66.5 1.0 NZ A:LYS175 4.5 23.1 1.0 CD A:LYS175 4.6 23.7 1.0 OP2 0:G1878 4.8 28.7 1.0 CG A:LYS178 5.0 31.3 1.0

Chlorine binding site 2 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl8819 b:56.4 occ:1.00 O 0:HOH3566 3.1 39.4 1.0 O 0:HOH3502 3.3 28.9 1.0 O 0:HOH7000 3.4 67.6 1.0 N B:LYS224 3.4 28.6 1.0 CA B:ARG223 3.5 29.6 1.0 CB B:HIS227 3.5 21.7 1.0 CB B:ARG223 3.6 30.9 1.0 O B:HOH9059 3.8 34.2 1.0 O2' 0:U2545 3.8 25.0 1.0 CG B:HIS227 3.8 22.8 1.0 CD2 B:HIS227 3.8 23.5 1.0 CG B:ARG223 3.9 33.6 1.0 C B:ARG223 4.0 29.2 1.0 CD B:ARG223 4.2 34.8 1.0 C4' 0:U2546 4.3 23.4 1.0 O4' 0:U2546 4.4 23.1 1.0 O B:LYS224 4.5 26.7 1.0 C5' 0:U2546 4.5 23.7 1.0 CA B:LYS224 4.6 26.7 1.0 N2 0:G2613 4.7 26.2 1.0 N B:ARG223 4.7 30.0 1.0 ND1 B:HIS227 4.8 23.8 1.0 O B:LYS222 4.8 32.6 1.0 NE2 B:HIS227 4.8 23.7 1.0 CB B:LYS224 4.9 27.1 1.0 C2' 0:U2545 4.9 24.4 1.0 CA B:HIS227 5.0 22.8 1.0

Chlorine binding site 3 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl8801 b:58.1 occ:1.00 N J:ILE127 2.7 45.4 1.0 N J:LYS128 3.1 40.8 1.0 O J:HOH4038 3.3 0.7 1.0 O J:HOH4193 3.3 52.0 1.0 O 0:HOH4781 3.3 66.6 1.0 CA J:ILE127 3.6 44.2 1.0 CA J:ASN126 3.6 48.6 1.0 C J:ASN126 3.6 47.1 1.0 CB J:ILE127 3.8 45.5 1.0 C J:ILE127 3.8 42.3 1.0 CB J:LYS128 3.9 38.1 1.0 CG E:PRO36 3.9 43.8 1.0 CG J:LYS128 4.0 36.1 1.0 OD1 J:ASN126 4.0 55.7 1.0 CA J:LYS128 4.1 39.2 1.0 CB J:ASN126 4.3 51.6 1.0 O 0:HOH7334 4.3 45.4 1.0 CG2 J:ILE127 4.4 46.4 1.0 O J:SER125 4.6 49.8 1.0 CG J:ASN126 4.6 54.4 1.0 CD J:LYS128 4.7 34.4 1.0 N J:ASN126 4.8 48.5 1.0 O J:ASN126 4.8 47.1 1.0 C J:LYS128 4.9 38.8 1.0 CB E:PRO36 4.9 44.0 1.0 CD E:PRO36 5.0 44.2 1.0 O J:LYS128 5.0 38.1 1.0

Chlorine binding site 4 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl8802 b:66.2 occ:1.00 N J:LYS90 3.0 41.9 1.0 C J:PRO88 3.2 38.9 1.0 CA J:PRO88 3.3 39.9 1.0 CB J:LYS90 3.3 40.8 1.0 O J:PRO88 3.5 38.2 1.0 CA J:LYS90 3.6 43.2 1.0 N J:HIS89 3.6 39.0 1.0 CG J:LYS91 3.6 54.0 1.0 CB J:PRO88 3.7 39.8 1.0 N J:LYS91 3.9 47.7 1.0 C J:LYS90 4.0 45.4 1.0 C J:HIS89 4.1 40.8 1.0 CG J:LYS90 4.4 38.0 1.0 CA J:HIS89 4.4 39.7 1.0 CD J:LYS91 4.4 57.6 1.0 ND1 J:HIS89 4.7 38.4 1.0 N J:PRO88 4.7 40.3 1.0 CB J:LYS91 4.8 50.2 1.0 CD J:LYS90 4.9 33.0 1.0 O J:LYS90 4.9 45.9 1.0 O J:LEU87 4.9 40.2 1.0 CA J:LYS91 4.9 50.2 1.0

Chlorine binding site 5 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl8821 b:61.5 occ:1.00 O J:HOH4949 3.2 31.3 1.0 CA J:GLY64 3.4 37.7 1.0 N J:ASN65 3.6 36.5 1.0 N J:TYR69 3.6 43.1 1.0 O J:ASN65 3.8 34.2 1.0 CA J:GLY68 3.9 40.9 1.0 C J:GLY64 3.9 37.8 1.0 O J:ILE63 4.0 41.3 1.0 OP1 0:A2678 4.1 40.2 1.0 NA J:NA8538 4.3 31.6 1.0 C J:GLY68 4.3 41.4 1.0 O3' 0:A2677 4.4 36.8 1.0 N J:GLY64 4.5 38.7 1.0 CA J:TYR69 4.6 46.2 1.0 C J:TYR69 4.6 48.8 1.0 C5' 0:A2677 4.6 42.5 1.0 C J:ASN65 4.6 35.3 1.0 CA J:ASN65 4.7 35.6 1.0 C J:ILE63 4.7 40.4 1.0 O J:TYR69 4.8 50.6 1.0 P 0:A2678 4.9 37.3 1.0 CB J:TYR69 4.9 44.7 1.0 N J:GLY68 4.9 39.5 1.0 O J:GLY64 5.0 38.6 1.0

Chlorine binding site 6 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ K:Cl8812 b:43.8 occ:1.00 O 0:HOH5965 3.2 13.6 1.0 NZ K:LYS14 3.4 31.1 1.0 OG K:SER33 3.4 42.2 1.0 CD K:LYS14 3.4 27.1 1.0 N2 0:G2582 3.4 24.4 1.0 C2 0:A2596 3.5 25.6 1.0 O K:ILE32 3.5 37.3 1.0 CE K:LYS14 3.6 28.1 1.0 N3 0:A2596 3.6 25.6 1.0 CG K:PRO45 3.8 30.5 1.0 O 0:HOH9389 4.0 56.3 1.0 CB K:SER33 4.2 39.2 1.0 CA K:SER33 4.2 37.9 1.0 C1' 0:U2597 4.2 33.1 1.0 CB K:PRO45 4.2 29.9 1.0 N3 0:A2583 4.3 27.5 1.0 O2' 0:U2597 4.4 35.4 1.0 CG K:LYS14 4.5 26.9 1.0 C K:ILE32 4.6 37.7 1.0 O2 0:U2597 4.6 31.4 1.0 N1 0:A2596 4.7 25.4 1.0 O4' 0:U2597 4.7 33.3 1.0 C2 0:G2582 4.8 25.4 1.0 C1' 0:A2583 4.8 25.9 1.0 C2 0:A2583 4.9 27.3 1.0 C2' 0:U2597 4.9 32.3 1.0 N K:SER33 4.9 37.5 1.0 C4 0:A2583 4.9 27.1 1.0 C4 0:A2596 5.0 27.4 1.0 CD K:PRO45 5.0 29.5 1.0

Chlorine binding site 7 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl8814 b:49.4 occ:1.00 O2' 0:G644 3.0 29.3 1.0 ND1 L:HIS13 3.1 20.5 1.0 O L:HOH8902 3.1 0.7 1.0 CG L:GLN7 3.5 26.8 1.0 C2' 0:G644 3.8 25.3 1.0 CG L:HIS13 3.9 18.3 1.0 N9 0:G644 3.9 19.9 1.0 CE1 L:HIS13 4.0 19.0 1.0 CB L:HIS13 4.0 19.3 1.0 C4 0:G644 4.0 18.9 1.0 O 0:HOH4085 4.1 43.9 1.0 CB L:GLN7 4.2 21.8 1.0 C1' 0:G644 4.2 23.4 1.0 C8 0:G644 4.2 19.3 1.0 N3 0:G644 4.4 20.2 1.0 C5 0:G644 4.4 18.9 1.0 CG L:LYS4 4.4 39.4 1.0 CD L:GLN7 4.5 29.9 1.0 N7 0:G644 4.5 20.2 1.0 O L:HIS13 4.6 21.3 1.0 CA L:LYS4 4.9 30.8 1.0 OE1 L:GLN7 4.9 29.9 1.0

Chlorine binding site 8 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl8810 b:52.7 occ:1.00 N L:ARG53 3.0 39.5 1.0 CA L:LYS52 3.7 37.1 1.0 C5' 0:A693 3.8 41.7 1.0 CB L:ARG53 3.8 40.3 1.0 C L:LYS52 3.9 37.6 1.0 NE2 L:GLN58 4.0 73.3 1.0 CA L:ARG53 4.0 40.5 1.0 CG L:ARG53 4.2 40.3 1.0 O L:ARG53 4.2 42.2 1.0 CD L:GLN58 4.2 73.0 1.0 CB L:LYS52 4.3 35.9 1.0 C4' 0:A693 4.4 41.9 1.0 O L:PHE51 4.5 34.7 1.0 C L:ARG53 4.5 41.2 1.0 OP1 0:A693 4.6 40.9 1.0 O3' 0:A693 4.6 44.1 1.0 OE1 L:GLN58 4.6 72.9 1.0 O 0:HOH4187 4.7 66.8 1.0 CG L:GLN58 4.8 72.8 1.0 CD L:ARG53 4.8 39.6 1.0 CG L:LYS52 4.9 38.9 1.0 N L:LYS52 4.9 36.5 1.0 O5' 0:A693 5.0 41.7 1.0

Chlorine binding site 9 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ M:Cl8818 b:33.4 occ:1.00 N M:VAL114 3.0 32.4 1.0 O M:HOH8936 3.1 42.0 1.0 CG1 M:VAL159 3.2 28.3 1.0 OG M:SER106 3.4 27.1 1.0 CG2 M:VAL114 3.5 29.1 1.0 CA M:ARG113 3.5 32.1 1.0 N M:VAL159 3.6 31.0 1.0 CB M:VAL159 3.7 29.6 1.0 C M:ARG113 3.7 32.3 1.0 CG M:ARG158 3.8 24.4 1.0 CB M:VAL114 3.8 31.1 1.0 N M:ARG158 3.9 33.9 1.0 CA M:VAL114 4.0 32.4 1.0 CA M:ASP157 4.0 39.1 1.0 CB M:ARG113 4.0 29.7 1.0 C M:ASP157 4.1 37.5 1.0 CB M:SER106 4.2 31.4 1.0 CA M:VAL159 4.3 30.5 1.0 N M:ASP157 4.4 38.2 1.0 O M:LEU112 4.5 37.9 1.0 CD M:ARG158 4.6 23.1 1.0 CG M:ARG113 4.6 27.3 1.0 C M:ARG158 4.6 32.4 1.0 CA M:ARG158 4.7 32.3 1.0 O M:VAL114 4.7 35.0 1.0 N M:ARG113 4.8 33.7 1.0 NA M:NA8539 4.8 33.8 1.0 CB M:ARG158 4.8 29.4 1.0 O M:ASP157 4.8 38.6 1.0 C M:VAL114 4.9 33.5 1.0 O M:ARG113 4.9 33.8 1.0

Chlorine binding site 10 out of 22 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ N:Cl8807 b:62.9 occ:1.00 N N:LYS38 3.3 54.1 1.0 CD N:ARG37 3.5 58.8 1.0 OD1 N:ASN107 3.5 50.8 1.0 CD D:LYS146 3.7 64.1 1.0 NZ D:LYS146 3.7 66.0 1.0 CB N:ARG37 3.7 52.6 1.0 O N:LYS38 3.7 58.9 1.0 CA N:ARG37 3.8 51.8 1.0 C N:ARG37 4.0 52.3 1.0 O 9:HOH9026 4.1 42.0 1.0 CE D:LYS146 4.1 65.6 1.0 CG N:ARG37 4.2 55.4 1.0 CA N:LYS38 4.2 56.0 1.0 C N:LYS38 4.3 57.6 1.0 CG N:ASN107 4.5 51.4 1.0 CB N:LYS38 4.6 56.0 1.0 NE N:ARG37 4.7 59.5 1.0 ND2 N:ASN107 4.8 52.2 1.0 CG D:LYS146 5.0 62.3 1.0

M.Simonovic, T.A.Steitz. Peptidyl-Cca Deacylation on the Ribosome Promoted By Induced Fit and the O3'-Hydroxyl Group of A76 of the Unacylated A-Site Trna. Rna V. 14 2372 2008.
ISSN: ISSN 1355-8382
PubMed: 18818369
DOI: 10.1261/RNA.1118908