Chlorine in PDB 1vq4: The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq4 was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.998, 301.034, 575.272, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23

The structure of The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	3 atoms
Cadmium	(Cd)	5 atoms
Sodium	(Na)	86 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vq4). 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq4:
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 the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9303 b:64.5 occ:1.00 N2 0:G1676 3.3 51.8 1.0 O 0:HOH6090 3.3 78.4 1.0 O 0:HOH9741 3.5 63.4 1.0 CE 2:LYS2 3.7 44.6 1.0 O 0:HOH3870 3.7 64.5 1.0 C1' 0:G1452 3.8 52.6 1.0 O2' 0:G1452 3.9 52.2 1.0 O 0:HOH7763 4.0 58.9 1.0 N3 0:A1486 4.2 45.6 1.0 C2 0:A1486 4.2 43.8 1.0 C2 0:G1676 4.3 51.8 1.0 O4' 0:G1452 4.3 54.1 1.0 C2' 0:G1452 4.4 51.4 1.0 O 0:HOH5010 4.5 77.1 1.0 N3 0:G1676 4.5 52.6 1.0 NZ 2:LYS2 4.5 45.4 1.0 O 0:HOH7021 4.6 64.3 1.0 CD 2:LYS2 4.6 43.1 1.0 O2 0:C1451 4.7 51.0 1.0 N9 0:G1452 4.7 53.9 1.0 N3 0:G1452 4.8 53.5 1.0

Chlorine binding site 2 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9305 b:71.2 occ:1.00 O 0:HOH5206 2.9 60.2 1.0 N2 0:G201 3.0 52.2 1.0 O 0:HOH3491 3.1 37.3 1.0 O 0:HOH4835 3.2 41.1 1.0 C5 0:C197 3.6 51.0 1.0 C5' 0:G229 3.8 56.0 1.0 O4' 0:U202 3.8 61.4 1.0 C1' 0:U202 3.9 59.5 1.0 C2 0:G201 4.1 53.2 1.0 C6 0:C197 4.2 52.0 1.0 N3 0:G201 4.2 53.5 1.0 C4' 0:G229 4.2 54.8 1.0 O3' 0:G229 4.3 53.3 1.0 N1 0:U202 4.5 59.6 1.0 O2 0:U202 4.6 62.1 1.0 O2 0:C195 4.7 48.7 1.0 N1 0:A199 4.7 65.0 1.0 O2' 0:U202 4.7 59.9 1.0 O 0:HOH3063 4.7 43.1 1.0 C4 0:C197 4.8 51.6 1.0 C2 0:A199 4.8 64.9 1.0 C2 0:U202 4.8 60.1 1.0 C3' 0:G229 4.9 54.9 1.0 N4 0:C197 4.9 53.2 1.0 C4' 0:U202 4.9 59.6 1.0 OP1 0:G229 5.0 54.7 1.0 C2' 0:U202 5.0 59.8 1.0

Chlorine binding site 3 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9311 b:52.5 occ:1.00 O Q:HOH1479 3.1 35.7 1.0 N Q:HIS53 3.2 44.2 1.0 O2' 0:C2388 3.2 38.6 1.0 CB Q:PHE52 3.6 43.2 1.0 CA Q:PHE52 3.7 44.2 1.0 O4' 0:C2388 3.7 40.2 1.0 C4' 0:C2388 3.8 38.6 1.0 CE2 Q:PHE56 3.8 40.6 1.0 O Q:HOH3082 3.8 38.1 1.0 C Q:PHE52 3.9 44.9 1.0 C1' 0:C2388 3.9 40.2 1.0 CB Q:HIS53 4.0 44.2 1.0 CD2 Q:PHE56 4.0 39.0 1.0 CG2 Q:ILE84 4.0 42.6 1.0 C2' 0:C2388 4.1 39.7 1.0 CA Q:HIS53 4.2 43.4 1.0 O 0:HOH3887 4.2 61.5 1.0 C3' 0:C2388 4.5 40.5 1.0 CG1 Q:ILE84 4.6 44.8 1.0 CB Q:ILE84 4.8 43.7 1.0 O 0:HOH3456 4.8 52.7 1.0 C5' 0:C2388 4.9 40.5 1.0 CD1 Q:ILE84 4.9 48.6 1.0 O3' 0:C2388 4.9 39.7 1.0 CG Q:PHE52 5.0 42.9 1.0

Chlorine binding site 4 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9313 b:61.1 occ:1.00 O 0:HOH4957 2.6 0.6 1.0 N1 0:A1329 2.9 41.1 1.0 N6 0:A1328 3.6 35.8 1.0 O 0:HOH5249 3.6 65.1 1.0 C2 0:A1329 3.6 39.8 1.0 O 0:HOH3942 3.6 32.7 1.0 O2' 0:G1300 3.7 38.9 1.0 O Y:HOH8123 3.8 43.9 1.0 C6 0:A1329 3.8 39.1 1.0 O 0:HOH5134 3.9 44.8 1.0 N6 0:A1329 3.9 41.2 1.0 N2 0:G1299 3.9 36.3 1.0 C1' 0:G1300 4.2 39.3 1.0 O4' 0:G1300 4.3 38.4 1.0 N1 0:A1330 4.3 39.1 1.0 C2' 0:G1300 4.6 39.9 1.0 N3 0:G1299 4.7 38.2 1.0 C2 0:A1330 4.8 39.7 1.0 C2 0:G1299 4.8 37.4 1.0 C4' 0:G1300 4.8 40.1 1.0 C6 0:A1328 4.9 34.0 1.0 N3 0:A1329 4.9 41.0 1.0 NH2 Y:ARG169 5.0 42.6 1.0

Chlorine binding site 5 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9314 b:54.0 occ:1.00 O2' 0:G644 3.0 34.2 1.0 ND1 L:HIS13 3.1 31.4 1.0 O 0:HOH7895 3.2 46.3 1.0 C2' 0:G644 3.5 32.9 1.0 N9 0:G644 3.6 31.6 1.0 C4 0:G644 3.7 31.2 1.0 C8 0:G644 3.9 34.5 1.0 C1' 0:G644 4.0 32.5 1.0 CE1 L:HIS13 4.0 29.6 1.0 CG L:GLN7 4.0 38.2 1.0 CG L:HIS13 4.1 32.6 1.0 C5 0:G644 4.1 32.4 1.0 N3 0:G644 4.2 33.6 1.0 N7 0:G644 4.2 33.6 1.0 CB L:HIS13 4.2 28.9 1.0 CG L:LYS4 4.4 42.1 1.0 O 0:HOH3490 4.6 52.6 1.0 CB L:GLN7 4.6 36.2 1.0 C2 0:G644 4.8 34.6 1.0 C6 0:G644 4.9 34.1 1.0 C3' 0:G644 5.0 34.3 1.0

Chlorine binding site 6 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9315 b:84.6 occ:1.00 N6 0:A1598 3.1 48.4 1.0 N6 0:A1597 3.4 49.7 1.0 N2 0:G1646 3.4 61.6 1.0 O 0:HOH7018 4.0 63.0 1.0 N7 0:A1597 4.0 52.0 1.0 C1' 0:G1647 4.0 55.9 1.0 O4' 0:G1647 4.1 55.4 1.0 C6 0:A1598 4.1 49.3 1.0 C1' 0:G1540 4.3 64.6 1.0 C6 0:A1597 4.4 50.7 1.0 C2 0:G1646 4.4 62.1 1.0 C5 0:A1597 4.6 52.1 1.0 N3 0:G1646 4.6 62.4 1.0 O4' 0:G1540 4.8 62.2 1.0 O2' 0:U1596 4.8 63.3 1.0 C5 0:A1598 4.8 49.2 1.0 N3 0:G1540 4.8 67.3 1.0 N9 0:G1647 4.9 57.8 1.0 N1 0:A1598 4.9 50.1 1.0 N7 0:A1598 4.9 50.2 1.0 O2' 0:G1647 4.9 51.7 1.0 N9 0:G1540 5.0 66.0 1.0 O2' 0:G1540 5.0 66.2 1.0

Chlorine binding site 7 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9316 b:61.1 occ:1.00 NZ J:LYS56 3.2 44.5 1.0 O2' 0:G1119 3.3 38.1 1.0 N4 0:C1243 3.3 37.0 1.0 C8 0:G1119 3.3 37.6 1.0 CD J:LYS56 3.8 43.9 1.0 NE2 J:GLN52 3.9 51.6 1.0 N7 0:G1119 3.9 37.8 1.0 C2' 0:G1119 3.9 37.9 1.0 CE J:LYS56 4.0 43.5 1.0 OE1 J:GLN52 4.0 51.5 1.0 N9 0:G1119 4.1 36.6 1.0 CD J:GLN52 4.4 52.4 1.0 C4 0:C1243 4.4 39.9 1.0 C1' 0:G1119 4.5 36.9 1.0 C5 0:C1243 4.6 39.7 1.0 N6 0:A1242 4.7 38.6 1.0 O 0:HOH7160 4.9 68.0 1.0 NA 0:NA9102 4.9 45.0 1.0 C5 0:G1119 4.9 34.4 1.0 O 0:HOH3753 4.9 41.0 1.0 O6 0:G1121 4.9 37.2 1.0

Chlorine binding site 8 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9317 b:64.7 occ:1.00 O Y:HOH8145 2.8 86.3 1.0 O2' 0:C594 2.9 48.2 1.0 O Y:HOH8183 3.1 48.5 1.0 O Y:HOH8125 3.1 56.1 1.0 CG Y:ARG115 3.5 51.9 1.0 O4' 0:U595 3.6 54.1 1.0 C5' 0:U595 3.7 49.4 1.0 C4' 0:U595 3.7 53.2 1.0 CD Y:ARG115 3.8 53.2 1.0 NE Y:ARG115 3.8 57.2 1.0 NH2 Y:ARG122 3.8 50.0 1.0 C2' 0:C594 3.9 50.3 1.0 O Y:HOH8177 4.2 67.5 1.0 O2 0:C594 4.6 55.5 1.0 C1' 0:C594 4.7 52.1 1.0 CZ Y:ARG115 4.8 59.0 1.0 C1' 0:U595 4.8 55.0 1.0 O5' 0:U595 4.9 47.2 1.0 CB Y:ARG115 4.9 49.7 1.0 CZ Y:ARG122 4.9 48.7 1.0 NE2 Y:GLN119 5.0 36.5 1.0

Chlorine binding site 9 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9320 b:49.0 occ:1.00 O 0:HOH5235 3.0 40.3 1.0 O 0:HOH3942 3.3 32.7 1.0 O 0:HOH3680 3.4 52.0 1.0 NE Y:ARG169 3.5 39.2 1.0 NH2 Y:ARG169 3.6 42.6 1.0 C5' 0:G1269 3.8 47.0 1.0 N6 0:A1328 3.8 35.8 1.0 CZ Y:ARG169 4.0 41.9 1.0 C4' 0:G1269 4.1 45.9 1.0 O3' 0:G1269 4.2 42.8 1.0 C6 0:A1328 4.2 34.0 1.0 MG 0:MG8075 4.5 43.6 1.0 N1 0:A1328 4.5 32.9 1.0 CG Y:ARG169 4.7 40.2 1.0 CD Y:ARG169 4.7 39.5 1.0 C3' 0:G1269 4.8 44.2 1.0 C5 0:A1328 4.8 32.8 1.0 OP1 0:U1270 4.9 41.0 1.0 O5' 0:G1269 5.0 47.2 1.0 OP1 0:G1269 5.0 48.8 1.0

Chlorine binding site 10 out of 22 in the The Structure of the Transition State Analogue "Daa" 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 the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl9322 b:93.0 occ:1.00 N1 0:G1072 3.0 33.0 1.0 C8 0:G1087 3.3 38.1 1.0 O 0:HOH5615 3.5 53.2 1.0 O2' 0:G1087 3.5 48.8 1.0 N2 0:G1072 3.5 30.6 1.0 N7 0:G1087 3.7 39.0 1.0 C2 0:G1072 3.8 32.7 1.0 O6 0:G1072 3.8 37.4 1.0 C6 0:G1072 3.9 33.9 1.0 N7 0:A1291 3.9 40.4 1.0 N9 0:G1087 3.9 39.3 1.0 C2' 0:G1087 3.9 44.1 1.0 C5 0:A1291 4.1 40.2 1.0 N6 0:A1291 4.2 40.1 1.0 O 0:HOH9463 4.3 40.6 1.0 C6 0:A1291 4.3 40.4 1.0 OE2 W:GLU10 4.3 55.2 1.0 C1' 0:G1087 4.4 42.9 1.0 C5 0:G1087 4.4 39.0 1.0 C8 0:A1291 4.5 38.5 1.0 C4 0:G1087 4.6 38.3 1.0 C4 0:A1291 4.9 40.4 1.0 O 0:HOH4335 4.9 63.4 1.0

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006