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Chlorine in PDB 2otj: 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj was solved by G.Blaha, S.J.Schroeder, J.Tirado-Rives, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.70 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.738, 299.519, 573.593, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.8

Other elements in 2otj:

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 117 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Sodium (Na) 86 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui (pdb code 2otj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 2otj

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Chlorine binding site 1 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8803

b:56.4
occ:1.00
N2 0:G1676 3.2 47.1 1.0
O 0:HOH9430 3.4 53.0 1.0
O 0:HOH3584 3.4 52.5 1.0
O 0:HOH5852 3.5 51.3 1.0
CE 2:LYS2 3.7 43.7 1.0
C1' 0:G1452 3.8 50.9 1.0
O2' 0:G1452 3.8 52.0 1.0
O 0:HOH7579 4.0 63.5 1.0
N3 0:A1486 4.1 43.4 1.0
C2 0:A1486 4.2 42.5 1.0
C2 0:G1676 4.3 46.5 1.0
C2' 0:G1452 4.4 50.7 1.0
N3 0:G1676 4.4 47.1 1.0
O4' 0:G1452 4.4 50.8 1.0
O2 0:C1451 4.6 48.5 1.0
CD 2:LYS2 4.6 43.9 1.0
O 2:HOH3526 4.6 47.9 1.0
N3 0:G1452 4.6 51.8 1.0
N9 0:G1452 4.7 51.3 1.0
NZ 2:LYS2 4.7 45.8 1.0

Chlorine binding site 2 out of 22 in 2otj

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Chlorine binding site 2 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8805

b:71.6
occ:1.00
O 0:HOH4937 3.3 60.5 1.0
O 0:HOH4569 3.4 46.3 1.0
N2 0:G201 3.4 56.8 1.0
C5 0:C197 3.4 60.2 1.0
O 0:HOH3199 3.6 49.6 1.0
C5' 0:G229 3.8 48.8 1.0
O4' 0:U202 3.8 55.9 1.0
C1' 0:U202 3.9 55.2 1.0
O3' 0:G229 4.0 48.3 1.0
C4' 0:G229 4.1 47.6 1.0
C6 0:C197 4.2 59.8 1.0
N4 0:C197 4.3 60.8 1.0
C4 0:C197 4.3 60.5 1.0
C2 0:G201 4.4 56.7 1.0
N3 0:G201 4.5 57.2 1.0
O2' 0:U202 4.7 56.2 1.0
N1 0:U202 4.7 54.4 1.0
OP1 0:G229 4.7 50.7 1.0
C3' 0:G229 4.7 47.6 1.0
O2 0:U202 4.7 53.8 1.0
OP1 0:C230 4.7 50.4 1.0
O2 0:C195 4.8 48.3 1.0
C4' 0:U202 4.8 56.2 1.0
N1 0:A199 4.8 67.0 1.0
O5' 0:G229 4.9 50.3 1.0
C2 0:U202 5.0 53.9 1.0
C2' 0:U202 5.0 55.9 1.0
P 0:C230 5.0 49.5 1.0

Chlorine binding site 3 out of 22 in 2otj

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Chlorine binding site 3 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8811

b:58.5
occ:1.00
N Q:HIS53 2.9 47.7 1.0
O 0:HOH3178 2.9 32.8 1.0
O2' 0:C2388 3.2 42.7 1.0
CB Q:HIS53 3.6 47.1 1.0
CA Q:PHE52 3.6 47.5 1.0
CE2 Q:PHE56 3.6 42.9 1.0
CB Q:PHE52 3.6 47.2 1.0
C Q:PHE52 3.7 47.8 1.0
CD2 Q:PHE56 3.8 42.9 1.0
CA Q:HIS53 3.8 47.0 1.0
C4' 0:C2388 3.9 42.8 1.0
O 0:HOH3603 4.0 51.3 1.0
O4' 0:C2388 4.0 43.3 1.0
C1' 0:C2388 4.1 43.6 1.0
O Q:HOH3082 4.1 58.2 1.0
C2' 0:C2388 4.1 42.9 1.0
CG2 Q:ILE84 4.2 47.9 1.0
C3' 0:C2388 4.6 42.0 1.0
CG1 Q:ILE84 4.7 47.7 1.0
O Q:PHE52 4.9 47.9 1.0
CB Q:ILE84 4.9 47.5 1.0
C Q:HIS53 4.9 46.0 1.0
CG Q:PHE52 4.9 47.5 1.0
CZ Q:PHE56 4.9 42.0 1.0
O3' 0:C2388 4.9 40.7 1.0
O Q:HIS53 5.0 46.5 1.0
CG Q:HIS53 5.0 48.1 1.0

Chlorine binding site 4 out of 22 in 2otj

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Chlorine binding site 4 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8812

b:49.3
occ:1.00
O 0:HOH5126 2.8 37.4 1.0
NZ K:LYS14 3.1 40.8 1.0
N2 0:G2582 3.4 38.5 1.0
C2 0:A2596 3.5 42.3 1.0
OG K:SER33 3.5 49.5 1.0
N3 0:A2596 3.6 42.5 1.0
O K:ILE32 3.7 47.2 1.0
CD K:LYS14 3.8 40.3 1.0
O 0:HOH7590 3.9 60.0 1.0
CG K:PRO45 4.0 44.6 1.0
CE K:LYS14 4.0 41.0 1.0
CB K:SER33 4.0 48.1 1.0
CA K:SER33 4.1 48.2 1.0
C1' 0:U2597 4.1 44.0 1.0
CB K:PRO45 4.2 44.8 1.0
O2' 0:U2597 4.4 45.1 1.0
N3 0:A2583 4.5 40.4 1.0
O2 0:U2597 4.5 45.2 1.0
N1 0:A2596 4.6 42.9 1.0
O 0:HOH7359 4.6 0.1 1.0
C2 0:G2582 4.7 38.2 1.0
C K:ILE32 4.7 47.0 1.0
O4' 0:U2597 4.8 44.1 1.0
C1' 0:A2583 4.8 39.8 1.0
C2' 0:U2597 4.8 43.6 1.0
CG K:LYS14 4.9 41.4 1.0
N K:SER33 4.9 47.6 1.0
N1 0:U2597 4.9 44.5 1.0
N K:VAL34 4.9 48.2 1.0
C4 0:A2596 5.0 42.8 1.0
C4 0:A2583 5.0 40.2 1.0

Chlorine binding site 5 out of 22 in 2otj

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Chlorine binding site 5 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8813

b:54.8
occ:1.00
O 0:HOH4691 2.5 0.4 1.0
O 0:HOH4980 2.8 66.4 1.0
N1 0:A1329 3.0 33.5 1.0
O 0:HOH3656 3.4 39.7 1.0
N6 0:A1328 3.6 25.4 1.0
C2 0:A1329 3.6 33.0 1.0
O2' 0:G1300 3.8 38.2 1.0
O Y:HOH8836 3.9 30.1 1.0
C6 0:A1329 4.0 34.0 1.0
N2 0:G1299 4.0 37.7 1.0
C1' 0:G1300 4.1 37.0 1.0
N6 0:A1329 4.1 35.2 1.0
O4' 0:G1300 4.2 38.4 1.0
O 0:HOH4865 4.3 46.1 1.0
N1 0:A1330 4.4 34.1 1.0
C2' 0:G1300 4.6 37.2 1.0
N3 0:G1299 4.7 39.0 1.0
O 0:HOH3943 4.7 55.2 1.0
C4' 0:G1300 4.8 37.9 1.0
C2 0:G1299 4.8 38.0 1.0
C6 0:A1328 4.9 24.3 1.0
C2 0:A1330 4.9 34.0 1.0
N3 0:A1329 5.0 34.1 1.0

Chlorine binding site 6 out of 22 in 2otj

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Chlorine binding site 6 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8814

b:57.0
occ:1.00
O2' 0:G644 2.7 34.8 1.0
ND1 L:HIS13 3.0 30.9 1.0
O L:HOH8893 3.2 53.8 1.0
C2' 0:G644 3.4 32.5 1.0
N9 0:G644 3.7 28.2 1.0
C4 0:G644 3.8 27.6 1.0
CE1 L:HIS13 3.9 31.4 1.0
C1' 0:G644 3.9 30.7 1.0
CG L:GLN7 4.0 42.4 1.0
CG L:HIS13 4.0 31.2 1.0
C8 0:G644 4.0 29.8 1.0
CB L:HIS13 4.1 32.0 1.0
C5 0:G644 4.2 28.1 1.0
N3 0:G644 4.2 26.9 1.0
N7 0:G644 4.3 30.1 1.0
CG L:LYS4 4.4 42.3 1.0
CB L:GLN7 4.5 40.2 1.0
O 0:HOH3198 4.7 42.9 1.0
C2 0:G644 4.8 26.9 1.0
O L:HIS13 4.9 34.6 1.0
C3' 0:G644 4.9 32.7 1.0
C6 0:G644 4.9 28.5 1.0
CD L:GLN7 4.9 44.5 1.0
OE1 L:GLN7 5.0 45.3 1.0

Chlorine binding site 7 out of 22 in 2otj

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Chlorine binding site 7 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8815

b:89.6
occ:1.00
N6 0:A1598 3.2 54.6 1.0
N2 0:G1646 3.3 57.3 1.0
N6 0:A1597 3.7 53.0 1.0
O4' 0:G1647 3.7 54.0 1.0
C1' 0:G1647 3.8 54.4 1.0
C2 0:G1646 4.3 57.6 1.0
C6 0:A1598 4.3 53.4 1.0
N3 0:G1646 4.3 57.5 1.0
O 0:HOH6801 4.4 65.5 1.0
N7 0:A1597 4.5 51.2 1.0
C1' 0:G1540 4.5 58.9 1.0
N3 0:G1540 4.6 60.2 1.0
N9 0:G1647 4.6 55.3 1.0
O2' 0:G1647 4.7 53.4 1.0
C6 0:A1597 4.7 52.0 1.0
C4' 0:G1647 4.8 53.4 1.0
C2' 0:G1647 4.9 53.6 1.0

Chlorine binding site 8 out of 22 in 2otj

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Chlorine binding site 8 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8816

b:69.6
occ:1.00
O2' 0:G1119 3.1 38.2 1.0
NZ J:LYS56 3.2 48.6 1.0
N4 0:C1243 3.2 37.2 1.0
C8 0:G1119 3.6 34.5 1.0
CD J:LYS56 3.6 49.5 1.0
NE2 J:GLN52 3.9 56.2 1.0
CE J:LYS56 3.9 48.7 1.0
C2' 0:G1119 3.9 38.2 1.0
N7 0:G1119 4.1 34.1 1.0
OE1 J:GLN52 4.3 55.5 1.0
N9 0:G1119 4.3 34.6 1.0
O 0:HOH6955 4.3 66.6 1.0
C4 0:C1243 4.4 38.6 1.0
O 0:HOH3462 4.5 36.7 1.0
N6 0:A1242 4.6 36.9 1.0
CD J:GLN52 4.6 55.5 1.0
C1' 0:G1119 4.6 37.3 1.0
C5 0:C1243 4.7 39.3 1.0
O6 0:G1121 4.9 39.5 1.0
N7 0:A1242 4.9 39.5 1.0

Chlorine binding site 9 out of 22 in 2otj

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Chlorine binding site 9 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8822

b:90.8
occ:1.00
O 0:HOH5362 2.9 47.6 1.0
N1 0:G1072 3.1 29.9 1.0
O2' 0:G1087 3.3 43.7 1.0
N2 0:G1072 3.5 29.9 1.0
C8 0:G1087 3.6 39.6 1.0
N7 0:A1291 3.7 43.3 1.0
C2 0:G1072 3.8 30.5 1.0
C2' 0:G1087 3.9 42.7 1.0
N7 0:G1087 4.1 39.5 1.0
N9 0:G1087 4.1 39.9 1.0
O6 0:G1072 4.1 30.0 1.0
C6 0:G1072 4.1 29.8 1.0
C5 0:A1291 4.1 42.8 1.0
C8 0:A1291 4.3 42.5 1.0
O 0:HOH9147 4.4 55.0 1.0
OE2 W:GLU10 4.4 52.1 1.0
N6 0:A1291 4.4 44.8 1.0
O 0:HOH4057 4.5 64.9 1.0
C6 0:A1291 4.5 43.4 1.0
C1' 0:G1087 4.5 41.7 1.0
O 0:HOH5169 4.7 64.5 1.0
C5 0:G1087 4.7 39.2 1.0
C4 0:G1087 4.8 39.4 1.0
C4 0:A1291 4.9 42.7 1.0
N9 0:A1291 5.0 42.5 1.0

Chlorine binding site 10 out of 22 in 2otj

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Chlorine binding site 10 out of 22 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8809

b:82.8
occ:1.00
NZ A:LYS178 3.1 43.3 1.0
O 0:HOH5259 3.6 39.5 1.0
O 0:HOH6420 3.7 24.3 1.0
CE A:LYS178 3.7 43.1 1.0
CD A:LYS178 3.8 42.9 1.0
CE A:LYS175 3.8 36.4 1.0
O 0:HOH6671 4.2 52.1 1.0
CZ A:PHE169 4.2 41.4 1.0
CE1 A:PHE169 4.4 42.2 1.0
SD A:MET179 4.4 44.7 1.0
O A:HOH8869 4.7 52.1 1.0
CE A:MET179 4.7 46.3 1.0
CD A:LYS175 4.7 35.6 1.0
OP2 0:G1878 4.7 40.3 1.0
O 0:HOH3061 4.9 54.4 1.0
NZ A:LYS175 4.9 34.9 1.0
O 0:HOH5416 4.9 89.3 1.0

Reference:

S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, P.B.Moore. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula Marismortui: 13-Deoxytedanolide and Girodazole. J.Mol.Biol. V. 367 1471 2007.
ISSN: ISSN 0022-2836
PubMed: 17321546
DOI: 10.1016/J.JMB.2007.01.081
Page generated: Sat Dec 12 09:14:04 2020

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