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Chlorine in PDB 1vq7: The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq7 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 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.150, 300.130, 573.290, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.5

Other elements in 1vq7:

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

Magnesium (Mg) 118 atoms
Potassium (K) 3 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 The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vq7). 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 1vq7

Go back to Chlorine Binding Sites List in 1vq7
Chlorine binding site 1 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9303

b:54.8
occ:1.00
 O 0:HOH9746 3.4 35.9 1.0
N2 0:G1676 3.4 42.3 1.0
CE 2:LYS2 3.5 41.1 1.0
O 0:HOH6104 3.7 51.2 1.0
O 0:HOH3889 3.7 52.5 1.0
O 0:HOH7793 3.7 63.8 1.0
C1' 0:G1452 4.0 44.9 1.0
O2' 0:G1452 4.2 45.2 1.0
C2 0:A1486 4.2 41.0 1.0
N3 0:A1486 4.2 41.9 1.0
NZ 2:LYS2 4.3 44.8 1.0
C2 0:G1676 4.4 42.5 1.0
N3 0:G1676 4.5 43.7 1.0
O 0:HOH5029 4.5 53.9 1.0
CD 2:LYS2 4.5 42.0 1.0
O4' 0:G1452 4.6 44.4 1.0
C2' 0:G1452 4.6 43.4 1.0
N3 0:G1452 4.8 44.1 1.0
O2 0:C1451 4.8 49.5 1.0
N9 0:G1452 4.9 44.4 1.0

Chlorine binding site 2 out of 22 in 1vq7

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Chlorine binding site 2 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9305

b:52.1
occ:1.00
 N2 0:G201 3.1 50.2 1.0
O 0:HOH5221 3.3 59.6 1.0
O 0:HOH4857 3.5 40.3 1.0
O 0:HOH3506 3.5 32.4 1.0
C5 0:C197 3.7 43.3 1.0
C5' 0:G229 3.8 47.8 1.0
C1' 0:U202 3.9 51.5 1.0
O4' 0:U202 4.0 53.5 1.0
C2 0:G201 4.1 51.0 1.0
C4' 0:G229 4.2 48.4 1.0
O3' 0:G229 4.3 46.4 1.0
N3 0:G201 4.3 52.1 1.0
C6 0:C197 4.4 44.6 1.0
O2 0:U202 4.5 51.6 1.0
N1 0:U202 4.5 50.7 1.0
O2 0:C195 4.6 41.0 1.0
O2' 0:U202 4.6 50.6 1.0
N1 0:A199 4.7 52.8 1.0
C2 0:U202 4.7 50.0 1.0
C4 0:C197 4.7 44.7 1.0
N4 0:C197 4.8 46.0 1.0
C2 0:A199 4.8 54.0 1.0
O 0:HOH3069 4.9 56.6 1.0
C3' 0:G229 4.9 47.9 1.0
C2' 0:U202 4.9 52.8 1.0
OP1 0:G229 4.9 49.3 1.0
O5' 0:G229 5.0 49.5 1.0

Chlorine binding site 3 out of 22 in 1vq7

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Chlorine binding site 3 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9311

b:51.2
occ:1.00
 N Q:HIS53 3.1 43.4 1.0
O2' 0:C2388 3.1 37.3 1.0
O 0:HOH3486 3.2 31.9 1.0
CB Q:PHE52 3.6 42.1 1.0
CA Q:PHE52 3.6 43.2 1.0
O 0:HOH4718 3.7 38.8 1.0
CE2 Q:PHE56 3.8 35.3 1.0
O4' 0:C2388 3.8 36.2 1.0
C Q:PHE52 3.8 43.8 1.0
C4' 0:C2388 3.8 38.2 1.0
CB Q:HIS53 3.9 42.4 1.0
CD2 Q:PHE56 4.0 34.9 1.0
C1' 0:C2388 4.0 37.0 1.0
CA Q:HIS53 4.0 41.8 1.0
C2' 0:C2388 4.1 37.3 1.0
CG2 Q:ILE84 4.2 40.5 1.0
O 0:HOH3908 4.4 50.8 1.0
C3' 0:C2388 4.5 38.1 1.0
CG1 Q:ILE84 4.6 42.4 1.0
O3' 0:C2388 4.9 38.5 1.0
CB Q:ILE84 4.9 43.0 1.0
CD1 Q:ILE84 4.9 47.5 1.0
C5' 0:C2388 5.0 38.7 1.0
CG Q:PHE52 5.0 43.5 1.0

Chlorine binding site 4 out of 22 in 1vq7

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Chlorine binding site 4 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9312

b:53.0
occ:1.00
 O K:HOH4058 3.0 52.3 1.0
NZ K:LYS14 3.2 43.2 1.0
N2 0:G2582 3.3 43.3 1.0
OG K:SER33 3.3 53.1 1.0
C2 0:A2596 3.4 43.9 1.0
N3 0:A2596 3.6 44.4 1.0
O K:ILE32 3.6 51.2 1.0
CB K:SER33 3.9 49.9 1.0
O K:HOH7499 4.0 67.6 1.0
CA K:SER33 4.1 49.2 1.0
CG K:PRO45 4.1 44.6 1.0
CD K:LYS14 4.1 39.0 1.0
C1' 0:U2597 4.1 50.3 1.0
CE K:LYS14 4.1 39.6 1.0
N3 0:A2583 4.4 44.8 1.0
CB K:PRO45 4.4 42.4 1.0
O2' 0:U2597 4.4 50.1 1.0
N1 0:A2596 4.5 43.0 1.0
C K:ILE32 4.6 50.2 1.0
C2 0:G2582 4.6 41.0 1.0
O4' 0:U2597 4.7 50.9 1.0
O2 0:U2597 4.7 48.3 1.0
CG K:LYS14 4.9 38.5 1.0
C1' 0:A2583 4.9 41.1 1.0
N K:SER33 4.9 49.5 1.0
C2' 0:U2597 4.9 49.2 1.0
N1 0:U2597 4.9 50.9 1.0
C4 0:A2596 4.9 45.7 1.0
C2 0:A2583 5.0 41.8 1.0
C4 0:A2583 5.0 43.9 1.0

Chlorine binding site 5 out of 22 in 1vq7

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Chlorine binding site 5 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9313

b:62.4
occ:1.00
 O 0:HOH4978 2.7 0.3 1.0
N1 0:A1329 2.9 39.2 1.0
O 0:HOH5264 3.0 65.7 1.0
N6 0:A1328 3.4 33.3 1.0
C2 0:A1329 3.5 34.9 1.0
O 0:HOH3961 3.6 35.5 1.0
O2' 0:G1300 3.8 37.6 1.0
C6 0:A1329 3.9 37.0 1.0
N2 0:G1299 4.0 36.8 1.0
O Y:HOH8121 4.0 39.8 1.0
N6 0:A1329 4.1 39.0 1.0
C1' 0:G1300 4.2 39.5 1.0
O4' 0:G1300 4.4 40.7 1.0
N1 0:A1330 4.4 35.7 1.0
C2' 0:G1300 4.7 39.9 1.0
O 0:HOH5148 4.7 51.6 1.0
N3 0:G1299 4.7 39.9 1.0
C6 0:A1328 4.7 31.2 1.0
C2 0:G1299 4.8 37.6 1.0
N3 0:A1329 4.8 35.3 1.0
C2 0:A1330 4.8 34.5 1.0
C4' 0:G1300 4.9 40.0 1.0
NH2 Y:ARG169 4.9 36.7 1.0

Chlorine binding site 6 out of 22 in 1vq7

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Chlorine binding site 6 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9314

b:51.0
occ:1.00
 O2' 0:G644 3.0 35.1 1.0
O L:HOH9392 3.0 36.1 1.0
ND1 L:HIS13 3.1 26.4 1.0
C2' 0:G644 3.6 32.4 1.0
N9 0:G644 3.7 27.2 1.0
C4 0:G644 3.9 24.6 1.0
CG L:GLN7 3.9 36.4 1.0
CE1 L:HIS13 3.9 25.0 1.0
C8 0:G644 4.0 26.9 1.0
C1' 0:G644 4.1 31.4 1.0
CG L:HIS13 4.1 27.6 1.0
C5 0:G644 4.2 25.6 1.0
CB L:HIS13 4.2 28.1 1.0
CG L:LYS4 4.3 41.9 1.0
N3 0:G644 4.3 23.2 1.0
N7 0:G644 4.3 27.8 1.0
O 0:HOH3505 4.5 58.2 1.0
CB L:GLN7 4.6 35.5 1.0
CA L:LYS4 4.9 37.0 1.0
O 0:HOH7338 4.9 67.5 1.0
CD L:GLN7 5.0 40.3 1.0
C2 0:G644 5.0 25.2 1.0
C6 0:G644 5.0 25.2 1.0

Chlorine binding site 7 out of 22 in 1vq7

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Chlorine binding site 7 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9315

b:69.7
occ:1.00
 N2 0:G1646 3.1 54.2 1.0
N6 0:A1598 3.2 47.5 1.0
N6 0:A1597 3.5 41.0 1.0
O 0:HOH7032 3.9 68.5 1.0
O4' 0:G1647 4.0 50.0 1.0
C1' 0:G1647 4.0 51.5 1.0
C2 0:G1646 4.1 54.6 1.0
N7 0:A1597 4.2 43.7 1.0
C6 0:A1598 4.2 46.3 1.0
N3 0:G1646 4.3 54.9 1.0
C1' 0:G1540 4.3 57.4 1.0
C6 0:A1597 4.6 43.2 1.0
N3 0:G1540 4.6 58.5 1.0
C5 0:A1597 4.8 44.3 1.0
N9 0:G1647 4.8 53.9 1.0
O2' 0:G1540 4.9 57.5 1.0
O4' 0:G1540 4.9 55.9 1.0
O2' 0:G1647 4.9 50.5 1.0
O2' 0:U1596 4.9 58.8 1.0
C5 0:A1598 4.9 47.0 1.0
N9 0:G1540 5.0 58.4 1.0

Chlorine binding site 8 out of 22 in 1vq7

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Chlorine binding site 8 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9316

b:56.4
occ:1.00
 O2' 0:G1119 3.0 41.6 1.0
N4 0:C1243 3.2 36.3 1.0
NZ J:LYS56 3.2 41.7 1.0
C8 0:G1119 3.4 34.3 1.0
CD J:LYS56 3.7 44.5 1.0
C2' 0:G1119 3.7 41.7 1.0
NE2 J:GLN52 3.8 51.9 1.0
CE J:LYS56 4.0 43.4 1.0
N7 0:G1119 4.0 33.9 1.0
N9 0:G1119 4.0 35.9 1.0
O 0:HOH7181 4.1 74.9 1.0
OE1 J:GLN52 4.3 51.5 1.0
C4 0:C1243 4.3 36.5 1.0
C1' 0:G1119 4.4 39.6 1.0
CD J:GLN52 4.4 52.3 1.0
N6 0:A1242 4.6 42.3 1.0
C5 0:C1243 4.6 36.3 1.0
O6 0:G1121 4.9 41.0 1.0
C5 0:G1119 4.9 33.1 1.0
C4 0:G1119 4.9 32.4 1.0
NA 0:NA9102 4.9 42.7 1.0

Chlorine binding site 9 out of 22 in 1vq7

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Chlorine binding site 9 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9317

b:61.9
occ:1.00
 O2' 0:C594 2.9 54.6 1.0
O Y:HOH8142 3.0 0.2 1.0
O Y:HOH8123 3.4 48.1 1.0
O Y:HOH8185 3.5 46.4 1.0
O4' 0:U595 3.5 58.4 1.0
CG Y:ARG115 3.6 47.1 1.0
CD Y:ARG115 3.7 45.6 1.0
C4' 0:U595 3.7 56.7 1.0
NE Y:ARG115 3.7 45.4 1.0
C5' 0:U595 3.8 53.0 1.0
C2' 0:C594 3.8 57.1 1.0
O 0:HOH6786 3.9 69.7 1.0
NH2 Y:ARG122 4.1 49.7 1.0
O Y:HOH8174 4.2 86.1 1.0
O2 0:C594 4.4 60.9 1.0
C1' 0:C594 4.6 59.1 1.0
C1' 0:U595 4.7 58.9 1.0
CZ Y:ARG115 4.9 46.6 1.0
O5' 0:U595 4.9 50.5 1.0

Chlorine binding site 10 out of 22 in 1vq7

Go back to Chlorine Binding Sites List in 1vq7
Chlorine binding site 10 out of 22 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl9320

b:48.1
occ:1.00
 O 0:HOH5250 3.1 35.4 1.0
O 0:HOH3961 3.2 35.5 1.0
O 0:HOH3696 3.4 37.4 1.0
NE Y:ARG169 3.5 39.7 1.0
NH2 Y:ARG169 3.5 36.7 1.0
C5' 0:G1269 3.7 48.0 1.0
N6 0:A1328 3.8 33.3 1.0
O3' 0:G1269 4.0 44.2 1.0
CZ Y:ARG169 4.0 38.4 1.0
C4' 0:G1269 4.0 46.0 1.0
C6 0:A1328 4.2 31.2 1.0
MG 0:MG8075 4.3 40.0 1.0
N1 0:A1328 4.5 31.3 1.0
O 0:HOH8148 4.6 40.7 1.0
C3' 0:G1269 4.6 44.6 1.0
CG Y:ARG169 4.7 41.3 1.0
CD Y:ARG169 4.7 41.3 1.0
OP1 0:U1270 4.8 48.3 1.0
C5 0:A1328 4.9 30.9 1.0
P 0:U1270 5.0 44.0 1.0
O5' 0:G1269 5.0 49.3 1.0

Reference:

T.M.Schmeing, K.S.Huang, S.A.Strobel, T.A.Steitz. An Induced-Fit Mechanism to Promote Peptide Bond Formation and Exclude Hydrolysis of Peptidyl-Trna. Nature V. 438 520 2005.
ISSN: ISSN 0028-0836
PubMed: 16306996
DOI: 10.1038/NATURE04152
Page generated: Sat Jul 20 03:07:56 2024

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