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Chlorine in PDB 1jj2: Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution

Protein crystallography data

The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2 was solved by D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.660, 299.670, 573.770, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.2

Other elements in 1jj2:

The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution 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 Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution (pdb code 1jj2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 1jj2

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Chlorine binding site 1 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8503

b:40.4
occ:1.00
 O 0:HOH8939 3.3 24.6 1.0
N2 0:G1676 3.4 26.0 1.0
O 0:HOH5357 3.4 34.7 1.0
CE 1:LYS2 3.7 31.0 1.0
C1' 0:G1452 3.8 31.7 1.0
O 0:HOH3092 3.9 40.5 1.0
O 0:HOH7131 4.1 38.3 1.0
O2' 0:G1452 4.1 28.3 1.0
C2 0:A1486 4.2 32.0 1.0
N3 0:A1486 4.2 33.5 1.0
C2 0:G1676 4.3 29.1 1.0
O 0:HOH4244 4.4 26.1 1.0
NZ 1:LYS2 4.4 33.5 1.0
O4' 0:G1452 4.4 33.4 1.0
N3 0:G1676 4.4 28.3 1.0
C2' 0:G1452 4.6 28.9 1.0
CD 1:LYS2 4.6 29.2 1.0
O2 0:C1451 4.6 38.9 1.0
N3 0:G1452 4.7 32.9 1.0
N9 0:G1452 4.7 32.1 1.0
O 0:HOH6333 4.9 51.4 1.0

Chlorine binding site 2 out of 22 in 1jj2

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Chlorine binding site 2 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8505

b:42.0
occ:1.00
 N2 0:G201 3.1 31.4 1.0
O 0:HOH4443 3.1 42.8 1.0
O 0:HOH4072 3.3 27.9 1.0
O 0:HOH9706 3.3 26.6 1.0
C1' 0:U202 3.6 41.2 1.0
C5' 0:G229 3.7 30.9 1.0
O4' 0:U202 3.8 40.9 1.0
C5 0:C197 3.9 36.0 1.0
C4' 0:G229 4.2 31.8 1.0
C2 0:G201 4.2 34.3 1.0
O3' 0:G229 4.2 30.9 1.0
O2 0:U202 4.3 38.8 1.0
O2' 0:U202 4.3 42.3 1.0
N1 0:U202 4.4 40.1 1.0
N3 0:G201 4.4 35.6 1.0
O2 0:C195 4.5 25.6 1.0
O 0:HOH9272 4.6 29.9 1.0
C6 0:C197 4.6 35.8 1.0
C2 0:U202 4.6 38.3 1.0
C2' 0:U202 4.7 41.5 1.0
N4 0:C197 4.8 35.6 1.0
C3' 0:G229 4.8 31.2 1.0
C4' 0:U202 4.8 40.5 1.0
C4 0:C197 4.8 36.4 1.0
OP1 0:C230 4.8 37.8 1.0
OP1 0:G229 4.9 33.9 1.0
O5' 0:G229 4.9 33.2 1.0
N1 0:A199 4.9 39.9 1.0

Chlorine binding site 3 out of 22 in 1jj2

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Chlorine binding site 3 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8511

b:37.1
occ:1.00
 N P:HIS53 3.1 30.9 1.0
O P:HOH1479 3.2 25.3 1.0
O2' 0:C2388 3.2 25.0 1.0
CB P:PHE52 3.6 27.8 1.0
CA P:PHE52 3.7 29.6 1.0
C4' 0:C2388 3.9 28.2 1.0
O4' 0:C2388 3.9 27.9 1.0
C P:PHE52 3.9 31.4 1.0
CB P:HIS53 3.9 30.2 1.0
O 0:HOH3926 3.9 35.4 1.0
CE2 P:PHE56 3.9 22.9 1.0
CD2 P:PHE56 4.0 24.5 1.0
C1' 0:C2388 4.0 26.9 1.0
CA P:HIS53 4.1 29.1 1.0
C2' 0:C2388 4.1 28.0 1.0
CG2 P:ILE84 4.1 27.5 1.0
O 0:HOH3111 4.4 30.9 1.0
C3' 0:C2388 4.6 27.9 1.0
CG1 P:ILE84 4.7 31.0 1.0
O 0:HOH9670 4.8 40.0 1.0
CB P:ILE84 4.9 31.4 1.0
O3' 0:C2388 4.9 28.6 1.0
C5' 0:C2388 4.9 28.8 1.0
CG P:PHE52 5.0 27.8 1.0

Chlorine binding site 4 out of 22 in 1jj2

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Chlorine binding site 4 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8512

b:34.9
occ:1.00
 O 0:HOH4634 2.9 25.5 1.0
NZ J:LYS14 3.2 25.1 1.0
OG J:SER33 3.2 34.2 1.0
N2 0:G2582 3.4 31.0 1.0
C2 0:A2596 3.4 30.3 1.0
O 0:HOH7142 3.5 46.0 1.0
N3 0:A2596 3.6 31.4 1.0
O J:ILE32 3.7 36.9 1.0
CB J:SER33 3.7 32.9 1.0
CG J:PRO45 3.9 35.6 1.0
CD J:LYS14 3.9 26.7 1.0
CA J:SER33 4.0 33.5 1.0
CE J:LYS14 4.0 27.2 1.0
C1' 0:U2597 4.0 35.6 1.0
CB J:PRO45 4.2 33.5 1.0
O2' 0:U2597 4.4 37.2 1.0
O2 0:U2597 4.4 34.6 1.0
N3 0:A2583 4.5 28.6 1.0
N1 0:A2596 4.6 31.9 1.0
C J:ILE32 4.6 35.5 1.0
O J:HOH7169 4.6 0.8 1.0
O4' 0:U2597 4.6 36.0 1.0
C2 0:G2582 4.7 30.2 1.0
CG J:LYS14 4.8 28.0 1.0
N1 0:U2597 4.8 35.0 1.0
N J:SER33 4.8 33.8 1.0
C2' 0:U2597 4.8 35.4 1.0
C4 0:A2596 4.9 32.1 1.0
C1' 0:A2583 4.9 27.5 1.0
N J:VAL34 4.9 33.1 1.0
C2 0:U2597 4.9 34.0 1.0

Chlorine binding site 5 out of 22 in 1jj2

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Chlorine binding site 5 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8513

b:44.1
occ:1.00
 O 0:HOH4193 2.9 90.6 1.0
N1 0:A1329 3.1 24.1 1.0
O 0:HOH4487 3.3 49.5 1.0
N2 0:G1299 3.5 21.5 1.0
O 0:HOH3163 3.6 23.2 1.0
O2' 0:G1300 3.6 28.5 1.0
C2 0:A1329 3.7 20.8 1.0
N6 0:A1328 3.7 20.8 1.0
C1' 0:G1300 3.9 28.2 1.0
O4' 0:G1300 4.0 29.9 1.0
O X:HOH8534 4.2 31.7 1.0
C6 0:A1329 4.2 23.2 1.0
N3 0:G1299 4.3 27.2 1.0
N1 0:A1330 4.4 19.4 1.0
C2 0:G1299 4.4 27.1 1.0
C2' 0:G1300 4.4 29.3 1.0
N6 0:A1329 4.4 26.0 1.0
C4' 0:G1300 4.6 29.7 1.0
C2 0:A1330 4.6 17.7 1.0
C6 0:A1328 5.0 22.6 1.0
N3 0:A1329 5.0 22.8 1.0

Chlorine binding site 6 out of 22 in 1jj2

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Chlorine binding site 6 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8514

b:36.8
occ:1.00
 O2' 0:G644 3.0 24.9 1.0
ND1 K:HIS13 3.0 15.0 1.0
O K:HOH8590 3.0 41.6 1.0
C2' 0:G644 3.5 22.6 1.0
N9 0:G644 3.6 19.1 1.0
C4 0:G644 3.7 15.4 1.0
CE1 K:HIS13 3.9 14.5 1.0
C8 0:G644 3.9 18.5 1.0
C1' 0:G644 3.9 20.1 1.0
CG K:HIS13 3.9 17.1 1.0
CG K:GLN7 4.0 25.1 1.0
N3 0:G644 4.1 15.7 1.0
CB K:HIS13 4.1 18.9 1.0
C5 0:G644 4.1 17.0 1.0
N7 0:G644 4.3 20.2 1.0
CG K:LYS4 4.3 32.5 1.0
CB K:GLN7 4.5 22.1 1.0
C2 0:G644 4.8 17.8 1.0
CE K:LYS4 4.8 38.7 1.0
CD K:LYS4 4.9 36.0 1.0
C6 0:G644 4.9 17.7 1.0
CA K:LYS4 4.9 25.2 1.0
C3' 0:G644 4.9 21.7 1.0

Chlorine binding site 7 out of 22 in 1jj2

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Chlorine binding site 7 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8515

b:48.3
occ:1.00
 N6 0:A1598 3.2 35.8 1.0
N2 0:G1646 3.3 39.5 1.0
N6 0:A1597 3.5 34.3 1.0
O 0:HOH6329 3.6 56.1 1.0
C1' 0:G1647 4.0 39.8 1.0
O4' 0:G1647 4.0 41.0 1.0
N7 0:A1597 4.1 34.3 1.0
C6 0:A1598 4.2 36.9 1.0
C2 0:G1646 4.3 41.4 1.0
C1' 0:G1540 4.3 45.0 1.0
N3 0:G1646 4.4 42.6 1.0
C6 0:A1597 4.5 35.5 1.0
N3 0:G1540 4.6 45.5 1.0
C5 0:A1597 4.7 34.1 1.0
O2' 0:U1596 4.8 38.7 1.0
O4' 0:G1540 4.8 44.1 1.0
N9 0:G1647 4.8 41.0 1.0
O2' 0:G1647 4.9 39.2 1.0
N9 0:G1540 4.9 46.3 1.0
C5 0:A1598 4.9 36.4 1.0
O2' 0:G1540 4.9 47.4 1.0
N1 0:A1598 5.0 35.1 1.0

Chlorine binding site 8 out of 22 in 1jj2

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Chlorine binding site 8 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8516

b:42.4
occ:1.00
 O2' 0:G1119 3.1 30.2 1.0
NZ I:LYS56 3.3 29.6 1.0
N4 0:C1243 3.3 29.4 1.0
C8 0:G1119 3.4 24.9 1.0
CD I:LYS56 3.6 30.1 1.0
C2' 0:G1119 3.9 28.7 1.0
NE2 I:GLN52 3.9 40.3 1.0
CE I:LYS56 4.0 29.1 1.0
N7 0:G1119 4.0 25.6 1.0
N9 0:G1119 4.1 25.9 1.0
OE1 I:GLN52 4.1 40.4 1.0
C4 0:C1243 4.4 30.5 1.0
CD I:GLN52 4.5 39.7 1.0
C1' 0:G1119 4.5 28.4 1.0
C5 0:C1243 4.6 29.7 1.0
N6 0:A1242 4.7 25.8 1.0
O 0:HOH6479 4.8 67.4 1.0
C5 0:G1119 5.0 24.3 1.0
O6 0:G1121 5.0 30.1 1.0
CG I:LYS56 5.0 32.7 1.0

Chlorine binding site 9 out of 22 in 1jj2

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Chlorine binding site 9 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8517

b:50.2
occ:1.00
 O2' 0:C594 2.9 38.0 1.0
O X:HOH8557 2.9 82.2 1.0
O X:HOH8600 3.4 39.4 1.0
O X:HOH8536 3.4 31.5 1.0
O4' 0:U595 3.5 43.9 1.0
C2' 0:C594 3.7 41.7 1.0
CG X:ARG115 3.8 37.3 1.0
C4' 0:U595 3.8 43.6 1.0
C5' 0:U595 3.8 41.8 1.0
NH2 X:ARG122 3.9 40.6 1.0
NE X:ARG115 3.9 42.2 1.0
CD X:ARG115 4.0 38.2 1.0
O2 0:C594 4.2 43.9 1.0
O 0:HOH6072 4.3 44.0 1.0
O 0:HOH5823 4.3 64.0 1.0
C1' 0:C594 4.5 42.3 1.0
C1' 0:U595 4.7 44.8 1.0
O5' 0:U595 5.0 41.2 1.0
O X:HOH8560 5.0 35.7 1.0
CZ X:ARG115 5.0 42.4 1.0
CZ X:ARG122 5.0 39.3 1.0

Chlorine binding site 10 out of 22 in 1jj2

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Chlorine binding site 10 out of 22 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8522

b:44.6
occ:1.00
 N1 0:G1072 2.9 25.1 1.0
O 0:HOH4867 3.0 53.2 1.0
N2 0:G1072 3.3 23.6 1.0
O2' 0:G1087 3.4 28.8 1.0
C8 0:G1087 3.5 25.6 1.0
N7 0:A1291 3.5 27.5 1.0
C2 0:G1072 3.6 24.5 1.0
C5 0:A1291 3.8 27.5 1.0
N7 0:G1087 3.9 27.8 1.0
C6 0:G1072 3.9 24.5 1.0
O6 0:G1072 3.9 24.3 1.0
N9 0:G1087 4.0 26.3 1.0
C2' 0:G1087 4.0 28.2 1.0
C8 0:A1291 4.1 26.9 1.0
O 0:HOH8663 4.1 48.3 1.0
N6 0:A1291 4.2 26.5 1.0
C6 0:A1291 4.2 28.4 1.0
C1' 0:G1087 4.5 26.7 1.0
C5 0:G1087 4.5 26.8 1.0
C4 0:A1291 4.6 26.6 1.0
OE2 V:GLU10 4.6 37.4 1.0
C4 0:G1087 4.7 26.0 1.0
O 0:HOH3555 4.7 56.0 1.0
N9 0:A1291 4.7 27.6 1.0
N3 0:G1072 4.9 25.2 1.0

Reference:

D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz. The Kink-Turn: A New Rna Secondary Structure Motif. Embo J. V. 20 4214 2001.
ISSN: ISSN 0261-4189
PubMed: 11483524
DOI: 10.1093/EMBOJ/20.15.4214
Page generated: Fri Jul 19 23:02:57 2024

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