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Chlorine in PDB 1q81: Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.

Protein crystallography data

The structure of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit., PDB code: 1q81 was solved by J.L.Hansen, 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) 20.00 / 2.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.163, 301.288, 575.397, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.9

Other elements in 1q81:

The structure of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. 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 Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. (pdb code 1q81). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit., PDB code: 1q81:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 1q81

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Chlorine binding site 1 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8503

b:65.6
occ:1.00
O A:HOH5324 3.1 57.8 1.0
N2 A:G1676 3.4 51.1 1.0
O A:HOH3077 3.4 89.5 1.0
C1' A:G1452 3.5 52.1 1.0
O A:HOH8932 3.7 53.1 1.0
CE 3:LYS2 3.9 46.9 1.0
O2' A:G1452 4.0 53.0 1.0
O4' A:G1452 4.0 49.9 1.0
N3 A:A1486 4.3 46.4 1.0
O2 A:C1451 4.3 55.5 1.0
C2' A:G1452 4.3 52.3 1.0
O A:HOH4219 4.3 55.8 1.0
N9 A:G1452 4.4 53.4 1.0
C2 A:A1486 4.4 47.4 1.0
C2 A:G1676 4.5 51.1 1.0
N3 A:G1452 4.7 54.5 1.0
O A:HOH6281 4.7 59.3 1.0
N3 A:G1676 4.8 51.0 1.0
NZ 3:LYS2 4.8 47.3 1.0
C4 A:G1452 4.9 54.2 1.0
CD 3:LYS2 4.9 45.4 1.0

Chlorine binding site 2 out of 22 in 1q81

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Chlorine binding site 2 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8505

b:68.6
occ:1.00
N2 A:G201 2.7 65.8 1.0
O A:HOH4417 2.8 94.5 1.0
O A:HOH9696 3.5 32.4 1.0
C5 A:C197 3.7 60.0 1.0
C5' A:G229 3.7 54.0 1.0
O A:HOH4044 3.8 26.2 1.0
C2 A:G201 3.8 65.3 1.0
N3 A:G201 4.1 65.7 1.0
C1' A:U202 4.1 61.5 1.0
O2 A:C195 4.2 57.2 1.0
C6 A:C197 4.2 59.0 1.0
O2 A:U202 4.2 60.2 1.0
O4' A:U202 4.3 62.3 1.0
O A:HOH9262 4.3 51.7 1.0
C4' A:G229 4.3 55.3 1.0
N1 A:A199 4.4 76.7 1.0
C2 A:U202 4.5 60.0 1.0
N1 A:U202 4.6 60.4 1.0
C2 A:A199 4.6 76.6 1.0
O3' A:G229 4.7 55.5 1.0
C4 A:C197 4.8 59.5 1.0
OP1 A:G229 4.8 52.9 1.0
O5' A:G229 4.9 52.0 1.0
N1 A:G201 5.0 65.3 1.0
N4 A:C197 5.0 60.2 1.0

Chlorine binding site 3 out of 22 in 1q81

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Chlorine binding site 3 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8510

b:83.5
occ:1.00
N M:ARG53 3.2 57.0 1.0
C5' A:A693 3.5 60.2 1.0
CB M:ARG53 3.8 57.0 1.0
O3' A:A693 3.9 61.2 1.0
CA M:LYS52 3.9 54.5 1.0
CG M:ARG53 4.0 56.7 1.0
C4' A:A693 4.0 60.8 1.0
C M:LYS52 4.1 56.0 1.0
CA M:ARG53 4.1 57.9 1.0
NE2 M:GLN58 4.3 92.3 1.0
CD M:ARG53 4.4 54.8 1.0
OP1 A:A693 4.4 59.7 1.0
CD M:GLN58 4.5 91.9 1.0
O M:ARG53 4.5 58.8 1.0
CB M:LYS52 4.5 54.4 1.0
C3' A:A693 4.5 60.9 1.0
O5' A:A693 4.6 58.3 1.0
OP1 A:A694 4.6 61.9 1.0
O M:PHE51 4.7 51.7 1.0
C M:ARG53 4.8 59.4 1.0
CG M:GLN58 4.8 92.3 1.0
P A:A694 4.8 61.0 1.0
OE1 M:GLN58 4.8 91.5 1.0

Chlorine binding site 4 out of 22 in 1q81

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Chlorine binding site 4 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8511

b:73.4
occ:1.00
O2' A:C2388 3.1 35.7 1.0
N R:HIS53 3.2 46.8 1.0
O A:HOH9673 3.3 39.6 1.0
CB R:PHE52 3.6 48.2 1.0
CA R:PHE52 3.6 48.6 1.0
CE2 R:PHE56 3.8 38.0 1.0
CD2 R:PHE56 3.9 39.2 1.0
C R:PHE52 3.9 48.1 1.0
O4' A:C2388 4.0 39.7 1.0
C4' A:C2388 4.0 39.3 1.0
CB R:HIS53 4.1 45.0 1.0
C1' A:C2388 4.1 38.7 1.0
CG2 R:ILE84 4.1 51.2 1.0
C2' A:C2388 4.1 38.7 1.0
O R:HOH3082 4.1 21.1 1.0
CA R:HIS53 4.2 44.6 1.0
CG1 R:ILE84 4.6 51.5 1.0
O A:HOH3097 4.6 49.6 1.0
C3' A:C2388 4.7 40.0 1.0
CD1 R:ILE84 4.8 53.5 1.0
CB R:ILE84 4.8 51.0 1.0
CG R:PHE52 4.9 48.2 1.0
O3' A:C2388 5.0 42.6 1.0

Chlorine binding site 5 out of 22 in 1q81

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Chlorine binding site 5 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8512

b:43.6
occ:1.00
NZ L:LYS14 3.1 35.4 1.0
O A:HOH4608 3.1 54.8 1.0
C2 A:A2596 3.4 47.2 1.0
N2 A:G2582 3.4 45.1 1.0
N3 A:A2596 3.6 48.4 1.0
O A:HOH7080 3.6 87.0 1.0
OG L:SER33 3.6 53.1 1.0
O L:ILE32 3.7 46.6 1.0
CE L:LYS14 3.8 33.8 1.0
CG L:PRO45 3.9 53.0 1.0
CD L:LYS14 3.9 34.1 1.0
CB L:SER33 4.1 49.8 1.0
CA L:SER33 4.1 48.6 1.0
CB L:PRO45 4.2 52.5 1.0
N3 A:A2583 4.3 44.4 1.0
C1' A:U2597 4.3 53.5 1.0
N1 A:A2596 4.5 46.7 1.0
O2 A:U2597 4.6 56.6 1.0
C2 A:G2582 4.6 44.1 1.0
C L:ILE32 4.7 45.7 1.0
CG L:LYS14 4.7 35.1 1.0
O2' A:U2597 4.7 53.5 1.0
C1' A:A2583 4.7 42.3 1.0
O4' A:U2597 4.8 52.3 1.0
C4 A:A2596 4.9 50.1 1.0
C2 A:A2583 4.9 44.1 1.0
CD L:PRO45 4.9 52.8 1.0
C4 A:A2583 4.9 45.6 1.0
N L:SER33 4.9 46.9 1.0

Chlorine binding site 6 out of 22 in 1q81

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Chlorine binding site 6 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8513

b:74.3
occ:1.00
O A:HOH4164 2.7 1.0 1.0
N1 A:A1329 3.0 36.0 1.0
O A:HOH4460 3.0 74.3 1.0
O A:HOH3150 3.3 63.3 1.0
N6 A:A1328 3.4 38.0 1.0
C2 A:A1329 3.6 34.7 1.0
N2 A:G1299 3.6 38.1 1.0
O2' A:G1300 3.8 36.4 1.0
C6 A:A1329 4.0 36.6 1.0
C1' A:G1300 4.0 38.0 1.0
N6 A:A1329 4.1 39.1 1.0
O4' A:G1300 4.2 38.3 1.0
N3 A:G1299 4.3 39.4 1.0
MG A:MG8075 4.4 44.4 1.0
C2 A:G1299 4.4 38.4 1.0
C2' A:G1300 4.6 37.4 1.0
N1 A:A1330 4.6 32.8 1.0
C6 A:A1328 4.7 36.0 1.0
O Z:HOH8533 4.8 60.9 1.0
O2' A:A907 4.9 36.5 1.0
C2 A:A1330 4.9 33.7 1.0
C4' A:G1300 4.9 40.0 1.0
N3 A:A1329 4.9 36.3 1.0

Chlorine binding site 7 out of 22 in 1q81

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Chlorine binding site 7 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8514

b:62.1
occ:1.00
O A:HOH7207 2.8 46.7 1.0
O2' A:G644 2.9 38.5 1.0
ND1 M:HIS13 3.1 28.5 1.0
C2' A:G644 3.5 35.4 1.0
C4 A:G644 3.7 31.7 1.0
N9 A:G644 3.7 32.4 1.0
CG M:GLN7 3.9 31.4 1.0
CE1 M:HIS13 3.9 27.9 1.0
N3 A:G644 3.9 29.6 1.0
CG M:HIS13 4.0 30.2 1.0
C1' A:G644 4.0 34.1 1.0
C8 A:G644 4.1 32.4 1.0
C5 A:G644 4.1 32.2 1.0
CB M:HIS13 4.2 31.1 1.0
CG M:LYS4 4.3 37.1 1.0
N7 A:G644 4.4 33.6 1.0
CB M:GLN7 4.4 29.5 1.0
C2 A:G644 4.6 29.1 1.0
C6 A:G644 4.8 31.7 1.0
CA M:LYS4 4.9 34.1 1.0
O A:HOH9695 4.9 31.3 1.0
C3' A:G644 4.9 35.3 1.0
N1 A:G644 5.0 30.2 1.0
CD M:GLN7 5.0 34.5 1.0
O M:HIS13 5.0 32.5 1.0
CB M:LYS4 5.0 35.2 1.0

Chlorine binding site 8 out of 22 in 1q81

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Chlorine binding site 8 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8515

b:0.4
occ:1.00
N6 A:A1598 2.8 52.4 1.0
N6 A:A1597 3.5 48.8 1.0
N2 A:G1646 3.6 58.9 1.0
C1' A:G1647 3.8 58.1 1.0
O4' A:G1647 3.8 58.4 1.0
C6 A:A1598 4.0 49.7 1.0
N7 A:A1597 4.3 51.3 1.0
O A:HOH6277 4.3 31.5 1.0
C6 A:A1597 4.5 49.2 1.0
O2' A:G1647 4.6 54.9 1.0
C2 A:G1646 4.6 60.2 1.0
N3 A:G1646 4.6 60.2 1.0
N9 A:G1647 4.7 59.0 1.0
N1 A:A1598 4.7 49.1 1.0
O2' A:U1596 4.8 64.0 1.0
C5 A:A1597 4.8 51.1 1.0
C5 A:A1598 4.8 50.5 1.0
C2' A:G1647 4.8 57.2 1.0
C1' A:G1540 4.9 62.1 1.0
C4' A:G1647 4.9 57.7 1.0
N7 A:A1598 5.0 50.7 1.0

Chlorine binding site 9 out of 22 in 1q81

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Chlorine binding site 9 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8516

b:57.2
occ:1.00
NZ K:LYS56 2.9 31.4 1.0
O2' A:G1119 2.9 43.5 1.0
N4 A:C1243 3.6 40.0 1.0
CD K:LYS56 3.6 38.5 1.0
C8 A:G1119 3.7 42.6 1.0
CE K:LYS56 3.8 36.1 1.0
C2' A:G1119 3.8 42.4 1.0
O A:HOH6430 4.1 37.8 1.0
OE1 K:GLN52 4.1 48.8 1.0
NE2 K:GLN52 4.2 51.6 1.0
N9 A:G1119 4.3 40.8 1.0
N7 A:G1119 4.3 41.7 1.0
O A:HOH5192 4.4 40.9 1.0
C1' A:G1119 4.5 41.5 1.0
NA A:NA8302 4.6 36.8 1.0
N6 A:A1242 4.6 41.8 1.0
CD K:GLN52 4.6 50.0 1.0
O K:HOH2828 4.7 22.7 1.0
C4 A:C1243 4.7 41.7 1.0
O6 A:G1121 4.8 44.0 1.0
C5 A:C1243 4.9 41.9 1.0
CG K:LYS56 5.0 39.5 1.0
N7 A:A1242 5.0 42.8 1.0

Chlorine binding site 10 out of 22 in 1q81

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Chlorine binding site 10 out of 22 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8517

b:75.6
occ:1.00
O2' A:C594 2.9 60.5 1.0
O4' A:U595 3.3 65.8 1.0
O Z:HOH8558 3.3 0.7 1.0
O Z:HOH8535 3.6 58.7 1.0
O A:HOH5790 3.6 64.5 1.0
NE Z:ARG115 3.8 54.8 1.0
C2' A:C594 3.8 60.5 1.0
CD Z:ARG115 3.8 54.6 1.0
O Z:HOH8602 3.8 52.0 1.0
C4' A:U595 3.9 63.9 1.0
O2 A:C594 4.0 62.5 1.0
CG Z:ARG115 4.0 54.3 1.0
O A:HOH6026 4.1 55.4 1.0
C5' A:U595 4.1 60.9 1.0
NH2 Z:ARG122 4.3 54.9 1.0
C1' A:C594 4.4 61.7 1.0
C1' A:U595 4.5 66.1 1.0
O Z:HOH8561 4.6 45.9 1.0
CZ Z:ARG115 4.9 55.5 1.0
C2 A:C594 4.9 63.5 1.0

Reference:

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz. Structural Insights Into Peptide Bond Formation Proc.Natl.Acad.Sci.Usa V. 99 11670 2002.
ISSN: ISSN 0027-8424
PubMed: 12185246
DOI: 10.1073/PNAS.172404099
Page generated: Sat Dec 12 08:46:38 2020

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