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Chlorine in PDB 1m1k: Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1m1k was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, 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 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.751, 301.566, 574.436, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25

Other elements in 1m1k:

The structure of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1m1k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1m1k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 1m1k

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Chlorine binding site 1 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8503

b:74.9
occ:1.00
O A:HOH9012 3.4 52.3 1.0
N2 A:G1676 3.4 55.1 1.0
O A:HOH3161 3.5 47.8 1.0
O A:HOH5418 3.7 61.7 1.0
CE 3:LYS2 3.7 46.0 1.0
C1' A:G1452 3.7 56.6 1.0
O2' A:G1452 4.0 56.2 1.0
N3 A:A1486 4.1 54.1 1.0
O A:HOH7170 4.1 73.2 1.0
C2 A:A1486 4.1 55.1 1.0
O A:HOH4306 4.2 50.4 1.0
O4' A:G1452 4.4 55.7 1.0
C2' A:G1452 4.4 56.1 1.0
C2 A:G1676 4.4 53.6 1.0
N3 A:G1676 4.5 53.5 1.0
CD 3:LYS2 4.6 44.1 1.0
N9 A:G1452 4.6 58.5 1.0
N3 A:G1452 4.6 59.2 1.0
O2 A:C1451 4.7 61.3 1.0
NZ 3:LYS2 4.7 45.5 1.0
O A:HOH6387 4.8 65.9 1.0
C4 A:G1452 5.0 59.2 1.0

Chlorine binding site 2 out of 22 in 1m1k

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Chlorine binding site 2 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8505

b:93.0
occ:1.00
O A:HOH4137 3.2 52.2 1.0
O A:HOH4505 3.3 62.9 1.0
N2 A:G201 3.3 61.9 1.0
O A:HOH9782 3.6 38.5 1.0
C5 A:C197 3.6 59.6 1.0
O4' A:U202 3.7 64.1 1.0
C1' A:U202 3.8 64.2 1.0
C5' A:G229 3.9 59.4 1.0
O3' A:G229 4.2 59.1 1.0
C2 A:G201 4.2 62.8 1.0
C4' A:G229 4.2 60.9 1.0
N3 A:G201 4.3 63.5 1.0
C6 A:C197 4.4 57.9 1.0
O2' A:U202 4.4 61.5 1.0
N4 A:C197 4.5 61.2 1.0
N1 A:U202 4.5 65.8 1.0
C4 A:C197 4.5 60.0 1.0
O2 A:U202 4.6 68.2 1.0
C4' A:U202 4.6 63.6 1.0
C2' A:U202 4.8 62.3 1.0
C2 A:U202 4.8 67.6 1.0
C3' A:G229 4.8 61.5 1.0
OP1 A:C230 4.8 59.5 1.0
N1 A:A199 4.9 75.7 1.0
O A:HOH9343 4.9 44.7 1.0
C2 A:A199 4.9 76.5 1.0
O2 A:C195 4.9 55.7 1.0

Chlorine binding site 3 out of 22 in 1m1k

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Chlorine binding site 3 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8510

b:97.6
occ:1.00
N M:ARG53 3.4 61.4 1.0
C5' A:A693 3.5 59.1 1.0
CB M:ARG53 4.0 61.0 1.0
CA M:LYS52 4.1 60.0 1.0
OP1 A:A693 4.1 55.5 1.0
O3' A:A693 4.1 59.9 1.0
C4' A:A693 4.2 59.7 1.0
CG M:ARG53 4.2 59.1 1.0
C M:LYS52 4.3 61.0 1.0
CA M:ARG53 4.3 62.2 1.0
NE2 M:GLN58 4.3 93.8 1.0
CD M:GLN58 4.4 93.1 1.0
O M:ARG53 4.5 62.9 1.0
O5' A:A693 4.5 58.7 1.0
OE1 M:GLN58 4.5 94.1 1.0
CB M:LYS52 4.6 60.4 1.0
O M:PHE51 4.7 56.3 1.0
C3' A:A693 4.7 59.6 1.0
OP1 A:A694 4.8 60.1 1.0
CD M:ARG53 4.9 57.5 1.0
C M:ARG53 4.9 63.4 1.0
CG M:GLN58 4.9 92.0 1.0
P A:A694 5.0 61.0 1.0
CG M:LYS52 5.0 59.9 1.0
P A:A693 5.0 57.3 1.0

Chlorine binding site 4 out of 22 in 1m1k

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Chlorine binding site 4 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8513

b:67.1
occ:1.00
O A:HOH4259 2.5 0.4 1.0
N1 A:A1329 2.7 46.7 1.0
C2 A:A1329 3.3 46.0 1.0
O2' A:G1300 3.4 43.7 1.0
N6 A:A1328 3.6 47.9 1.0
N2 A:G1299 3.6 43.9 1.0
C6 A:A1329 3.7 47.5 1.0
O A:HOH3231 3.8 39.1 1.0
O A:HOH4549 3.8 65.1 1.0
C1' A:G1300 3.9 45.4 1.0
O A:HOH9392 3.9 35.2 1.0
N1 A:A1330 3.9 48.9 1.0
N6 A:A1329 3.9 50.3 1.0
O4' A:G1300 4.1 43.7 1.0
C2' A:G1300 4.3 44.5 1.0
C2 A:A1330 4.3 47.6 1.0
O A:HOH4426 4.5 67.7 1.0
C2 A:G1299 4.6 45.8 1.0
N3 A:A1329 4.6 46.3 1.0
N3 A:G1299 4.7 47.5 1.0
C4' A:G1300 4.7 44.6 1.0
C6 A:A1330 4.8 48.8 1.0
C6 A:A1328 4.9 47.0 1.0
C5 A:A1329 5.0 46.5 1.0

Chlorine binding site 5 out of 22 in 1m1k

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Chlorine binding site 5 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8514

b:57.9
occ:1.00
O A:HOH7312 2.7 73.4 1.0
O2' A:G644 3.2 37.3 1.0
ND1 M:HIS13 3.5 44.6 1.0
CG M:GLN7 3.8 39.5 1.0
CG M:LYS4 4.0 45.1 1.0
C2' A:G644 4.0 35.8 1.0
N9 A:G644 4.0 40.2 1.0
C8 A:G644 4.2 41.3 1.0
C4 A:G644 4.3 42.4 1.0
O A:HOH9781 4.3 45.1 1.0
CB M:HIS13 4.3 39.4 1.0
CG M:HIS13 4.3 43.2 1.0
C1' A:G644 4.4 36.9 1.0
CE1 M:HIS13 4.4 45.6 1.0
O A:HOH6688 4.4 64.7 1.0
CA M:LYS4 4.5 43.6 1.0
CB M:GLN7 4.6 39.3 1.0
N7 A:G644 4.6 42.0 1.0
C5 A:G644 4.6 43.8 1.0
CB M:LYS4 4.6 43.3 1.0
CD M:GLN7 4.7 39.7 1.0
CE M:LYS4 4.7 48.8 1.0
CD M:LYS4 4.7 47.4 1.0
N3 A:G644 4.7 44.0 1.0
O M:HIS13 4.8 35.4 1.0

Chlorine binding site 6 out of 22 in 1m1k

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Chlorine binding site 6 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8515

b:0.6
occ:1.00
O A:HOH6383 3.2 84.0 1.0
N6 A:A1598 3.4 65.7 1.0
N2 A:G1646 3.6 60.6 1.0
N6 A:A1597 3.7 59.7 1.0
N7 A:A1597 3.9 59.4 1.0
C1' A:G1540 4.2 65.0 1.0
C6 A:A1598 4.4 63.5 1.0
O4' A:G1647 4.4 66.2 1.0
O2' A:U1596 4.5 68.1 1.0
C1' A:G1647 4.5 64.2 1.0
O2' A:G1540 4.6 63.2 1.0
C6 A:A1597 4.6 59.6 1.0
N3 A:G1540 4.6 70.8 1.0
C5 A:A1597 4.6 59.4 1.0
C2 A:G1646 4.6 62.8 1.0
N3 A:G1646 4.7 63.1 1.0
O4' A:G1540 4.8 65.3 1.0
N9 A:G1540 4.9 66.8 1.0
C5 A:A1598 5.0 63.3 1.0

Chlorine binding site 7 out of 22 in 1m1k

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Chlorine binding site 7 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8517

b:52.8
occ:1.00
O2' A:C594 2.8 55.7 1.0
O4' A:U595 3.2 60.2 1.0
O Z:HOH8145 3.3 0.6 1.0
O Z:HOH8182 3.4 34.1 1.0
C4' A:U595 3.5 59.6 1.0
C5' A:U595 3.5 57.3 1.0
C2' A:C594 3.6 57.0 1.0
O Z:HOH8122 3.6 50.6 1.0
CG Z:ARG115 3.7 61.4 1.0
NH2 Z:ARG122 3.8 56.5 1.0
CD Z:ARG115 3.9 63.0 1.0
NE Z:ARG115 4.1 62.8 1.0
O2 A:C594 4.2 62.1 1.0
O A:HOH5879 4.4 79.0 1.0
O A:HOH6125 4.4 77.6 1.0
C1' A:U595 4.5 61.1 1.0
C1' A:C594 4.5 59.6 1.0
O5' A:U595 4.6 56.0 1.0
C3' A:C594 4.8 55.8 1.0
O3' A:C594 4.9 54.6 1.0
CZ Z:ARG122 4.9 56.9 1.0
C3' A:U595 5.0 60.0 1.0

Chlorine binding site 8 out of 22 in 1m1k

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Chlorine binding site 8 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8520

b:65.3
occ:1.00
O A:HOH4534 2.8 64.6 1.0
O A:HOH9973 3.1 77.5 1.0
C5' A:G1269 3.3 53.4 1.0
O A:HOH3231 3.5 39.1 1.0
NH2 Z:ARG169 3.6 47.2 1.0
NE Z:ARG169 3.6 45.1 1.0
C4' A:G1269 3.8 51.0 1.0
O3' A:G1269 3.8 47.9 1.0
CZ Z:ARG169 4.1 46.6 1.0
N6 A:A1328 4.2 47.9 1.0
C6 A:A1328 4.4 47.0 1.0
C3' A:G1269 4.4 49.5 1.0
N1 A:A1328 4.4 46.7 1.0
MG A:MG8075 4.5 56.6 1.0
O5' A:G1269 4.6 55.2 1.0
OP1 A:G1269 4.7 54.1 1.0
CG Z:ARG169 4.7 46.0 1.0
CD Z:ARG169 4.7 45.1 1.0
OP1 A:U1270 4.8 45.0 1.0
P A:U1270 4.9 46.3 1.0

Chlorine binding site 9 out of 22 in 1m1k

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Chlorine binding site 9 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl8522

b:83.7
occ:1.00
O2' A:G1087 3.4 44.2 1.0
N1 A:G1072 3.4 38.0 1.0
O A:HOH4930 3.4 87.1 1.0
N2 A:G1072 3.5 35.1 1.0
N7 A:A1291 3.6 50.7 1.0
C8 A:G1087 3.7 46.5 1.0
C2' A:G1087 3.9 44.2 1.0
O A:HOH8740 3.9 64.6 1.0
C2 A:G1072 4.0 37.5 1.0
C5 A:A1291 4.1 49.2 1.0
C8 A:A1291 4.2 47.6 1.0
N9 A:G1087 4.2 45.6 1.0
N7 A:G1087 4.2 44.0 1.0
N6 A:A1291 4.3 49.5 1.0
OE2 X:GLU10 4.3 58.7 1.0
C6 A:G1072 4.4 39.6 1.0
O6 A:G1072 4.5 41.9 1.0
C6 A:A1291 4.5 48.6 1.0
C1' A:G1087 4.5 45.2 1.0
O A:HOH3623 4.5 61.8 1.0
C5 A:G1087 4.9 45.5 1.0
C4 A:A1291 4.9 47.3 1.0
C4 A:G1087 5.0 45.4 1.0
N9 A:A1291 5.0 46.5 1.0

Chlorine binding site 10 out of 22 in 1m1k

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Chlorine binding site 10 out of 22 in the Co-Crystal Structure of Azithromycin Bound to the 50S 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl8509

b:69.6
occ:1.00
NZ C:LYS178 3.1 50.1 1.0
O A:HOH5997 3.5 43.1 1.0
CD C:LYS178 3.6 49.0 1.0
CE C:LYS178 3.6 50.4 1.0
CE C:LYS175 3.9 34.0 1.0
CZ C:PHE169 4.1 41.7 1.0
O A:HOH4829 4.1 45.4 1.0
SD C:MET179 4.3 45.6 1.0
CE C:MET179 4.3 43.6 1.0
CD C:LYS175 4.4 36.9 1.0
CE1 C:PHE169 4.4 43.3 1.0
O C:HOH8577 4.6 75.7 1.0
OP2 A:G1878 4.7 44.0 1.0
CG C:LYS178 4.8 48.0 1.0
O A:HOH9650 4.9 64.0 1.0

Reference:

J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz. The Structures of Four Macrolide Antibiotics Bound to the Large Ribosomal Subunit. Mol.Cell V. 10 117 2002.
ISSN: ISSN 1097-2765
PubMed: 12150912
DOI: 10.1016/S1097-2765(02)00570-1
Page generated: Sat Dec 12 08:42:23 2020

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