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Potassium 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
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1m1k:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 1m1k

Go back to Potassium Binding Sites List in 1m1k
Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K8201

b:70.8
occ:1.00
O6 A:G2482 2.7 40.2 1.0
O6 A:G2102 2.7 49.1 1.0
O2 A:C2536 3.0 45.1 1.0
N7 A:G2482 3.0 43.1 1.0
O4' A:C2536 3.3 43.7 1.0
C6 A:G2482 3.3 39.0 1.0
N7 A:G2102 3.3 51.5 1.0
C6 A:G2102 3.4 49.5 1.0
C5 A:G2482 3.5 40.9 1.0
C2 A:C2536 3.5 44.4 1.0
C1' A:C2536 3.6 43.7 1.0
C5 A:G2102 3.6 50.7 1.0
N1 A:C2536 3.8 45.1 1.0
N6 A:A2486 3.9 61.0 1.0
C4' A:C2536 4.1 41.8 1.0
C8 A:G2482 4.2 42.4 1.0
O2 A:U2535 4.3 44.7 1.0
N3 A:C2536 4.4 43.2 1.0
C2 A:U2535 4.5 44.8 1.0
C8 A:G2102 4.5 52.0 1.0
N1 A:G2102 4.6 49.2 1.0
N1 A:G2482 4.7 38.9 1.0
N3 A:U2535 4.7 45.7 1.0
C5' A:C2536 4.8 40.0 1.0
C4 A:G2482 4.8 41.6 1.0
C2' A:U2535 4.8 40.7 1.0
C6 A:C2536 4.9 44.7 1.0
C4 A:G2102 4.9 51.7 1.0
OP1 A:U2539 5.0 44.8 1.0

Potassium binding site 2 out of 2 in 1m1k

Go back to Potassium Binding Sites List in 1m1k
Potassium binding site 2 out of 2 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 Potassium with other atoms in the K 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:K8202

b:61.0
occ:1.00
O A:HOH8707 2.5 49.6 1.0
O A:HOH4522 2.8 58.0 1.0
O A:HOH8613 2.9 37.7 1.0
O4 A:U172 3.0 47.4 1.0
O4 A:U163 3.0 38.8 1.0
O A:HOH8742 3.2 52.5 1.0
OP2 A:C162 3.3 30.6 1.0
O A:HOH7411 3.4 57.3 1.0
CD N:ARG82 3.5 45.0 1.0
C4 A:U172 3.9 46.7 1.0
N3 A:U172 4.0 47.5 1.0
C4 A:U163 4.1 39.1 1.0
O A:HOH8915 4.1 42.0 1.0
NE N:ARG82 4.2 47.5 1.0
N4 A:C171 4.2 50.7 1.0
O A:HOH7410 4.3 29.2 1.0
P A:C162 4.5 34.4 1.0
OP2 A:A169 4.6 42.3 1.0
C5 A:U163 4.6 40.7 1.0
CG N:ARG82 4.7 42.7 1.0
OP1 A:A169 4.7 40.7 1.0
CB N:ARG82 4.7 41.6 1.0
O6 A:G164 4.7 43.1 1.0
OP1 A:C162 4.8 31.7 1.0
N3 A:C173 4.9 42.7 1.0
MG A:MG8054 5.0 52.0 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: Sun Dec 13 22:50:24 2020

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