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Potassium in PDB 1kc8: Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit, PDB code: 1kc8 was solved by J.L.Hansen, 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) 19.99 / 3.01
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.5

Other elements in 1kc8:

The structure of Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit 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 Blasticidin S Bound to the 50S Ribosomal Subunit (pdb code 1kc8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit, PDB code: 1kc8:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 1kc8

Go back to Potassium Binding Sites List in 1kc8
Potassium binding site 1 out of 3 in the Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit


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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K8201

b:52.7
occ:1.00
O2' A:C2104 2.7 34.7 1.0
C2' A:C2104 3.6 35.1 1.0
C2 A:A2485 3.6 26.1 1.0
N3 A:A2486 3.7 42.8 1.0
O2 A:C2104 3.7 29.9 1.0
C1' A:A2486 3.8 36.5 1.0
C2' A:BLS9001 4.1 39.1 1.0
C4 A:A2486 4.1 41.8 1.0
C3' A:BLS9001 4.1 37.5 1.0
N9 A:A2486 4.2 39.4 1.0
N1 A:A2485 4.2 26.1 1.0
C1' A:C2104 4.2 34.3 1.0
O A:HOH5695 4.3 28.7 1.0
O4' A:A2486 4.3 35.7 1.0
O4' A:C2105 4.4 30.1 1.0
C2 A:A2486 4.5 45.0 1.0
N3 A:A2485 4.5 25.9 1.0
O A:HOH6666 4.6 82.1 1.0
C2 A:C2104 4.7 30.7 1.0
O2' A:A2486 4.7 34.1 1.0
C5' A:C2105 4.7 30.5 1.0
C2' A:A2486 4.8 34.5 1.0
C4' A:C2105 5.0 29.9 1.0
C3' A:C2104 5.0 35.6 1.0
N1 A:C2104 5.0 32.5 1.0

Potassium binding site 2 out of 3 in 1kc8

Go back to Potassium Binding Sites List in 1kc8
Potassium binding site 2 out of 3 in the Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit


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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K8202

b:91.2
occ:1.00
O6 A:G2482 2.7 25.7 1.0
O6 A:G2102 2.8 44.6 1.0
N7 A:G2482 2.9 27.5 1.0
O2 A:C2536 3.1 28.1 1.0
O4' A:C2536 3.4 31.7 1.0
C6 A:G2482 3.4 25.1 1.0
C5 A:G2482 3.4 27.1 1.0
N7 A:G2102 3.6 43.0 1.0
C6 A:G2102 3.6 44.8 1.0
C2 A:C2536 3.7 30.1 1.0
C1' A:C2536 3.8 31.0 1.0
C5 A:G2102 3.9 44.4 1.0
O2 A:U2535 4.0 33.0 1.0
N1 A:C2536 4.0 31.1 1.0
N6 A:A2486 4.0 43.2 1.0
C8 A:G2482 4.1 27.2 1.0
C4' A:C2536 4.1 30.6 1.0
C2 A:U2535 4.2 31.8 1.0
OP1 A:U2539 4.5 32.3 1.0
N3 A:U2535 4.5 30.7 1.0
N3 A:C2536 4.5 30.2 1.0
C2' A:U2535 4.6 31.2 1.0
C5' A:C2536 4.7 30.7 1.0
N1 A:G2482 4.7 24.2 1.0
C8 A:G2102 4.7 42.9 1.0
C4 A:G2482 4.8 27.4 1.0
N1 A:U2535 4.8 31.6 1.0
N1 A:G2102 4.9 44.7 1.0

Potassium binding site 3 out of 3 in 1kc8

Go back to Potassium Binding Sites List in 1kc8
Potassium binding site 3 out of 3 in the Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K8203

b:79.1
occ:1.00
O A:HOH7822 2.8 36.1 1.0
O A:HOH4925 2.8 75.0 1.0
O A:HOH9017 2.9 28.8 1.0
O A:HOH9114 2.9 39.1 1.0
OP2 A:C162 3.2 15.9 1.0
O4 A:U172 3.3 31.0 1.0
CD N:ARG82 3.3 92.7 1.0
O A:HOH9150 3.3 20.2 1.0
O4 A:U163 3.3 28.4 1.0
O A:HOH9326 4.0 46.2 1.0
O A:HOH7821 4.0 45.5 1.0
C4 A:U172 4.2 30.3 1.0
NE N:ARG82 4.3 93.1 1.0
C4 A:U163 4.3 26.4 1.0
N3 A:U172 4.4 29.9 1.0
CG N:ARG82 4.4 92.2 1.0
P A:C162 4.4 16.2 1.0
OP2 A:A169 4.5 26.8 1.0
CB N:ARG82 4.5 92.8 1.0
OP1 A:A169 4.6 30.7 1.0
C5 A:U163 4.6 25.2 1.0
N4 A:C171 4.7 27.1 1.0
OP1 A:C162 4.7 17.1 1.0
MG A:MG8054 4.7 32.8 1.0
P A:A169 4.9 26.3 1.0

Reference:

J.Hansen, P.B.Moore, T.A.Steitz. Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit J.Mol.Biol. V. 330 1061 2003.
ISSN: ISSN 0022-2836
PubMed: 12860128
DOI: 10.1016/S0022-2836(03)00668-5
Page generated: Sun Dec 13 22:48:17 2020

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