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Potassium in PDB 4lf9: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

Protein crystallography data

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4lf9 was solved by H.Demirci, R.Belardinelli, J.Carr, F.Murphy Iv, G.Jogl, A.E.Dahlberg, S.T.Gregory, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.48 / 3.28
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.042, 402.042, 176.388, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.1

Other elements in 4lf9:

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus also contains other interesting chemical elements:

Magnesium (Mg) 143 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 4lf9). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4lf9:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 4lf9

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Potassium binding site 1 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1712

b:0.2
occ:1.00
 O6 A:G293 3.1 83.9 1.0
O6 A:G305 3.2 91.8 1.0
O4 A:U304 3.3 98.7 1.0
C6 A:G305 4.0 85.3 1.0
N6 A:A303 4.1 86.2 1.0
N1 A:G305 4.1 78.2 1.0
C6 A:G293 4.2 80.1 1.0
C4 A:U304 4.2 92.7 1.0
N7 A:G293 4.4 77.7 1.0
N3 A:U304 4.4 91.4 1.0
OP2 A:G292 4.5 82.2 1.0
O4 A:U294 4.7 92.5 1.0
C5 A:G293 4.7 76.0 1.0
OP1 A:G292 4.9 89.0 1.0

Potassium binding site 2 out of 8 in 4lf9

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Potassium binding site 2 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1713

b:0.3
occ:1.00
 OP1 A:G576 2.7 86.6 1.0
P A:G576 3.7 84.2 1.0
OP2 A:G576 3.9 89.1 1.0
OP1 A:G575 4.2 74.2 1.0
OP2 A:G577 4.3 85.8 1.0
O5' A:G576 4.5 68.2 1.0
OP2 A:G575 4.6 75.3 1.0
OP1 A:A815 4.6 73.0 1.0
P A:G575 4.8 74.8 1.0
C5' A:G576 4.9 68.9 1.0
OP2 A:A815 4.9 83.0 1.0

Potassium binding site 3 out of 8 in 4lf9

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Potassium binding site 3 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1714

b:0.1
occ:1.00
 N7 A:G898 4.4 91.6 1.0
O6 A:G898 4.5 0.5 1.0

Potassium binding site 4 out of 8 in 4lf9

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Potassium binding site 4 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1715

b:0.2
occ:1.00
 MG A:MG1609 3.1 94.7 1.0
O6 A:G475 3.3 0.3 1.0
O6 A:G474 3.6 0.5 1.0
N7 A:G474 3.9 0.6 1.0
C6 A:G474 4.1 0.6 1.0
N7 A:G475 4.2 0.3 1.0
C5 A:G474 4.2 0.1 1.0
C6 A:G475 4.3 0.5 1.0
OP2 A:A463 4.4 0.2 1.0
C5 A:G475 4.6 0.9 1.0
C8 A:G474 4.9 0.9 1.0

Potassium binding site 5 out of 8 in 4lf9

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Potassium binding site 5 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1716

b:1.0
occ:1.00
 O6 A:G231 3.7 97.4 1.0
O6 A:G230 4.1 94.6 1.0
N7 A:G231 4.6 87.7 1.0
C6 A:G231 4.7 88.1 1.0

Potassium binding site 6 out of 8 in 4lf9

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Potassium binding site 6 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1717

b:0.6
occ:1.00
 O2 A:C1336 3.9 0.9 1.0
N3 A:C1336 3.9 0.7 1.0
OP1 A:G942 4.0 0.7 1.0
C2 A:C1336 4.3 0.1 1.0
N4 A:C1237 4.6 87.3 1.0
OP2 A:G942 4.8 0.9 1.0
P A:G942 5.0 0.1 1.0
C4 A:C1336 5.0 0.5 1.0

Potassium binding site 7 out of 8 in 4lf9

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Potassium binding site 7 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1718

b:0.6
occ:1.00
 OP1 A:G529 4.1 0.5 1.0
OP1 A:G530 4.2 0.6 1.0
OP2 A:G530 4.3 0.4 1.0
OE2 C:GLU161 4.5 0.9 1.0
C5' A:A533 4.5 0.3 1.0
OE1 C:GLU161 4.6 0.8 1.0
OP2 A:A533 4.6 0.5 1.0
P A:G530 4.8 1.0 1.0
C4' A:A533 4.9 0.2 1.0
O4' A:A533 5.0 0.1 1.0
CD C:GLU161 5.0 0.2 1.0

Potassium binding site 8 out of 8 in 4lf9

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Potassium binding site 8 out of 8 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1719

b:0.6
occ:1.00
 O2 A:U531 3.0 0.4 1.0
O6 A:G517 3.6 0.8 1.0
C2 A:U531 3.8 0.8 1.0
N3 A:U531 3.9 0.2 1.0
OP2 A:PSU516 4.0 0.9 1.0
OP2 A:G515 4.2 0.3 1.0
C6 A:G517 4.6 1.0 1.0
N7 A:G517 4.6 0.3 1.0
OP1 A:G515 4.8 0.6 1.0
P A:G515 4.9 0.8 1.0
N1 A:PSU516 4.9 0.9 1.0

Reference:

H.Demirci, R.Belardinelli, J.Carr, F.Murphy Iv, G.Jogl, A.E.Dahlberg, S.T.Gregory. Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus To Be Published 2013.
Page generated: Mon Aug 12 11:24:48 2024

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