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Potassium in PDB 3oto: Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)

Protein crystallography data

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto was solved by H.Demirci, F.Murphy Iv, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, S.T.Gregory, A.E.Dahlberg, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 3.69
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.089, 402.089, 173.254, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 23.1

Other elements in 3oto:

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) also contains other interesting chemical elements:

Magnesium (Mg) 94 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) (pdb code 3oto). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 42 binding sites of Potassium where determined in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 42 in 3oto

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Potassium binding site 1 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1631

b:0.6
occ:1.00
O6 A:G305 3.4 95.9 1.0
O6 A:G293 3.7 79.8 1.0
O4 A:U304 3.8 75.3 1.0
OP2 A:G292 4.2 77.5 1.0
C6 A:G305 4.2 88.2 1.0
N1 A:G305 4.3 78.5 1.0
N6 A:A303 4.6 88.5 1.0
OP1 A:G292 4.7 82.7 1.0
C6 A:G293 4.7 80.8 1.0
N7 A:G293 4.8 83.5 1.0
C4 A:U304 4.9 76.4 1.0
P A:G292 4.9 78.9 1.0

Potassium binding site 2 out of 42 in 3oto

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Potassium binding site 2 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1632

b:0.4
occ:1.00
O6 A:G895 3.5 85.2 1.0
N7 A:G894 4.2 74.8 1.0
N7 A:G895 4.2 60.4 1.0
C6 A:G895 4.4 72.8 1.0
O6 A:G894 4.5 73.5 1.0
N4 A:C896 4.7 79.4 1.0
C5 A:G895 4.7 63.1 1.0
C5 A:G894 4.8 67.0 1.0
C6 A:G894 4.9 68.1 1.0

Potassium binding site 3 out of 42 in 3oto

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Potassium binding site 3 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1633

b:0.8
occ:1.00
OP2 A:G1343 3.3 0.5 1.0
OP2 A:C936 3.6 0.9 1.0
O3' A:C934 3.7 0.6 1.0
O2' A:C934 3.7 0.6 1.0
OP2 A:A935 3.8 94.5 1.0
O3' A:A935 3.9 94.1 1.0
C5' A:A935 4.0 79.5 1.0
OP1 A:G1343 4.0 0.1 1.0
P A:G1343 4.0 0.6 1.0
P A:C936 4.1 0.8 1.0
P A:A935 4.2 98.3 1.0
O5' A:A935 4.2 79.8 1.0
OP1 A:C936 4.4 0.5 1.0
C3' A:A935 4.5 88.4 1.0
O5' A:G1343 4.6 0.4 1.0
C2' A:C934 4.6 0.2 1.0
C3' A:C934 4.7 0.5 1.0
C4' A:A935 4.8 80.9 1.0
OP2 A:C1344 4.8 1.0 1.0
C1' A:C934 4.9 0.3 1.0

Potassium binding site 4 out of 42 in 3oto

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Potassium binding site 4 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1634

b:0.4
occ:1.00
N7 A:G837 4.0 1.0 1.0
O6 A:G838 4.0 0.5 1.0
O6 A:G837 4.2 0.7 1.0
OP2 A:G837 4.6 0.8 1.0
N7 A:G838 4.7 0.3 1.0
C5 A:G837 4.7 0.3 1.0
N3 A:C840 4.7 0.2 1.0
C6 A:G837 4.8 0.7 1.0
O2 A:C840 4.9 0.7 1.0
C6 A:G838 4.9 0.8 1.0
C8 A:G837 4.9 97.6 1.0

Potassium binding site 5 out of 42 in 3oto

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Potassium binding site 5 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1635

b:0.4
occ:1.00
OP2 A:C536 3.6 0.7 1.0
OP1 A:A535 3.8 0.5 1.0
O6 A:G538 4.0 0.6 1.0
O6 A:G537 4.1 0.5 1.0
O3' A:U534 4.8 0.5 1.0
C6 A:G537 4.8 0.7 1.0
N7 A:G537 4.8 0.7 1.0
P A:A535 4.9 0.6 1.0
C5' A:A535 4.9 80.4 1.0
N6 A:A539 4.9 0.6 1.0
P A:C536 5.0 0.8 1.0

Potassium binding site 6 out of 42 in 3oto

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Potassium binding site 6 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1636

b:0.5
occ:1.00
O6 A:G595 3.9 0.5 1.0
O6 A:G594 4.1 90.0 1.0
N7 A:G593 4.1 89.9 1.0
O2' A:U641 4.3 72.3 1.0
O6 A:G593 4.3 88.5 1.0
N1 A:G595 4.5 93.2 1.0
C6 A:G595 4.5 0.1 1.0
OP2 A:A642 4.7 83.2 1.0
N7 A:G592 4.8 0.9 1.0
OP2 A:G593 4.9 88.6 1.0
N7 A:G594 4.9 79.2 1.0
C5 A:G593 4.9 87.3 1.0
C6 A:G593 4.9 88.9 1.0

Potassium binding site 7 out of 42 in 3oto

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Potassium binding site 7 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1637

b:0.7
occ:1.00
O6 A:G475 3.7 0.8 1.0
MG A:MG1551 3.9 50.3 1.0
OP2 A:A463 4.1 0.2 1.0
O6 A:G474 4.2 0.6 1.0
NE P:ARG75 4.6 0.2 1.0
C6 A:G475 4.7 0.1 1.0
CZ P:ARG75 4.7 0.5 1.0
NH2 P:ARG75 4.8 0.5 1.0
N7 A:G474 4.8 0.1 1.0
C6 A:G474 4.8 0.3 1.0
N7 A:G475 4.9 0.8 1.0
OP2 A:G474 4.9 0.3 1.0

Potassium binding site 8 out of 42 in 3oto

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Potassium binding site 8 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1638

b:0.3
occ:1.00
O6 A:G231 3.8 99.9 1.0
O6 A:G230 4.4 0.5 1.0
N7 A:G231 4.6 96.8 1.0
C6 A:G231 4.8 91.5 1.0
O4 A:U129 4.8 0.4 1.0

Potassium binding site 9 out of 42 in 3oto

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Potassium binding site 9 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1639

b:81.5
occ:1.00
O6 A:G800 4.2 88.3 1.0
O6 A:G799 4.3 67.7 1.0
N7 A:G798 4.5 72.4 1.0
N7 A:G799 4.6 76.1 1.0
OP2 A:A781 4.7 99.7 1.0
C6 A:G800 4.8 94.5 1.0
OP1 A:A781 4.8 0.1 1.0
O6 A:G798 4.9 81.7 1.0

Potassium binding site 10 out of 42 in 3oto

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Potassium binding site 10 out of 42 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1640

b:1.0
occ:1.00
OP2 A:G21 3.9 82.6 1.0
OP2 A:U20 4.4 51.0 1.0
OP1 A:U561 4.4 72.8 1.0
N7 A:G21 4.6 67.5 1.0
O E:GLY124 4.8 87.2 1.0
C E:GLY124 4.8 82.2 1.0

Reference:

H.Demirci, F.Murphy, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, S.T.Gregory, A.E.Dahlberg, G.Jogl. Modification of 16S Ribosomal Rna By the Ksga Methyltransferase Restructures the 30S Subunit to Optimize Ribosome Function. Rna V. 16 2319 2010.
ISSN: ISSN 1355-8382
PubMed: 20962038
DOI: 10.1261/RNA.2357210
Page generated: Sun Dec 13 23:20:58 2020

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