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Magnesium in PDB 4lf6: 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: 4lf6 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) 34.90 / 3.31
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 403.178, 403.178, 176.492, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21

Other elements in 4lf6:

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

Potassium (K) 30 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 220 in 4lf6

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Magnesium binding site 1 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1601

b:76.4
occ:1.00
O2 A:C701 2.7 0.8 1.0
O6 A:G703 3.2 98.4 1.0
OP2 A:A702 3.9 0.7 1.0
C2 A:C701 4.0 99.6 1.0
C6 A:G703 4.1 94.2 1.0
C1' A:C701 4.3 94.2 1.0
O2' A:C701 4.5 0.1 1.0
N1 A:C701 4.7 94.3 1.0
N1 A:G703 4.8 95.9 1.0
N3 A:C701 4.9 95.8 1.0
C5 A:G703 5.0 90.8 1.0

Magnesium binding site 2 out of 220 in 4lf6

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Magnesium binding site 2 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1602

b:0.7
occ:1.00
MG A:MG1829 3.7 0.3 1.0
O6 A:G157 4.1 0.1 1.0
O6 A:G158 4.2 0.8 1.0
O6 A:G159 4.5 1.0 1.0
N7 A:G157 4.5 1.0 1.0
C6 A:G157 4.8 0.9 1.0
C5 A:G157 4.9 0.1 1.0

Magnesium binding site 3 out of 220 in 4lf6

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Magnesium binding site 3 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1603

b:69.3
occ:1.00
K A:K1738 3.3 0.9 1.0
O6 A:G258 4.0 0.9 1.0
O6 A:G259 4.0 89.7 1.0
N7 A:G258 4.2 0.3 1.0
OP2 A:G265 4.4 82.0 1.0
OP1 A:G265 4.5 83.7 1.0
OP2 A:G266 4.6 76.0 1.0
C6 A:G258 4.7 96.0 1.0
C5 A:G258 4.7 97.6 1.0
P A:G265 4.8 82.6 1.0
O6 A:G260 4.9 91.4 1.0

Magnesium binding site 4 out of 220 in 4lf6

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Magnesium binding site 4 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1604

b:79.9
occ:1.00
O2 A:C519 2.7 79.9 1.0
O4' A:A520 3.3 79.3 1.0
O2' A:C519 3.3 75.0 1.0
C2 A:C519 3.9 75.8 1.0
C1' A:A520 3.9 77.3 1.0
C2' A:C519 4.0 73.4 1.0
O2' A:PSU516 4.2 87.0 1.0
C4' A:A520 4.2 80.5 1.0
C1' A:C519 4.4 74.9 1.0
O3' A:PSU516 4.5 98.0 1.0
N1 A:C519 4.7 75.4 1.0
OP1 A:G517 4.7 0.8 1.0
N9 A:A520 4.7 72.9 1.0
C5' A:A520 4.8 84.0 1.0
N3 A:C519 4.8 72.7 1.0

Magnesium binding site 5 out of 220 in 4lf6

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Magnesium binding site 5 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1605

b:44.2
occ:1.00
O6 A:G799 4.0 80.5 1.0
O6 A:G800 4.1 78.5 1.0
O6 A:G798 4.1 78.5 1.0
N7 A:G799 4.2 75.5 1.0
N7 A:G798 4.4 72.9 1.0
OP2 A:A781 4.6 77.0 1.0
C6 A:G800 4.6 75.6 1.0
C6 A:G799 4.8 74.4 1.0
C6 A:G798 4.8 78.0 1.0
N1 A:G800 4.8 73.4 1.0
C5 A:G799 4.9 72.2 1.0
C5 A:G798 4.9 74.1 1.0

Magnesium binding site 6 out of 220 in 4lf6

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Magnesium binding site 6 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1606

b:72.6
occ:1.00
OP2 A:G21 4.1 72.3 1.0
N7 A:G21 4.2 65.9 1.0
OP2 A:U20 4.3 62.9 1.0
O E:GLY124 4.6 81.3 1.0
C8 A:G21 4.8 62.1 1.0
OP2 A:U561 4.8 80.8 1.0

Magnesium binding site 7 out of 220 in 4lf6

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Magnesium binding site 7 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1607

b:59.5
occ:1.00
N7 A:G758 3.5 62.9 1.0
N7 A:G581 3.7 76.1 1.0
OP2 A:G758 3.9 67.9 1.0
OP2 A:U580 4.1 69.6 1.0
OP2 A:U757 4.1 62.2 1.0
O6 A:G581 4.3 71.5 1.0
C8 A:G758 4.4 61.8 1.0
O6 A:G758 4.5 61.8 1.0
C8 A:G581 4.6 77.7 1.0
C5 A:G581 4.6 70.6 1.0
C5 A:G758 4.6 58.2 1.0
O5' A:U757 4.6 53.7 1.0
P A:U757 4.8 61.0 1.0
C6 A:G581 4.9 69.3 1.0
OP2 A:G581 4.9 65.8 1.0
OP1 A:U757 5.0 59.8 1.0
C6 A:G758 5.0 57.1 1.0

Magnesium binding site 8 out of 220 in 4lf6

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Magnesium binding site 8 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1608

b:73.7
occ:1.00
O6 A:G593 2.7 85.2 1.0
O6 A:G592 2.9 84.0 1.0
O4 A:U646 3.2 87.1 1.0
O6 A:G594 3.6 87.5 1.0
C6 A:G592 3.7 83.1 1.0
C6 A:G593 3.7 80.7 1.0
K A:K1744 3.8 1.0 1.0
N4 A:C645 3.9 75.8 1.0
N7 A:G593 4.0 78.7 1.0
C5 A:G593 4.2 76.8 1.0
C4 A:U646 4.2 84.6 1.0
C5 A:G592 4.3 83.6 1.0
C6 A:G594 4.4 84.5 1.0
N7 A:G592 4.4 87.0 1.0
N3 A:U646 4.5 83.7 1.0
N4 A:C647 4.5 84.3 1.0
N1 A:G592 4.5 80.9 1.0
N1 A:G593 5.0 76.3 1.0

Magnesium binding site 9 out of 220 in 4lf6

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Magnesium binding site 9 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:

Magnesium binding site 10 out of 220 in 4lf6

Go back to Magnesium Binding Sites List in 4lf6
Magnesium binding site 10 out of 220 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:89.7
occ:1.00
N2 A:G484 3.6 87.9 1.0
N1 A:G485 4.5 0.7 1.0
C2 A:G485 4.6 0.8 1.0
N2 A:G485 4.6 0.7 1.0
C2 A:G484 4.8 86.4 1.0
OP2 A:A448 4.9 0.1 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 19 17:43:24 2024

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