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Magnesium in PDB 4lf8: 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: 4lf8 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) 34.62 / 3.15
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.445, 402.445, 176.924, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.5

Other elements in 4lf8:

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

Potassium (K) 20 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 202 in 4lf8

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Magnesium binding site 1 out of 202 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:91.9
occ:1.00
O6 A:G703 2.9 0.3 1.0
O2 A:C701 3.1 0.4 1.0
C6 A:G703 3.9 0.7 1.0
OP2 A:A702 4.2 0.7 1.0
C2 A:C701 4.3 0.6 1.0
N1 A:G703 4.6 0.6 1.0
C1' A:C701 4.8 0.2 1.0
C5 A:G703 4.9 0.1 1.0

Magnesium binding site 2 out of 202 in 4lf8

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Magnesium binding site 2 out of 202 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:77.0
occ:1.00
OP1 A:C1527 3.8 73.8 1.0
OP2 A:G731 4.3 75.1 1.0
OP1 A:G730 4.4 72.6 1.0
N7 A:G731 4.5 73.1 1.0
C8 A:G731 5.0 65.8 1.0

Magnesium binding site 3 out of 202 in 4lf8

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Magnesium binding site 3 out of 202 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:94.2
occ:1.00
O2 A:C519 2.5 98.7 1.0
O2' A:C519 3.2 76.6 1.0
O4' A:A520 3.2 87.0 1.0
C2 A:C519 3.7 88.5 1.0
C1' A:A520 3.9 82.7 1.0
C2' A:C519 3.9 72.0 1.0
C4' A:A520 4.2 83.9 1.0
O2' A:PSU516 4.2 0.5 1.0
C1' A:C519 4.3 79.8 1.0
O3' A:PSU516 4.5 1.0 1.0
N1 A:C519 4.5 81.6 1.0
N3 A:C519 4.6 89.2 1.0
N9 A:A520 4.7 82.7 1.0
OP1 A:G517 4.7 0.7 1.0
C5' A:A520 4.8 78.5 1.0
C5' A:G517 5.0 0.5 1.0

Magnesium binding site 4 out of 202 in 4lf8

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Magnesium binding site 4 out of 202 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:49.1
occ:1.00
O6 A:G799 4.1 74.2 1.0
O6 A:G798 4.3 82.6 1.0
O6 A:G800 4.3 93.5 1.0
N7 A:G799 4.5 78.1 1.0
OP2 A:A781 4.6 75.2 1.0
N7 A:G798 4.6 80.1 1.0
C6 A:G800 4.7 92.0 1.0
N1 A:G800 4.8 84.7 1.0
C6 A:G798 5.0 82.0 1.0
C6 A:G799 5.0 73.3 1.0

Magnesium binding site 5 out of 202 in 4lf8

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Magnesium binding site 5 out of 202 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:70.6
occ:1.00
N7 A:G21 4.1 70.3 1.0
OP2 A:G21 4.2 71.8 1.0
OP2 A:U20 4.5 59.2 1.0
C8 A:G21 4.7 65.1 1.0
O E:GLY124 4.8 86.6 1.0
OP2 A:U561 4.9 88.1 1.0

Magnesium binding site 6 out of 202 in 4lf8

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Magnesium binding site 6 out of 202 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:78.2
occ:1.00
O2 A:U871 3.8 0.4 1.0
MG A:MG1617 4.0 85.6 1.0
OP2 A:G855 4.4 76.3 1.0
N3 A:G818 4.6 71.3 1.0
C4 A:G818 4.6 70.9 1.0
C2 A:G818 4.8 61.4 1.0
C5 A:G818 4.9 69.6 1.0
C2 A:U871 4.9 89.9 1.0
N9 A:G818 5.0 65.9 1.0
N1 A:G818 5.0 64.7 1.0
O4' A:G818 5.0 68.6 1.0

Magnesium binding site 7 out of 202 in 4lf8

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Magnesium binding site 7 out of 202 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:72.1
occ:1.00
N7 A:G581 3.1 72.0 1.0
N7 A:G758 3.1 73.8 1.0
C8 A:G581 3.9 81.5 1.0
C8 A:G758 4.0 69.1 1.0
O6 A:G758 4.1 80.2 1.0
O6 A:G581 4.1 85.3 1.0
C5 A:G581 4.1 67.2 1.0
C5 A:G758 4.1 67.8 1.0
OP2 A:G758 4.2 58.9 1.0
OP2 A:U580 4.2 67.0 1.0
OP2 A:U757 4.3 75.3 1.0
C6 A:G581 4.4 77.2 1.0
OP2 A:G581 4.5 74.1 1.0
C6 A:G758 4.5 67.8 1.0
O5' A:U757 5.0 65.0 1.0

Magnesium binding site 8 out of 202 in 4lf8

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Magnesium binding site 8 out of 202 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:85.0
occ:1.00
O6 A:G309 2.7 71.1 1.0
C6 A:G309 3.3 67.6 1.0
N7 A:G309 3.4 68.1 1.0
MG A:MG1789 3.5 69.5 1.0
C5 A:G309 3.6 65.3 1.0
O6 A:G310 3.7 76.5 1.0
N4 A:C308 4.0 77.2 1.0
N7 A:G310 4.3 62.2 1.0
C4 A:C308 4.4 65.6 1.0
N1 A:G309 4.5 61.3 1.0
C8 A:G309 4.5 63.9 1.0
C5 A:C308 4.6 63.1 1.0
C6 A:G310 4.6 72.1 1.0
N4 A:C291 4.6 66.0 1.0
C5 A:G310 4.8 60.6 1.0
C4 A:G309 4.8 63.3 1.0
OP2 A:C307 4.9 0.9 1.0

Magnesium binding site 9 out of 202 in 4lf8

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Magnesium binding site 9 out of 202 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:
probe atom residue distance (Å) B Occ
A:Mg1609

b:78.0
occ:1.00
O6 A:G593 2.4 0.1 1.0
O4 A:U646 3.0 96.4 1.0
O6 A:G592 3.2 95.7 1.0
C6 A:G593 3.5 0.1 1.0
O6 A:G594 3.6 78.5 1.0
N4 A:C645 3.8 71.9 1.0
C6 A:G592 3.9 91.3 1.0
N7 A:G593 4.0 1.0 1.0
C4 A:U646 4.0 90.6 1.0
C5 A:G593 4.1 0.0 1.0
N3 A:U646 4.1 92.7 1.0
C6 A:G594 4.3 83.7 1.0
N4 A:C647 4.4 90.3 1.0
C5 A:G592 4.5 94.7 1.0
N1 A:G593 4.7 96.8 1.0
N7 A:G592 4.7 99.2 1.0
N1 A:G592 4.7 84.6 1.0
C4 A:C645 4.8 69.8 1.0
N1 A:G594 5.0 82.5 1.0
C5 A:G594 5.0 89.7 1.0

Magnesium binding site 10 out of 202 in 4lf8

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Magnesium binding site 10 out of 202 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:0.0
occ:1.00
OP1 A:U1049 3.6 0.4 1.0
O N:ALA2 3.6 0.1 1.0
OP1 A:G1048 3.8 0.1 1.0
OP2 A:A1204 4.1 0.8 1.0
OP1 A:A1204 4.2 0.1 1.0
OP1 A:C1203 4.3 0.4 1.0
OP2 A:G1048 4.5 0.9 1.0
C N:ALA2 4.6 0.3 1.0
P A:G1048 4.6 0.0 1.0
P A:A1204 4.7 0.1 1.0
P A:U1049 4.8 0.5 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 17:43:34 2024

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