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Magnesium in PDB 4x62: 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: 4x62 was solved by H.Demirci, J.Chen, J.Choi, M.Soltis, J.D.Puglisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.88 / 3.45
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.834, 400.834, 175.086, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 4x62:

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

Potassium (K) 29 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 280 in 4x62

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Magnesium binding site 1 out of 280 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:Mg1607

b:81.3
occ:1.00
N3 A:U203 4.7 0.8 1.0
O2 A:U203 4.8 1.0 1.0

Magnesium binding site 2 out of 280 in 4x62

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Magnesium binding site 2 out of 280 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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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:Mg1608

b:84.2
occ:1.00
O A:HOH1906 2.1 36.9 1.0
O A:HOH1908 2.1 31.8 1.0
O A:HOH1907 2.1 86.3 1.0
N7 A:G376 4.3 77.4 1.0
O6 A:G377 4.5 78.4 1.0
O6 A:G376 4.7 77.9 1.0
MG A:MG1809 4.7 42.5 1.0
MG A:MG1799 4.9 48.2 1.0
OP2 A:U375 4.9 80.1 1.0

Magnesium binding site 3 out of 280 in 4x62

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Magnesium binding site 3 out of 280 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:Mg1609

b:0.1
occ:1.00
O A:HOH1910 2.1 58.6 1.0
O A:HOH1909 2.1 96.6 1.0
OP2 A:A753 3.8 80.2 1.0
O6 A:G650 3.8 83.3 1.0
N7 A:G650 3.9 82.8 1.0
OP1 A:A753 4.6 79.6 1.0
C6 A:G650 4.6 81.6 1.0
P A:A753 4.6 79.6 1.0
C5 A:G650 4.6 82.6 1.0
O6 A:G649 4.7 90.0 1.0
N7 A:G649 4.8 90.8 1.0

Magnesium binding site 4 out of 280 in 4x62

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Magnesium binding site 4 out of 280 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:Mg1610

b:98.1
occ:1.00
O A:HOH1912 2.1 58.0 1.0
O A:HOH1911 2.1 94.6 1.0
OP2 A:G750 3.0 87.7 1.0
OP2 A:C749 3.0 0.2 1.0
OP1 A:C749 3.1 0.4 1.0
P A:C749 3.5 0.4 1.0
O2' A:C748 4.2 0.7 1.0
P A:G750 4.3 88.8 1.0
O3' A:C748 4.4 0.9 1.0
OP1 A:G750 4.7 89.8 1.0
O6 A:G752 4.8 91.2 1.0
O5' A:C749 4.9 0.1 1.0

Magnesium binding site 5 out of 280 in 4x62

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Magnesium binding site 5 out of 280 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:Mg1611

b:60.1
occ:1.00
O2 A:U871 3.5 78.1 1.0
MG A:MG1772 3.7 59.2 1.0
OP2 A:G855 3.9 68.2 1.0
C4 A:G818 4.5 65.5 1.0
C2 A:U871 4.5 69.0 1.0
N3 A:G818 4.6 65.6 1.0
C5 A:G818 4.6 65.6 1.0
C2 A:G818 4.8 65.8 1.0
N9 A:G818 4.9 65.3 1.0
N3 A:U871 4.9 69.0 1.0
C6 A:G818 4.9 69.8 1.0
O4' A:G818 4.9 65.4 1.0
N1 A:G818 4.9 66.1 1.0
OP1 A:G855 4.9 76.4 1.0
P A:G855 5.0 69.6 1.0

Magnesium binding site 6 out of 280 in 4x62

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Magnesium binding site 6 out of 280 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:Mg1612

b:63.7
occ:1.00
O A:HOH1914 2.1 0.9 1.0
O A:HOH1916 2.1 39.6 1.0
O A:HOH1915 2.1 29.4 1.0
O A:HOH1913 2.1 58.4 1.0
OP2 A:G117 2.8 66.5 1.0
OP2 A:G289 3.1 65.7 1.0
OP1 A:A116 3.4 66.6 1.0
OP1 A:G117 3.7 68.8 1.0
P A:G117 3.7 68.6 1.0
O5' A:A288 4.0 65.0 1.0
P A:G289 4.1 65.6 1.0
C3' A:A288 4.2 65.0 1.0
O4 A:U118 4.3 65.5 1.0
P A:A116 4.3 67.0 1.0
OP2 A:A116 4.4 66.9 1.0
C8 A:A288 4.4 71.0 1.0
OP2 A:A288 4.4 72.5 1.0
O3' A:A288 4.5 65.3 1.0
OP1 A:G289 4.6 65.9 1.0
C5 A:U118 4.6 65.7 1.0
N7 A:G117 4.7 66.7 1.0
P A:A288 4.7 69.1 1.0
O3' A:A116 4.8 67.2 1.0
N7 A:A288 4.8 69.0 1.0
C5' A:A116 4.8 67.3 1.0
O5' A:G117 4.9 77.0 1.0
C4 A:U118 4.9 65.6 1.0
C8 A:G117 4.9 66.8 1.0
C2' A:A288 4.9 64.9 1.0
C3' A:A116 5.0 67.4 1.0

Magnesium binding site 7 out of 280 in 4x62

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Magnesium binding site 7 out of 280 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:Mg1613

b:68.5
occ:1.00
OP2 A:C48 2.8 76.0 1.0
OP1 A:G115 3.4 68.6 1.0
OP1 A:A51 3.7 78.3 1.0
O23 A:PAR1603 3.7 0.6 1.0
P A:C48 4.0 72.3 1.0
OP2 A:U49 4.1 88.8 1.0
C23 A:PAR1603 4.2 0.3 1.0
O3' A:U114 4.2 69.1 1.0
OP1 A:C48 4.2 69.8 1.0
P A:G115 4.4 68.6 1.0
C5' A:G115 4.4 68.2 1.0
O5' A:A51 4.7 72.9 1.0
O3' A:C47 4.8 70.3 1.0
P A:A51 4.8 75.2 1.0
O2' A:C47 4.9 73.8 1.0
O5' A:G115 4.9 68.2 1.0
C5' A:A51 4.9 70.6 1.0

Magnesium binding site 8 out of 280 in 4x62

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Magnesium binding site 8 out of 280 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:Mg1614

b:77.7
occ:1.00
O A:HOH1920 2.1 66.8 1.0
O A:HOH1918 2.1 90.3 1.0
O A:HOH1919 2.1 0.4 1.0
O A:HOH1917 2.1 92.6 1.0
N7 A:G752 4.0 84.1 1.0
OP2 A:U652 4.0 92.5 1.0
OP2 A:U751 4.3 87.5 1.0
OP1 A:C651 4.4 96.2 1.0
OP2 A:G752 4.6 88.6 1.0
C8 A:G752 4.6 83.5 1.0
OP1 A:U751 4.7 92.5 1.0
P A:U751 4.9 87.4 1.0
OP2 A:C651 5.0 92.6 1.0

Magnesium binding site 9 out of 280 in 4x62

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Magnesium binding site 9 out of 280 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:Mg1615

b:47.4
occ:1.00
O A:HOH1922 2.1 31.6 1.0
O A:HOH1923 2.1 59.4 1.0
O A:HOH1921 2.1 84.6 1.0
O6 A:G800 3.4 70.5 1.0
O A:HOH2032 4.0 65.8 1.0
C6 A:G800 4.2 70.7 1.0
N7 A:G799 4.3 72.0 1.0
O6 A:G799 4.4 71.2 1.0
OP2 A:A781 4.5 69.4 1.0
N1 A:G800 4.6 70.4 1.0
OP1 A:A781 4.7 68.7 1.0
OP2 A:A780 4.8 70.0 1.0

Magnesium binding site 10 out of 280 in 4x62

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Magnesium binding site 10 out of 280 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:Mg1616

b:63.3
occ:1.00
OP2 A:G1508 3.5 64.6 1.0
O2 A:U1506 3.6 66.4 1.0
O2' A:U1506 3.7 75.0 1.0
OP2 A:U1522 3.9 64.0 1.0
C2 A:U1506 3.9 63.4 1.0
OP1 A:U1522 4.1 63.4 1.0
N1 A:U1506 4.4 63.6 1.0
N3 A:U1506 4.4 63.5 1.0
P A:U1522 4.6 63.7 1.0
C1' A:U1506 4.6 63.6 1.0
P A:G1508 4.6 65.0 1.0
OP1 A:G1508 4.7 65.1 1.0
C2' A:U1506 4.7 64.0 1.0

Reference:

J.Choi, K.W.Ieong, H.Demirci, J.Chen, A.Petrov, A.Prabhakar, S.E.O'leary, D.Dominissini, G.Rechavi, S.M.Soltis, M.Ehrenberg, J.D.Puglisi. N(6)-Methyladenosine in Mrna Disrupts Trna Selection and Translation-Elongation Dynamics. Nat.Struct.Mol.Biol. V. 23 110 2016.
ISSN: ESSN 1545-9985
PubMed: 26751643
DOI: 10.1038/NSMB.3148
Page generated: Mon Dec 14 19:43:37 2020

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