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Magnesium in PDB 4ji4: 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: 4ji4 was solved by H.Demirci, L.Wang, F.Murphy Iv, E.Murphy, J.Carr, S.Blanchard, 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) 48.30 / 3.69
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.081, 402.081, 174.609, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 21.4

Other elements in 4ji4:

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

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 274 in 4ji4

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Magnesium binding site 1 out of 274 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 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:0.1
occ:1.00
O2 A:C381 3.1 0.5 1.0
N3 A:C381 3.5 0.9 1.0
O4 A:U65 3.5 0.3 1.0
C2 A:C381 3.8 0.0 1.0
C4 A:U65 4.5 0.0 1.0
C4 A:C381 4.7 0.2 1.0
C1' A:A382 4.9 0.1 1.0
N3 A:A382 4.9 0.1 1.0

Magnesium binding site 2 out of 274 in 4ji4

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Magnesium binding site 2 out of 274 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:Mg1602

b:0.5
occ:1.00
O A:HOH1902 2.1 0.4 1.0
O A:HOH1903 2.1 60.7 1.0
O A:HOH1901 2.1 95.7 1.0
O6 A:G377 3.7 0.4 1.0
C6 A:G377 4.8 0.6 1.0
N7 A:G376 4.8 0.4 1.0
MG A:MG1809 4.9 0.6 1.0

Magnesium binding site 3 out of 274 in 4ji4

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Magnesium binding site 3 out of 274 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:0.4
occ:1.00
O A:HOH1906 2.1 76.1 1.0
O A:HOH1905 2.1 0.0 1.0
O A:HOH1904 2.1 0.7 1.0
O6 A:G650 3.6 0.5 1.0
OP2 A:A753 3.6 0.3 1.0
OP1 A:A753 4.0 0.3 1.0
N7 A:G650 4.1 0.1 1.0
P A:A753 4.3 0.2 1.0
N7 A:G649 4.3 0.1 1.0
O6 A:G649 4.5 0.7 1.0
C6 A:G650 4.5 0.7 1.0
C5 A:G650 4.7 0.5 1.0
C5 A:G649 4.9 0.8 1.0
C6 A:G649 4.9 0.5 1.0

Magnesium binding site 4 out of 274 in 4ji4

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Magnesium binding site 4 out of 274 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:0.7
occ:1.00
O A:HOH1908 2.1 91.7 1.0
O A:HOH1907 2.1 0.9 1.0
OP2 A:G750 2.7 0.0 1.0
OP2 A:C749 2.8 0.5 1.0
OP1 A:C749 3.3 0.6 1.0
P A:C749 3.6 0.0 1.0
MG A:MG1798 3.8 0.1 1.0
P A:G750 4.1 0.1 1.0
O2' A:C748 4.2 1.0 1.0
O3' A:C748 4.6 0.9 1.0
O5' A:C749 4.8 0.6 1.0
N7 A:G750 4.8 0.5 1.0
C3' A:C749 4.9 0.9 1.0
O3' A:C749 4.9 0.4 1.0
O6 A:G752 4.9 0.1 1.0
O5' A:G750 4.9 0.4 1.0

Magnesium binding site 5 out of 274 in 4ji4

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Magnesium binding site 5 out of 274 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:0.9
occ:1.00
O6 A:G664 3.0 0.6 1.0
O6 A:G741 3.1 0.6 1.0
N7 A:G741 3.5 0.5 1.0
O6 A:G742 3.7 0.6 1.0
MG A:MG1857 3.8 0.7 1.0
O6 A:G666 3.9 0.1 1.0
C6 A:G741 3.9 0.9 1.0
C5 A:G741 4.1 0.4 1.0
C6 A:G664 4.1 0.7 1.0
O4 A:U740 4.1 0.9 1.0
N1 A:G664 4.5 0.8 1.0
C6 A:G742 4.5 0.1 1.0
C6 A:G666 4.6 0.9 1.0
C4 A:U740 4.6 0.6 1.0
C8 A:G741 4.7 0.0 1.0
N3 A:U740 4.8 0.3 1.0
N6 A:A663 4.8 0.1 1.0
N7 A:G742 4.9 0.0 1.0
C5 A:G742 5.0 0.9 1.0

Magnesium binding site 6 out of 274 in 4ji4

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Magnesium binding site 6 out of 274 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:0.3
occ:1.00
O A:HOH1912 2.1 0.5 1.0
O A:HOH1910 2.1 0.9 1.0
O A:HOH1911 2.1 76.4 1.0
O A:HOH1909 2.1 0.3 1.0
OP2 A:G117 2.5 0.7 1.0
OP2 A:G289 3.1 0.1 1.0
P A:G117 3.3 0.9 1.0
OP1 A:G117 3.4 0.3 1.0
OP2 A:A116 3.6 0.7 1.0
OP1 A:A116 3.7 0.8 1.0
O3' A:A116 3.9 0.5 1.0
O5' A:A288 4.0 0.2 1.0
P A:A116 4.1 0.1 1.0
OP2 A:A288 4.2 0.7 1.0
P A:G289 4.2 0.1 1.0
OP1 A:G289 4.4 0.3 1.0
O4 A:U118 4.4 0.9 1.0
C8 A:A288 4.4 0.3 1.0
C3' A:A288 4.4 0.4 1.0
P A:A288 4.5 0.1 1.0
C3' A:A116 4.5 0.6 1.0
O5' A:G117 4.7 0.6 1.0
C5 A:U118 4.7 0.9 1.0
OP1 A:A288 4.8 0.9 1.0
N7 A:G117 4.8 0.7 1.0
O3' A:A288 4.8 0.2 1.0
N7 A:A288 4.8 0.0 1.0
O5' A:A116 4.9 0.2 1.0
C4 A:U118 5.0 0.7 1.0
C5' A:A288 5.0 0.1 1.0

Magnesium binding site 7 out of 274 in 4ji4

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Magnesium binding site 7 out of 274 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:0.7
occ:1.00
OP2 A:C48 2.6 0.9 1.0
OP1 A:G115 3.0 0.3 1.0
OP2 A:U49 3.1 0.7 1.0
O5' A:C48 3.4 0.1 1.0
P A:C48 3.5 0.6 1.0
O3' A:U114 3.9 0.0 1.0
P A:G115 4.0 0.8 1.0
OP1 A:A51 4.3 0.9 1.0
C5' A:G115 4.3 1.0 1.0
OP1 A:C48 4.4 0.0 1.0
P A:U49 4.5 1.0 1.0
C5' A:C48 4.6 0.9 1.0
O3' A:C47 4.7 0.3 1.0
O5' A:G115 4.7 0.9 1.0
O2' A:C47 4.8 0.7 1.0

Magnesium binding site 8 out of 274 in 4ji4

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Magnesium binding site 8 out of 274 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:0.3
occ:1.00
O A:HOH1916 2.1 99.9 1.0
O A:HOH1914 2.1 0.6 1.0
O A:HOH1915 2.1 0.3 1.0
O A:HOH1913 2.1 0.9 1.0
N7 A:G752 3.8 0.4 1.0
OP2 A:U652 4.1 0.8 1.0
OP2 A:U751 4.1 0.8 1.0
MG A:MG1798 4.3 0.1 1.0
C8 A:G752 4.4 0.7 1.0
OP1 A:U751 4.5 0.1 1.0
P A:U751 4.7 0.2 1.0
OP2 A:C651 4.7 0.2 1.0
OP2 A:G752 4.7 0.8 1.0
C5 A:G752 4.8 0.5 1.0
O5' A:U751 4.9 0.3 1.0

Magnesium binding site 9 out of 274 in 4ji4

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Magnesium binding site 9 out of 274 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:0.3
occ:1.00
O A:HOH1919 2.1 86.0 1.0
O A:HOH1918 2.1 87.9 1.0
O A:HOH1917 2.1 0.6 1.0
O6 A:G800 3.3 0.2 1.0
O6 A:G799 3.5 0.8 1.0
C6 A:G800 4.1 0.5 1.0
OP2 A:A781 4.1 0.7 1.0
N1 A:G800 4.3 0.4 1.0
O A:HOH2030 4.4 0.5 1.0
N7 A:G799 4.4 0.3 1.0
C6 A:G799 4.5 0.1 1.0
O6 A:G798 4.8 0.4 1.0
C5 A:G799 4.9 0.3 1.0
OP1 A:A781 4.9 0.9 1.0
P A:A781 5.0 0.2 1.0

Magnesium binding site 10 out of 274 in 4ji4

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Magnesium binding site 10 out of 274 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:0.9
occ:1.00
O A:HOH1920 2.1 0.2 1.0
O A:HOH1921 2.1 98.9 1.0
OP1 A:G1505 2.8 0.3 1.0
OP1 A:G1508 2.8 0.6 1.0
O3' A:A1507 2.8 0.0 1.0
OP1 A:A1500 2.9 0.8 1.0
OP1 A:G1504 3.3 0.0 1.0
P A:G1508 3.4 0.9 1.0
C5' A:G1505 3.5 0.8 1.0
C3' A:G1504 3.7 0.1 1.0
P A:G1505 3.9 0.3 1.0
C5' A:G1504 3.9 0.8 1.0
O5' A:G1505 3.9 0.2 1.0
C4' A:G1504 4.0 0.8 1.0
C3' A:A1507 4.1 0.1 1.0
O3' A:G1504 4.2 0.0 1.0
C5' A:G1508 4.2 0.2 1.0
P A:A1500 4.2 0.9 1.0
P A:G1504 4.2 0.9 1.0
O5' A:G1508 4.3 0.7 1.0
OP2 A:G1504 4.3 0.4 1.0
O2' A:A1507 4.4 0.7 1.0
C4' A:A1507 4.4 0.0 1.0
O2' A:U1506 4.4 0.1 1.0
OP2 A:C1501 4.4 0.6 1.0
OP2 A:G1508 4.5 0.9 1.0
O5' A:G1504 4.6 0.6 1.0
OP2 A:A1500 4.7 0.3 1.0
C4' A:G1505 4.8 0.8 1.0
C2' A:U1506 4.8 0.2 1.0
C2' A:A1507 4.8 0.9 1.0
MG A:MG1736 4.9 99.8 1.0
C5' A:A1507 4.9 0.2 1.0
C2' A:G1504 4.9 0.4 1.0

Reference:

H.Demirci, L.Wang, F.V.Murphy, E.L.Murphy, J.F.Carr, S.C.Blanchard, G.Jogl, A.E.Dahlberg, S.T.Gregory. The Central Role of Protein S12 in Organizing the Structure of the Decoding Site of the Ribosome. Rna V. 19 1791 2013.
ISSN: ISSN 1355-8382
PubMed: 24152548
DOI: 10.1261/RNA.040030.113
Page generated: Sat Aug 17 00:19:50 2024

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