Magnesium in PDB 5wns: 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: 5wns was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 3.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.000, 400.000, 173.000, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.5

Other elements in 5wns:

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 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 1 out of 254 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:0.7
occ:1.00
O4 A:U65 3.2 0.2 1.0
O2 A:C381 3.2 0.8 1.0
N3 A:C381 3.7 0.5 1.0
C2 A:C381 3.9 0.3 1.0
C4 A:U65 4.2 0.9 1.0
C5 A:U65 4.9 0.5 1.0
C4 A:C381 5.0 0.5 1.0

Magnesium binding site 2 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 2 out of 254 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:0.8
occ:1.00
O A:HOH2029 2.1 0.1 1.0
O A:HOH2090 2.1 0.7 1.0
O A:HOH2122 2.1 0.1 1.0
N7 A:G377 4.4 0.5 1.0
N7 A:G376 4.4 0.1 1.0
MG A:MG1834 4.4 0.4 1.0
O6 A:G377 4.5 0.6 1.0
C5 A:G376 4.9 0.8 1.0
O6 A:G376 4.9 0.1 1.0

Magnesium binding site 3 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 3 out of 254 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:0.5
occ:1.00
O A:HOH2096 2.1 0.2 1.0
O A:HOH2095 2.1 0.6 1.0
O A:HOH2066 2.1 0.7 1.0
O6 A:G650 3.8 0.5 1.0
N7 A:G650 3.8 0.9 1.0
OP2 A:A753 4.0 0.5 1.0
OP1 A:A753 4.4 0.5 1.0
N7 A:G649 4.4 0.1 1.0
O6 A:G649 4.5 0.3 1.0
C6 A:G650 4.5 0.0 1.0
C5 A:G650 4.5 0.9 1.0
P A:A753 4.6 0.5 1.0
C5 A:G649 4.9 0.0 1.0
C6 A:G649 4.9 0.2 1.0
N4 A:C651 4.9 0.9 1.0
C8 A:G650 4.9 0.1 1.0

Magnesium binding site 4 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 4 out of 254 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:0.1
occ:1.00
O A:HOH1925 2.1 97.1 1.0
O A:HOH2002 2.1 0.3 1.0
OP2 A:G750 3.0 0.8 1.0
OP2 A:C749 3.1 0.6 1.0
OP1 A:C749 3.4 0.1 1.0
P A:C749 3.8 0.3 1.0
P A:G750 4.4 0.5 1.0
MG A:MG1818 4.4 0.9 1.0
O6 A:G752 4.6 0.8 1.0
O3' A:C748 4.9 0.4 1.0
O2' A:C748 4.9 0.2 1.0
OP2 A:A653 4.9 99.6 1.0
O5' A:C749 4.9 0.5 1.0
OP1 A:G750 5.0 0.5 1.0

Magnesium binding site 5 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 5 out of 254 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:0.7
occ:1.00
O6 A:G741 3.2 0.1 1.0
O6 A:G742 3.4 0.8 1.0
O6 A:G664 3.6 0.5 1.0
N7 A:G741 3.7 0.9 1.0
C6 A:G741 3.9 0.9 1.0
C5 A:G741 4.1 0.5 1.0
C6 A:G742 4.2 0.6 1.0
N7 A:G742 4.6 0.2 1.0
C6 A:G664 4.6 0.9 1.0
O6 A:G666 4.7 0.5 1.0
C5 A:G742 4.7 0.3 1.0
N1 A:G664 4.8 0.0 1.0
C8 A:G741 4.8 0.6 1.0
N6 A:A663 5.0 0.3 1.0

Magnesium binding site 6 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 6 out of 254 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:0.5
occ:1.00
O A:HOH1908 2.1 0.7 1.0
O A:HOH1906 2.1 0.9 1.0
O A:HOH1915 2.1 0.5 1.0
O A:HOH1933 2.1 0.2 1.0
OP2 A:G117 2.8 0.5 1.0
OP2 A:G289 3.4 0.9 1.0
OP1 A:A116 3.6 1.0 1.0
P A:G117 3.7 0.6 1.0
OP1 A:G117 3.8 0.7 1.0
O4 A:U118 3.9 1.0 1.0
OP2 A:A288 4.2 0.8 1.0
O3' A:A116 4.2 0.1 1.0
C8 A:A288 4.3 0.9 1.0
C5 A:U118 4.3 0.3 1.0
O5' A:A288 4.3 0.5 1.0
C4 A:U118 4.5 0.2 1.0
N7 A:A288 4.5 1.0 1.0
C3' A:A288 4.6 0.9 1.0
P A:G289 4.6 0.7 1.0
P A:A116 4.7 0.2 1.0
C3' A:A116 4.7 0.9 1.0
N7 A:G117 4.7 0.7 1.0
OP2 A:A116 4.7 0.3 1.0
P A:A288 4.8 0.0 1.0
C8 A:G117 4.9 0.7 1.0

Magnesium binding site 7 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 7 out of 254 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:0.2
occ:1.00
OP2 A:C48 3.0 0.1 1.0
OP1 A:G115 3.2 0.6 1.0
OP2 A:U49 3.6 0.7 1.0
OP1 A:A51 3.6 0.3 1.0
O3' A:U114 4.0 0.4 1.0
O5' A:C48 4.1 0.7 1.0
P A:C48 4.1 0.1 1.0
P A:G115 4.2 0.2 1.0
C5' A:G115 4.5 0.7 1.0
O5' A:A51 4.7 0.7 1.0
P A:A51 4.7 0.7 1.0
O3' A:C47 4.7 1.0 1.0
C5' A:A51 4.8 0.7 1.0
O5' A:G115 4.9 0.7 1.0
P A:U49 5.0 0.3 1.0

Magnesium binding site 8 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 8 out of 254 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:0.7
occ:1.00
O A:HOH2038 2.1 0.6 1.0
O A:HOH2033 2.1 0.3 1.0
O A:HOH2049 2.1 0.8 1.0
O A:HOH2099 2.1 0.5 1.0
N7 A:G752 4.0 0.5 1.0
OP2 A:U652 4.2 0.1 1.0
OP1 A:C651 4.2 0.9 1.0
MG A:MG1818 4.3 0.9 1.0
OP2 A:G752 4.5 0.1 1.0
C8 A:G752 4.5 0.5 1.0
OP2 A:U751 4.5 0.2 1.0
OP2 A:C651 4.6 1.0 1.0
OP1 A:U751 4.7 0.5 1.0
P A:C651 4.8 0.4 1.0

Magnesium binding site 9 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 9 out of 254 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:HOH2071 2.1 0.9 1.0
O A:HOH2119 2.1 0.3 1.0
O A:HOH2115 2.1 0.3 1.0
O6 A:G800 3.5 0.9 1.0
O6 A:G799 4.0 0.9 1.0
C6 A:G800 4.1 0.1 1.0
O A:HOH2009 4.2 0.8 1.0
N7 A:G799 4.2 0.8 1.0
OP2 A:A781 4.3 0.9 1.0
N1 A:G800 4.4 0.2 1.0
O6 A:G798 4.6 0.7 1.0
OP1 A:A781 4.6 0.8 1.0
N7 A:G798 4.8 0.2 1.0
C6 A:G799 4.8 0.1 1.0
C5 A:G799 4.9 0.0 1.0
P A:A781 5.0 0.1 1.0

Magnesium binding site 10 out of 254 in 5wns

Go back to Magnesium Binding Sites List in 5wns
Magnesium binding site 10 out of 254 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
O2' A:C795 3.4 0.4 1.0
O3' A:C795 3.4 0.9 1.0
OP1 A:C796 3.6 0.4 1.0
O2 A:U1506 3.8 0.5 1.0
O4' A:U1506 3.9 0.3 1.0
C1' A:U1506 4.1 1.0 1.0
P A:C796 4.2 0.8 1.0
C2' A:C795 4.4 0.8 1.0
C3' A:C795 4.4 0.6 1.0
O3' A:U1506 4.5 0.7 1.0
C4' A:U1506 4.5 0.5 1.0
C2 A:U1506 4.6 0.4 1.0
N1 A:U1506 4.8 0.3 1.0
C5' A:C796 4.8 0.1 1.0

Reference:

J.Choi, G.Indrisiunaite, H.Demirci, K.W.Ieong, J.Wang, A.Petrov, A.Prabhakar, G.Rechavi, D.Dominissini, C.He, M.Ehrenberg, J.D.Puglisi. 2'-O-Methylation in Mrna Disrupts Trna Decoding During Translation Elongation. Nat. Struct. Mol. Biol. V. 25 208 2018.
ISSN: ESSN 1545-9985
PubMed: 29459784
DOI: 10.1038/S41594-018-0030-Z
Page generated: Mon Dec 14 21:22:53 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy