Atomistry » Magnesium » PDB 5fhe-5fsb » 5fjc
Atomistry »
  Magnesium »
    PDB 5fhe-5fsb »
      5fjc »

Magnesium in PDB 5fjc: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU

Protein crystallography data

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.134 / 1.71
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.398, 60.398, 152.950, 90.00, 90.00, 90.00
R / Rfree (%) 20.09 / 24.05

Other elements in 5fjc:

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU also contains other interesting chemical elements:

Potassium (K) 4 atoms
Barium (Ba) 21 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU (pdb code 5fjc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5fjc

Go back to Magnesium Binding Sites List in 5fjc
Magnesium binding site 1 out of 2 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg127

b:42.3
occ:1.00
O A:HOH2113 1.8 47.0 1.0
O A:HOH2114 2.2 54.2 1.0
O A:HOH2029 2.4 51.6 1.0
O A:HOH2027 2.5 48.2 1.0
OP1 A:A62 3.3 61.6 1.0
K A:K124 3.7 49.6 1.0
O3' A:A61 3.9 53.1 1.0
O A:HOH2030 4.0 50.8 1.0
OP2 A:A12 4.2 47.6 1.0
P A:A62 4.3 54.8 1.0
N7 A:A12 4.8 37.6 1.0

Magnesium binding site 2 out of 2 in 5fjc

Go back to Magnesium Binding Sites List in 5fjc
Magnesium binding site 2 out of 2 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg128

b:32.0
occ:1.00
O6 A:G74 2.4 36.9 1.0
O A:HOH2135 2.7 37.5 1.0
O A:HOH2137 2.8 30.4 1.0
O6 A:G73 3.0 28.3 1.0
O A:HOH2134 3.1 36.0 1.0
O A:HOH2142 3.3 43.5 1.0
C6 A:G74 3.3 34.2 1.0
N4 A:C72 3.5 30.0 1.0
C6 A:G73 4.0 34.0 1.0
N7 A:G73 4.1 26.1 1.0
N1 A:G74 4.1 32.8 1.0
BA A:BA119 4.1 26.5 0.8
C5 A:G74 4.3 39.4 1.0
C4 A:C72 4.3 26.7 1.0
C5 A:G73 4.4 33.9 1.0
N4 A:C78 4.6 39.5 1.0
O A:HOH2019 4.6 45.4 1.0
N7 A:G74 4.6 34.1 1.0
C5 A:C72 4.8 28.2 1.0
O A:HOH2143 4.8 42.4 1.0
O A:HOH2141 4.9 37.1 1.0
O6 A:G79 4.9 31.7 1.0
O A:HOH2126 4.9 33.7 1.0
O A:HOH2124 4.9 32.3 1.0

Reference:

L.Huang, J.Wang, D.M.J.Lilley. A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function. Nucleic Acids Res. V. 44 5390 2016.
ISSN: ISSN 0305-1048
PubMed: 27016741
DOI: 10.1093/NAR/GKW201
Page generated: Mon Dec 14 20:18:46 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy