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Magnesium in PDB 4yb0: 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp

Protein crystallography data

The structure of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp, PDB code: 4yb0 was solved by A.M.Ren, D.J.Patel, R.K.Rajashankar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.10 / 2.12
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.829, 44.901, 68.210, 90.00, 103.33, 90.00
R / Rfree (%) 22.8 / 26.2

Other elements in 4yb0:

The structure of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp (pdb code 4yb0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp, PDB code: 4yb0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4yb0

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Magnesium binding site 1 out of 5 in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg103

b:73.2
occ:1.00
O R:HOH226 1.8 49.6 1.0
O R:HOH205 2.0 47.2 1.0
O R:HOH208 2.1 58.3 1.0
O R:HOH214 2.3 55.4 1.0
OP1 R:G28 3.1 46.7 1.0
N7 R:G26 3.2 45.6 1.0
O6 R:G26 3.6 44.5 1.0
C5 R:G26 3.7 38.7 1.0
OP2 R:G28 3.7 62.7 1.0
P R:G28 3.8 54.5 1.0
C6 R:G26 3.9 43.4 1.0
C8 R:G26 4.1 47.0 1.0
O R:HOH202 4.3 55.5 1.0
O3' R:C27 4.6 45.3 1.0
C4 R:G26 4.8 45.3 1.0
O R:HOH215 4.9 47.1 1.0
N9 R:G26 5.0 47.6 1.0

Magnesium binding site 2 out of 5 in 4yb0

Go back to Magnesium Binding Sites List in 4yb0
Magnesium binding site 2 out of 5 in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg104

b:81.1
occ:1.00
OP2 R:A12 2.1 80.1 1.0
OP2 R:A11 2.5 94.8 1.0
OP1 R:A11 2.6 90.7 1.0
P R:A11 2.8 0.3 1.0
O5' R:A11 3.5 84.4 1.0
P R:A12 3.5 95.0 1.0
OP1 R:A12 4.2 92.5 1.0
O3' R:C10 4.3 88.7 1.0
O3' R:A11 4.4 75.3 1.0
C3' R:A11 4.4 76.4 1.0
O5' R:A12 4.5 77.1 1.0
O1P R:C2E102 4.6 71.8 1.0
C5' R:A11 4.6 79.5 1.0
N7 R:A12 5.0 71.6 1.0

Magnesium binding site 3 out of 5 in 4yb0

Go back to Magnesium Binding Sites List in 4yb0
Magnesium binding site 3 out of 5 in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg105

b:52.4
occ:1.00
O R:HOH213 1.9 63.7 1.0
O2' R:A41 2.6 62.2 1.0
O3' R:A41 2.9 55.0 1.0
OP2 R:A42 3.1 61.4 1.0
O61 R:C2E102 3.1 49.7 1.0
N7 R:G8 3.3 67.0 1.0
C2' R:A41 3.6 53.4 1.0
P R:A42 3.6 55.4 1.0
O6 R:G8 3.7 54.1 1.0
C3' R:A41 3.8 49.1 1.0
C5 R:G8 3.8 53.6 1.0
O5' R:A42 3.9 74.0 1.0
C1' R:A41 3.9 49.1 1.0
C6 R:G8 4.0 57.4 1.0
N71 R:C2E102 4.1 49.5 1.0
C61 R:C2E102 4.1 47.1 1.0
C8 R:G8 4.2 63.6 1.0
C51 R:C2E102 4.4 45.7 1.0
N4 R:C75 4.6 49.3 1.0
C4 R:G8 4.9 49.5 1.0
O4' R:A41 4.9 44.5 1.0
N9 R:A41 4.9 55.0 1.0
OP1 R:A42 4.9 59.4 1.0
C4' R:A41 4.9 40.7 1.0

Magnesium binding site 4 out of 5 in 4yb0

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Magnesium binding site 4 out of 5 in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:0.8
occ:1.00
O A:HOH203 2.0 0.7 1.0
O A:HOH208 2.2 0.8 1.0
OP1 A:G28 2.5 0.7 1.0
O A:HOH202 2.7 0.8 1.0
O6 A:G26 3.1 0.3 1.0
P A:G28 3.4 0.7 1.0
OP2 A:G28 3.6 0.8 1.0
N7 A:G26 3.6 0.2 1.0
C6 A:G26 3.6 0.1 1.0
C5 A:G26 3.8 0.7 1.0
O3' A:C27 4.2 0.7 1.0
C8 A:G26 4.7 0.4 1.0
N1 A:G26 4.7 0.3 1.0
O5' A:G28 4.7 0.0 1.0

Magnesium binding site 5 out of 5 in 4yb0

Go back to Magnesium Binding Sites List in 4yb0
Magnesium binding site 5 out of 5 in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:59.4
occ:1.00
O A:HOH215 2.4 57.5 1.0
O2' A:A41 2.9 57.8 1.0
O3' A:A41 3.1 57.3 1.0
O61 A:C2E102 3.2 55.9 1.0
OP2 A:A42 3.3 71.3 1.0
P A:A42 3.7 65.6 1.0
O5' A:A42 3.7 78.6 1.0
N7 A:G8 3.8 53.6 1.0
C2' A:A41 3.8 52.6 1.0
O6 A:G8 3.9 60.6 1.0
C1' A:A41 4.0 55.9 1.0
C3' A:A41 4.1 52.5 1.0
C61 A:C2E102 4.2 57.3 1.0
C5 A:G8 4.3 49.0 1.0
C6 A:G8 4.3 56.9 1.0
N4 A:C75 4.3 52.1 1.0
N71 A:C2E102 4.4 62.9 1.0
O6 A:G74 4.4 62.4 1.0
OP2 A:A6 4.6 92.6 1.0
C51 A:C2E102 4.7 59.6 1.0
C8 A:G8 4.7 55.5 1.0
N9 A:A41 4.9 55.6 1.0
O4' A:A41 4.9 54.2 1.0
C5' A:A42 5.0 59.5 1.0

Reference:

A.Ren, X.C.Wang, C.A.Kellenberger, K.R.Rajashankar, R.A.Jones, M.C.Hammond, D.J.Patel. Structural Basis For Molecular Discrimination By A 3',3'-Cgamp Sensing Riboswitch. Cell Rep V. 11 1 2015.
ISSN: ESSN 2211-1247
PubMed: 25818298
DOI: 10.1016/J.CELREP.2015.03.004
Page generated: Mon Dec 14 19:53:13 2020

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