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Magnesium in PDB 3mxh: Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae

Protein crystallography data

The structure of Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae, PDB code: 3mxh was solved by S.A.Strobel, K.D.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.34 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.243, 45.652, 80.248, 90.00, 93.74, 90.00
R / Rfree (%) 20.2 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae (pdb code 3mxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae, PDB code: 3mxh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3mxh

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Magnesium binding site 1 out of 5 in the Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg99

b:88.6
occ:1.00
O P:HOH110 2.2 88.0 1.0
O P:HOH112 2.2 87.9 1.0
O P:HOH114 2.2 88.2 1.0
O P:HOH109 2.2 87.3 1.0
O P:HOH113 2.2 88.2 1.0
O P:HOH111 2.2 88.3 1.0
NH1 P:ARG70 3.7 0.3 1.0
NH2 P:ARG70 4.2 0.2 1.0
CZ P:ARG70 4.4 0.7 1.0

Magnesium binding site 2 out of 5 in 3mxh

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Magnesium binding site 2 out of 5 in the Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg670

b:42.0
occ:1.00
O R:HOH732 2.2 45.3 1.0
O R:HOH731 2.2 45.9 1.0
O R:HOH733 2.2 41.7 1.0
O R:HOH729 2.2 41.9 1.0
O R:HOH730 2.2 42.0 1.0
OP2 R:A48 2.2 55.4 1.0
P R:A48 3.2 48.5 1.0
O5' R:A48 3.3 49.8 1.0
O3' R:A47 3.5 47.3 1.0
O6 R:G14 4.1 47.2 1.0
O2' R:A47 4.2 44.0 1.0
O6 R:C2E1 4.2 36.1 1.0
N7 R:G14 4.2 44.8 1.0
N1 R:A91 4.5 43.9 1.0
N4 R:C92 4.5 39.8 1.0
O R:HOH692 4.6 27.2 1.0
O R:HOH683 4.6 26.0 1.0
OP1 R:A48 4.6 47.6 1.0
N6 R:A91 4.6 45.1 1.0
C5' R:A48 4.6 46.3 1.0
O R:HOH105 4.7 26.2 1.0
C6 R:G14 4.7 45.2 1.0
C3' R:A47 4.8 42.8 1.0
C5 R:G14 4.8 44.3 1.0
N4 R:C13 4.9 46.7 1.0
C2' R:A47 4.9 42.3 1.0

Magnesium binding site 3 out of 5 in 3mxh

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Magnesium binding site 3 out of 5 in the Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2

b:61.0
occ:1.00
O R:HOH739 2.2 61.8 1.0
O R:HOH738 2.2 60.4 1.0
O R:HOH736 2.2 60.7 1.0
O R:HOH737 2.2 60.5 1.0
O R:HOH735 2.2 63.5 1.0
O R:HOH734 2.2 57.1 1.0
O21 R:C2E1 3.5 46.0 1.0
N7 R:G20 3.8 57.5 1.0
O R:HOH676 4.1 18.2 1.0
O11 R:C2E1 4.4 45.4 1.0
O6 R:G20 4.5 52.3 1.0
C8 R:G20 4.6 60.5 1.0
C5 R:G20 4.6 55.7 1.0
P11 R:C2E1 4.7 44.3 1.0
N7 R:G19 4.7 53.2 1.0
N7 R:A18 4.9 57.1 1.0
C6 R:G20 4.9 52.0 1.0

Magnesium binding site 4 out of 5 in 3mxh

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Magnesium binding site 4 out of 5 in the Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg4

b:57.0
occ:1.00
O R:HOH100 2.2 49.5 1.0
O R:HOH161 2.4 30.4 1.0
O R:HOH70 2.9 30.8 1.0
OP2 R:U81 3.1 49.4 1.0
OP1 R:U81 4.0 51.4 1.0
P R:U81 4.1 50.9 1.0
OP2 R:U53 4.8 47.5 1.0
OP1 R:C52 5.0 35.1 1.0

Magnesium binding site 5 out of 5 in 3mxh

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Magnesium binding site 5 out of 5 in the Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Native Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg5

b:49.1
occ:1.00
O R:HOH740 2.2 50.2 1.0
O R:HOH744 2.2 48.6 1.0
O R:HOH742 2.2 43.3 1.0
O R:HOH743 2.2 51.9 1.0
O R:HOH741 2.2 47.7 1.0
O6 R:G42 2.4 38.8 1.0
O R:HOH169 3.3 48.1 1.0
C6 R:G42 3.4 38.4 1.0
N7 R:G42 3.9 39.9 1.0
C5 R:G42 4.0 38.4 1.0
OP2 R:G41 4.2 50.4 1.0
N6 R:A43 4.4 36.8 1.0
O R:HOH166 4.4 22.2 1.0
OP2 R:A23 4.4 39.5 1.0
N1 R:G42 4.5 36.3 1.0
N7 R:G41 4.5 40.4 1.0
O R:HOH171 5.0 23.6 1.0

Reference:

K.D.Smith, S.V.Lipchock, A.L.Livingston, C.A.Shanahan, S.A.Strobel. Structural and Biochemical Determinants of Ligand Binding By the C-Di-Gmp Riboswitch . Biochemistry V. 49 7351 2010.
ISSN: ISSN 0006-2960
PubMed: 20690679
DOI: 10.1021/BI100671E
Page generated: Mon Dec 14 08:27:14 2020

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