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Magnesium in PDB 3f30: Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.

Protein crystallography data

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak., PDB code: 3f30 was solved by A.A.Serganov, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.15
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.156, 71.156, 138.421, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 23.4

Other elements in 3f30:

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. also contains other interesting chemical elements:

Cobalt (Co) 9 atoms
Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. (pdb code 3f30). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak., PDB code: 3f30:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3f30

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg303

b:82.9
occ:1.00
 N7 X:G93 2.4 94.0 1.0
O6 X:G93 3.3 93.5 1.0
C5 X:G93 3.4 93.3 1.0
C8 X:G93 3.5 93.5 1.0
C6 X:G93 3.7 93.3 1.0
OP1 X:G93 4.2 91.8 1.0
N7 X:G84 4.3 90.7 1.0
C4 X:G93 4.6 93.0 1.0
N9 X:G93 4.7 92.8 1.0
O4 X:U94 4.7 93.6 1.0
O6 X:G84 5.0 90.6 1.0

Magnesium binding site 2 out of 8 in 3f30

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg304

b:57.6
occ:1.00
 N7 X:G33 2.3 93.0 1.0
O1P X:FMN200 2.5 81.0 1.0
O3P X:FMN200 3.2 80.8 1.0
C8 X:G33 3.3 93.2 1.0
P X:FMN200 3.4 80.5 1.0
C5 X:G33 3.4 92.9 1.0
O6 X:G33 3.5 93.8 1.0
C6 X:G33 3.9 93.1 1.0
O2' X:G41 4.1 90.5 1.0
O4' X:G41 4.1 89.8 1.0
O5' X:FMN200 4.2 79.8 1.0
OP2 X:G33 4.3 95.8 1.0
C4' X:G41 4.4 90.4 1.0
O6 X:G62 4.5 97.2 1.0
N9 X:G33 4.5 92.9 1.0
N1 X:G10 4.5 98.9 1.0
C4 X:G33 4.6 92.5 1.0
N1 X:G62 4.6 95.9 1.0
O2P X:FMN200 4.6 80.0 1.0
C1' X:G41 4.6 88.0 1.0
C2' X:G41 4.9 89.2 1.0
N2 X:G10 4.9 99.6 1.0

Magnesium binding site 3 out of 8 in 3f30

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg305

b:91.4
occ:1.00
 O4 X:U89 2.0 94.5 1.0
OP2 X:A92 2.4 92.8 1.0
C4 X:U89 3.1 94.6 1.0
N7 X:G88 3.7 96.8 1.0
C5 X:U89 3.7 95.1 1.0
P X:A92 3.9 93.2 1.0
O6 X:G88 4.0 97.9 1.0
N3 X:U89 4.2 94.4 1.0
C5 X:G88 4.5 97.0 1.0
C6 X:G88 4.6 97.4 1.0
O5' X:A92 4.6 92.5 1.0
C5' X:G91 4.7 94.0 1.0
C8 X:G88 4.7 96.6 1.0
OP1 X:A92 4.7 93.2 1.0
C4' X:G91 4.8 94.7 1.0
O3' X:G91 4.8 94.1 1.0
C8 X:A92 4.8 92.5 1.0
C3' X:G91 4.9 94.6 1.0

Magnesium binding site 4 out of 8 in 3f30

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg307

b:95.6
occ:1.00
 OP1 X:G16 4.1 92.5 1.0
OP1 X:G15 4.5 93.0 1.0

Magnesium binding site 5 out of 8 in 3f30

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg309

b:0.8
occ:1.00
 O6 X:G68 3.7 97.1 1.0
O6 X:G67 4.1 86.9 1.0
N7 X:G67 4.4 87.2 1.0
C6 X:G68 4.8 97.2 1.0
C4' X:U74 4.8 94.7 1.0
C6 X:G67 4.8 86.6 1.0
OP2 X:U75 4.8 93.0 1.0
C5 X:G67 4.9 86.9 1.0
N7 X:G68 5.0 97.4 1.0
O4 X:U66 5.0 98.3 1.0

Magnesium binding site 6 out of 8 in 3f30

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg311

b:0.4
occ:1.00
 N7 X:G32 4.1 98.9 1.0
O6 X:G41 4.2 86.9 1.0
O6 X:G32 4.5 97.0 1.0
N7 X:G41 4.9 87.2 1.0
C5 X:G32 5.0 97.9 1.0

Magnesium binding site 7 out of 8 in 3f30

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg313

b:0.3
occ:1.00
 N3 X:A14 4.0 98.0 1.0
C2 X:A14 4.5 98.0 1.0
C4 X:A14 4.6 97.6 1.0
O2' X:A29 4.7 92.8 1.0
C1' X:A14 4.9 96.6 1.0
O3' X:A29 4.9 92.8 1.0
N9 X:A14 5.0 97.2 1.0

Magnesium binding site 8 out of 8 in 3f30

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Magnesium binding site 8 out of 8 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


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 the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg314

b:0.5
occ:1.00
 OP1 X:A22 2.4 99.3 1.0
OP2 X:U23 3.5 97.5 1.0
P X:A22 3.8 98.8 1.0
O3' X:A21 4.2 98.1 1.0
P X:U23 4.6 97.5 1.0
C5' X:A22 4.6 99.5 1.0
OP1 X:U23 4.7 97.6 1.0
O5' X:A22 4.7 99.0 1.0
OP2 X:A22 4.8 98.8 1.0

Reference:

A.Serganov, L.Huang, D.J.Patel. Coenzyme Recognition and Gene Regulation By A Flavin Mononucleotide Riboswitch. Nature V. 458 233 2009.
ISSN: ISSN 0028-0836
PubMed: 19169240
DOI: 10.1038/NATURE07642
Page generated: Wed Aug 14 13:28:49 2024

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