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Barium in PDB 3f2w: Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.

Protein crystallography data

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak., PDB code: 3f2w 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 / 3.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.003, 71.003, 139.745, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 21.7

Other elements in 3f2w:

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Barium atom in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. (pdb code 3f2w). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 16 binding sites of Barium where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak., PDB code: 3f2w:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 16 in 3f2w

Go back to Barium Binding Sites List in 3f2w
Barium binding site 1 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba401

b:0.2
occ:0.40
O6 X:G97 2.8 0.8 1.0
O4 X:U96 3.5 0.7 1.0
BA X:BA412 3.6 0.3 0.6
C6 X:G97 3.8 1.0 1.0
N6 X:A85 4.0 0.5 1.0
N7 X:G97 4.1 0.1 1.0
O6 X:G98 4.3 0.4 1.0
C5 X:G97 4.3 0.2 1.0
C4 X:U96 4.4 0.5 1.0
OP1 X:U94 4.7 0.6 1.0
O2 X:FMN200 4.7 82.1 1.0
N4 X:C86 4.8 0.9 1.0
C5 X:U96 4.9 0.5 1.0
N1 X:G97 5.0 0.7 1.0

Barium binding site 2 out of 16 in 3f2w

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Barium binding site 2 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba402

b:0.1
occ:1.00
O1P X:FMN200 2.7 77.2 1.0
N7 X:G33 2.9 0.7 1.0
O2' X:G41 3.1 0.8 1.0
O6 X:G62 3.2 0.5 1.0
O3P X:FMN200 3.5 77.2 1.0
O6 X:G33 3.7 0.9 1.0
P X:FMN200 3.7 77.4 1.0
C5 X:G33 3.9 1.0 1.0
C8 X:G33 3.9 0.4 1.0
N1 X:G62 3.9 0.3 1.0
C6 X:G62 4.0 0.1 1.0
C6 X:G33 4.2 0.9 1.0
C2' X:G41 4.4 0.6 1.0
O4' X:G41 4.5 0.0 1.0
C4' X:G41 4.5 0.6 1.0
C1' X:G41 4.6 0.4 1.0
O5' X:FMN200 4.7 77.3 1.0
N1 X:G10 4.7 0.3 1.0
O3' X:G41 4.8 0.1 1.0
O2P X:FMN200 4.8 76.8 1.0
N1 X:A63 4.9 0.0 1.0
C3' X:G41 4.9 0.4 1.0

Barium binding site 3 out of 16 in 3f2w

Go back to Barium Binding Sites List in 3f2w
Barium binding site 3 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba403

b:0.5
occ:1.00
OP2 X:G101 2.7 0.5 1.0
OP1 X:G101 3.0 0.5 1.0
P X:G101 3.1 0.5 1.0
O3' X:U100 3.6 0.2 1.0
N7 X:G9 4.0 0.1 1.0
C4' X:U100 4.4 0.6 1.0
C8 X:G9 4.4 1.0 1.0
BA X:BA404 4.4 0.6 1.0
C3' X:U100 4.6 0.1 1.0
OP2 X:G10 4.6 0.0 1.0
O5' X:G101 4.7 0.5 1.0
C5 X:G9 4.8 1.0 1.0
O6 X:G103 4.9 0.0 1.0

Barium binding site 4 out of 16 in 3f2w

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Barium binding site 4 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba404

b:0.6
occ:1.00
O6 X:G9 2.5 0.9 1.0
OP2 X:A102 2.5 0.1 1.0
OP1 X:G101 2.8 0.5 1.0
C6 X:G9 3.5 0.9 1.0
P X:G101 3.7 0.5 1.0
O5' X:G101 4.0 0.5 1.0
P X:A102 4.0 0.6 1.0
N7 X:G9 4.1 0.1 1.0
C5 X:G9 4.2 1.0 1.0
OP2 X:G101 4.2 0.5 1.0
BA X:BA403 4.4 0.5 1.0
N1 X:G9 4.6 0.6 1.0
O5' X:A102 4.7 0.4 1.0
O3' X:G101 4.8 0.1 1.0
N7 X:A102 4.8 1.0 1.0
OP1 X:A102 4.9 0.5 1.0
C3' X:G101 4.9 0.4 1.0

Barium binding site 5 out of 16 in 3f2w

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Barium binding site 5 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba405

b:0.0
occ:0.60
O6 X:GTP1 2.6 0.4 1.0
O4 X:U111 3.7 0.1 1.0
C6 X:GTP1 3.8 0.3 1.0
O4 X:U110 3.8 0.6 1.0
O6 X:G2 4.0 0.0 1.0
C5 X:GTP1 4.5 0.3 1.0
N7 X:GTP1 4.5 0.2 1.0
N1 X:GTP1 4.7 0.4 1.0
O2G X:GTP1 4.8 0.3 1.0
C4 X:U111 4.9 0.0 1.0
C4 X:U110 5.0 0.8 1.0

Barium binding site 6 out of 16 in 3f2w

Go back to Barium Binding Sites List in 3f2w
Barium binding site 6 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba406

b:0.9
occ:0.60
O6 X:G19 2.7 0.2 1.0
O4 X:U18 3.8 0.9 1.0
C6 X:G19 3.9 0.1 1.0
C4 X:U18 4.6 0.8 1.0
C5 X:G19 4.7 0.0 1.0
MG X:MG302 4.7 0.3 1.0
N7 X:G19 4.7 0.9 1.0
C5 X:U18 4.8 0.7 1.0
N1 X:G19 4.9 0.2 1.0

Barium binding site 7 out of 16 in 3f2w

Go back to Barium Binding Sites List in 3f2w
Barium binding site 7 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba407

b:0.5
occ:0.30
OP1 X:G15 4.3 0.7 1.0
OP1 X:G16 4.6 0.4 1.0
OP2 X:G16 4.7 0.5 1.0

Barium binding site 8 out of 16 in 3f2w

Go back to Barium Binding Sites List in 3f2w
Barium binding site 8 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba408

b:0.1
occ:0.70
O6 X:G16 2.6 0.8 1.0
O6 X:G17 3.5 0.5 1.0
C6 X:G16 3.5 0.8 1.0
N7 X:G16 3.7 0.9 1.0
C5 X:G16 3.9 0.8 1.0
O6 X:G15 4.4 0.9 1.0
C6 X:G17 4.5 0.1 1.0
N1 X:G16 4.8 0.8 1.0
N7 X:G17 4.8 0.8 1.0
C8 X:G16 4.9 0.0 1.0

Barium binding site 9 out of 16 in 3f2w

Go back to Barium Binding Sites List in 3f2w
Barium binding site 9 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba409

b:97.9
occ:0.50
O6 X:G28 2.6 0.2 1.0
C6 X:G28 3.8 0.2 1.0
N7 X:G28 4.4 0.5 1.0
C5 X:G28 4.4 0.3 1.0
OP2 X:C26 4.8 0.5 1.0
N6 X:A29 4.8 0.8 1.0
N1 X:G28 4.9 1.0 1.0

Barium binding site 10 out of 16 in 3f2w

Go back to Barium Binding Sites List in 3f2w
Barium binding site 10 out of 16 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ba410

b:0.9
occ:0.40
N7 X:G93 3.0 0.3 1.0
O6 X:G93 3.4 0.0 1.0
C5 X:G93 3.9 0.1 1.0
C6 X:G93 4.0 0.1 1.0
C8 X:G93 4.1 0.0 1.0
N7 X:G84 4.3 0.6 1.0
OP1 X:G93 4.6 0.2 1.0
O6 X:G84 4.7 0.9 1.0
O4 X:U94 4.8 0.8 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: Tue Oct 27 17:00:42 2020

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