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Cobalt 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:

Magnesium (Mg) 8 atoms
Potassium (K) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 9 binding sites of Cobalt where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak., PDB code: 3f30:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in 3f30

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Cobalt binding site 1 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co401

b:0.1
occ:1.00
CO X:NCO401 0.0 0.1 1.0
N1 X:NCO401 2.0 0.7 1.0
N3 X:NCO401 2.0 0.6 1.0
N2 X:NCO401 2.0 0.8 1.0
N5 X:NCO401 2.0 0.7 1.0
N6 X:NCO401 2.0 0.1 1.0
N4 X:NCO401 2.0 0.5 1.0
O2 X:FMN200 4.1 80.3 1.0
O6 X:G97 4.2 90.8 1.0
N7 X:G97 4.5 89.9 1.0
O6 X:G98 4.6 93.2 1.0
C6 X:G97 4.9 90.1 1.0

Cobalt binding site 2 out of 9 in 3f30

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Cobalt binding site 2 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co403

b:0.3
occ:1.00
CO X:NCO403 0.0 0.3 1.0
N1 X:NCO403 2.0 0.3 1.0
N2 X:NCO403 2.0 0.4 1.0
N6 X:NCO403 2.0 0.3 1.0
N4 X:NCO403 2.0 0.2 1.0
N3 X:NCO403 2.0 0.2 1.0
N5 X:NCO403 2.0 0.2 1.0
OP1 X:U39 3.8 91.8 1.0
OP2 X:U37 3.9 94.9 1.0
OP2 X:A38 4.0 94.5 1.0
OP1 X:U37 4.4 96.1 1.0
P X:U37 4.5 95.1 1.0
O5' X:U37 4.6 95.0 1.0
O5' X:A38 4.7 93.7 1.0

Cobalt binding site 3 out of 9 in 3f30

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Cobalt binding site 3 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co404

b:0.4
occ:1.00
CO X:NCO404 0.0 0.4 1.0
N6 X:NCO404 2.0 0.5 1.0
N1 X:NCO404 2.0 0.4 1.0
N4 X:NCO404 2.0 0.4 1.0
N2 X:NCO404 2.0 0.3 1.0
N5 X:NCO404 2.0 0.7 1.0
N3 X:NCO404 2.0 0.3 1.0
N7 X:G16 4.1 93.8 1.0
O6 X:G16 4.4 93.4 1.0
O6 X:G17 4.8 93.5 1.0
N7 X:G17 4.8 93.1 1.0
C5 X:G16 4.9 93.8 1.0

Cobalt binding site 4 out of 9 in 3f30

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Cobalt binding site 4 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co405

b:97.8
occ:0.50
CO X:NCO405 0.0 97.8 0.5
N4 X:NCO405 2.0 97.7 0.5
N5 X:NCO405 2.0 97.6 0.5
N3 X:NCO405 2.0 97.5 0.5
N2 X:NCO405 2.0 97.3 0.5
N6 X:NCO405 2.0 97.4 0.5
N1 X:NCO405 2.0 97.4 0.5
O4 X:U111 4.2 88.1 1.0
O4 X:U110 4.2 85.3 1.0
O6 X:GTP1 4.3 0.8 1.0
O6 X:G2 4.6 0.7 1.0
N7 X:GTP1 4.9 0.9 1.0

Cobalt binding site 5 out of 9 in 3f30

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Cobalt binding site 5 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co406

b:0.7
occ:0.50
CO X:NCO406 0.0 0.7 0.5
N4 X:NCO406 2.0 0.6 0.5
N6 X:NCO406 2.0 0.6 0.5
N5 X:NCO406 2.0 0.4 0.5
N1 X:NCO406 2.0 0.5 0.5
N2 X:NCO406 2.0 0.5 0.5
N3 X:NCO406 2.0 0.4 0.5
OP2 X:C58 3.7 95.9 1.0
OP2 X:G47 4.1 91.4 1.0
OP1 X:G47 4.2 91.2 1.0
O4 X:U60 4.5 0.7 1.0
OP1 X:C46 4.5 93.4 1.0
P X:C58 4.5 96.0 1.0
OP1 X:C58 4.6 96.0 1.0
P X:G47 4.7 91.5 1.0
OP2 X:G57 4.8 0.1 1.0
O5' X:C58 4.9 94.9 1.0
O4 X:U61 5.0 0.8 1.0

Cobalt binding site 6 out of 9 in 3f30

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Cobalt binding site 6 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co407

b:0.8
occ:1.00
CO X:NCO407 0.0 0.8 1.0
N1 X:NCO407 2.0 0.8 1.0
N6 X:NCO407 2.0 0.8 1.0
N4 X:NCO407 2.0 0.7 1.0
N2 X:NCO407 2.0 0.7 1.0
N3 X:NCO407 2.0 0.8 1.0
N5 X:NCO407 2.0 0.8 1.0
O4 X:U64 4.2 95.4 1.0
OP2 X:C76 4.5 91.1 1.0
O4 X:U42 4.9 96.7 1.0

Cobalt binding site 7 out of 9 in 3f30

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Cobalt binding site 7 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co408

b:0.2
occ:1.00
CO X:NCO408 0.0 0.2 1.0
N6 X:NCO408 2.0 0.0 1.0
N3 X:NCO408 2.0 0.1 1.0
N2 X:NCO408 2.0 0.1 1.0
N4 X:NCO408 2.0 0.2 1.0
N5 X:NCO408 2.0 0.1 1.0
N1 X:NCO408 2.0 0.2 1.0
OP2 X:A49 4.2 92.9 1.0
N7 X:A50 4.4 90.2 1.0
O4 X:U52 4.5 0.7 1.0
O6 X:G51 4.5 96.5 1.0
N6 X:A50 4.7 89.8 1.0
OP2 X:A50 4.8 89.1 1.0
N7 X:G51 4.9 96.5 1.0

Cobalt binding site 8 out of 9 in 3f30

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Cobalt binding site 8 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co409

b:0.7
occ:1.00
CO X:NCO409 0.0 0.7 1.0
N1 X:NCO409 2.0 0.7 1.0
N5 X:NCO409 2.0 0.8 1.0
N4 X:NCO409 2.0 0.8 1.0
N3 X:NCO409 2.0 0.8 1.0
N2 X:NCO409 2.0 0.8 1.0
N6 X:NCO409 2.0 0.7 1.0
OP1 X:G33 3.7 95.0 1.0
OP1 X:A40 4.1 92.9 1.0
OP2 X:G41 4.3 93.6 1.0
P X:G33 4.9 94.9 1.0

Cobalt binding site 9 out of 9 in 3f30

Go back to Cobalt Binding Sites List in 3f30
Cobalt binding site 9 out of 9 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Cobalt Hexammine Soak.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 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:Co410

b:0.8
occ:1.00
CO X:NCO410 0.0 0.8 1.0
N5 X:NCO410 2.0 0.8 1.0
N1 X:NCO410 2.0 0.7 1.0
N2 X:NCO410 2.0 0.7 1.0
N4 X:NCO410 2.0 0.5 1.0
N3 X:NCO410 2.0 0.7 1.0
N6 X:NCO410 2.0 0.5 1.0
N7 X:G19 4.4 96.6 1.0
OP1 X:A21 4.4 97.7 1.0
O6 X:G19 4.5 96.2 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: Sun Dec 13 10:40:11 2020

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