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Cobalt in PDB 3p59: First Crystal Structure of A Rna Nanosquare

Protein crystallography data

The structure of First Crystal Structure of A Rna Nanosquare, PDB code: 3p59 was solved by S.Dibrov, T.Hermann, J.Mclean, J.Parsons, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.06 / 2.18
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.378, 62.378, 126.268, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 19.2

Other elements in 3p59:

The structure of First Crystal Structure of A Rna Nanosquare also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the First Crystal Structure of A Rna Nanosquare (pdb code 3p59). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 10 binding sites of Cobalt where determined in the First Crystal Structure of A Rna Nanosquare, PDB code: 3p59:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 3p59

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Cobalt binding site 1 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1

b:0.3
occ:1.00
CO A:NCO1 0.0 0.3 1.0
N1 A:NCO1 2.0 0.2 1.0
N5 A:NCO1 2.0 0.3 1.0
N2 A:NCO1 2.0 0.8 1.0
N6 A:NCO1 2.0 0.5 1.0
N3 A:NCO1 2.0 88.9 1.0
N4 A:NCO1 2.0 28.9 1.0
N7 A:G49 3.6 36.7 1.0
N7 A:G48 3.6 28.8 1.0
O6 A:G48 3.9 36.0 1.0
O6 A:G49 4.2 44.2 1.0
C5 A:G48 4.3 28.5 1.0
C5 A:G49 4.4 37.3 1.0
C6 A:G48 4.4 27.7 1.0
C8 A:G49 4.5 26.1 1.0
C8 A:G48 4.5 27.5 1.0
C6 A:G49 4.6 38.2 1.0

Cobalt binding site 2 out of 10 in 3p59

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Cobalt binding site 2 out of 10 in the First Crystal Structure of A Rna Nanosquare


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1

b:61.6
occ:1.00
CO B:NCO1 0.0 61.6 1.0
N1 B:NCO1 2.0 30.9 1.0
N3 B:NCO1 2.0 0.7 1.0
N4 B:NCO1 2.0 39.5 1.0
N5 B:NCO1 2.0 0.2 1.0
N6 B:NCO1 2.0 0.6 1.0
N2 B:NCO1 2.0 27.4 1.0
O B:HOH62 3.7 50.1 1.0
O B:HOH19 4.1 34.0 1.0
O B:HOH79 4.3 41.1 1.0
O A:HOH65 4.3 36.3 1.0
O6 B:G107 4.4 22.0 1.0
O6 A:G60 4.4 27.6 1.0
O B:HOH25 4.7 24.9 1.0
O B:HOH81 4.7 35.5 1.0
O B:HOH27 4.8 33.8 1.0
O B:HOH91 4.8 37.4 1.0
N4 B:C105 4.8 38.3 1.0
N7 B:G107 5.0 16.0 1.0
N7 B:G106 5.0 26.8 1.0

Cobalt binding site 3 out of 10 in 3p59

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Cobalt binding site 3 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1

b:0.6
occ:1.00
CO C:NCO1 0.0 0.6 1.0
N2 C:NCO1 2.0 40.1 1.0
N3 C:NCO1 2.0 0.3 1.0
N4 C:NCO1 2.0 0.9 1.0
N6 C:NCO1 2.0 0.4 1.0
N1 C:NCO1 2.0 0.7 1.0
N5 C:NCO1 2.0 43.0 1.0
O C:HOH75 3.4 31.9 1.0
O C:HOH11 3.9 38.3 1.0
N7 C:G48 4.1 22.2 1.0
N7 C:G49 4.3 18.3 1.0
O6 C:G49 4.4 23.0 1.0
O C:HOH95 4.4 31.4 1.0
O6 C:G48 4.7 26.5 1.0
C5 C:G48 4.9 11.0 1.0
C8 C:G48 5.0 21.3 1.0

Cobalt binding site 4 out of 10 in 3p59

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Cobalt binding site 4 out of 10 in the First Crystal Structure of A Rna Nanosquare


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co61

b:0.4
occ:1.00
CO C:NCO61 0.0 0.4 1.0
N5 C:NCO61 2.0 0.7 1.0
N2 C:NCO61 2.0 42.9 1.0
N6 C:NCO61 2.0 0.7 1.0
N4 C:NCO61 2.0 50.7 1.0
N3 C:NCO61 2.0 47.4 1.0
N1 C:NCO61 2.0 48.6 1.0
O4' C:A54 3.9 54.5 1.0
C1' C:A54 3.9 53.9 1.0
O2' C:A54 4.2 66.5 1.0
O C:HOH62 4.2 47.6 1.0
C2 C:A53 4.3 28.9 1.0
N3 C:A53 4.6 28.3 1.0
C4' C:A54 4.7 62.6 1.0
C2' C:A54 4.7 62.8 1.0
N3 C:A54 4.9 43.4 1.0
N9 C:A54 5.0 39.1 1.0

Cobalt binding site 5 out of 10 in 3p59

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Cobalt binding site 5 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1

b:82.1
occ:1.00
CO D:NCO1 0.0 82.1 1.0
N4 D:NCO1 2.0 22.9 1.0
N6 D:NCO1 2.0 0.4 1.0
N5 D:NCO1 2.0 90.5 1.0
N2 D:NCO1 2.0 0.9 1.0
N1 D:NCO1 2.0 1.0 1.0
N3 D:NCO1 2.0 30.2 1.0
O6 D:G107 3.9 51.3 1.0
N7 D:G106 4.0 45.0 1.0
N7 D:G107 4.2 42.1 1.0
O6 D:G106 4.2 32.3 1.0
O D:HOH66 4.4 43.5 1.0
N4 D:C108 4.5 71.9 1.0
C5 D:G106 4.6 43.1 1.0
C6 D:G106 4.7 35.5 1.0
C6 D:G107 4.7 43.3 1.0
C5 D:G107 4.8 42.5 1.0
N4 D:C105 4.9 45.8 1.0
C8 D:G106 5.0 49.7 1.0

Cobalt binding site 6 out of 10 in 3p59

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Cobalt binding site 6 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co1

b:0.2
occ:1.00
CO E:NCO1 0.0 0.2 1.0
N2 E:NCO1 2.0 41.0 1.0
N6 E:NCO1 2.0 0.7 1.0
N5 E:NCO1 2.0 0.6 1.0
N1 E:NCO1 2.0 47.6 1.0
N3 E:NCO1 2.0 0.6 1.0
N4 E:NCO1 2.0 68.6 1.0
N7 E:G48 3.7 38.8 1.0
O6 E:G49 4.2 48.8 1.0
C8 E:G48 4.2 39.8 1.0
N7 E:G49 4.6 30.0 1.0
C5 E:G48 4.8 37.9 1.0

Cobalt binding site 7 out of 10 in 3p59

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Cobalt binding site 7 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co1

b:66.2
occ:1.00
CO F:NCO1 0.0 66.2 1.0
N3 F:NCO1 2.0 22.9 1.0
N1 F:NCO1 2.0 34.8 1.0
N4 F:NCO1 2.0 0.3 1.0
N2 F:NCO1 2.0 0.1 1.0
N5 F:NCO1 2.0 24.4 1.0
N6 F:NCO1 2.0 37.9 1.0
O6 E:G60 4.3 19.6 1.0
N7 F:G106 4.4 29.7 1.0
O6 F:G107 4.5 35.4 1.0
O6 F:G106 4.6 22.8 1.0
O4 E:5BU59 4.8 27.2 1.0

Cobalt binding site 8 out of 10 in 3p59

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Cobalt binding site 8 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co1

b:59.9
occ:1.00
CO G:NCO1 0.0 59.9 1.0
N2 G:NCO1 2.0 47.6 1.0
N5 G:NCO1 2.0 0.5 1.0
N4 G:NCO1 2.0 34.8 1.0
N6 G:NCO1 2.0 42.3 1.0
N1 G:NCO1 2.0 40.3 1.0
N3 G:NCO1 2.0 36.1 1.0
N7 G:G48 4.3 25.2 1.0
O G:HOH62 4.4 28.3 1.0
N7 G:G49 4.4 27.8 1.0
O6 G:G48 4.5 29.3 1.0
O6 G:G49 4.7 31.6 1.0
N4 G:C47 4.7 23.0 1.0
C5 G:G48 5.0 24.7 1.0

Cobalt binding site 9 out of 10 in 3p59

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Cobalt binding site 9 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co61

b:0.1
occ:1.00
CO G:NCO61 0.0 0.1 1.0
N1 G:NCO61 2.0 39.4 1.0
N4 G:NCO61 2.0 73.4 1.0
N5 G:NCO61 2.0 0.2 1.0
N6 G:NCO61 2.0 85.0 1.0
N2 G:NCO61 2.0 0.3 1.0
N3 G:NCO61 2.0 64.2 1.0
O G:HOH34 3.7 31.7 1.0
O6 G:G52 4.4 48.0 1.0
N7 G:G52 4.7 32.8 1.0
N7 G:G51 5.0 31.5 1.0

Cobalt binding site 10 out of 10 in 3p59

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Cobalt binding site 10 out of 10 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Co1

b:85.9
occ:1.00
CO H:NCO1 0.0 85.9 1.0
N5 H:NCO1 2.0 0.9 1.0
N1 H:NCO1 2.0 73.2 1.0
N4 H:NCO1 2.0 0.1 1.0
N6 H:NCO1 2.0 75.0 1.0
N2 H:NCO1 2.0 94.8 1.0
N3 H:NCO1 2.0 27.0 1.0
O6 H:G106 3.7 47.5 1.0
N7 H:G106 4.3 51.8 1.0
O6 H:G107 4.5 38.4 1.0
N4 H:C105 4.5 55.4 1.0
O H:HOH103 4.6 38.3 1.0
C6 H:G106 4.6 39.6 1.0
N4 E:C47 4.7 50.7 1.0
C5 H:G106 4.8 43.0 1.0
C4 H:C105 4.9 46.8 1.0

Reference:

S.M.Dibrov, J.Mclean, J.Parsons, T.Hermann. Self-Assembling Rna Square. Proc.Natl.Acad.Sci.Usa V. 108 6405 2011.
ISSN: ISSN 0027-8424
PubMed: 21464284
DOI: 10.1073/PNAS.1017999108
Page generated: Sun Dec 13 10:41:52 2020

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