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Magnesium 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:

Cobalt (Co) 10 atoms
Bromine (Br) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 3p59

Go back to Magnesium Binding Sites List in 3p59
Magnesium binding site 1 out of 2 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg61

b:29.1
occ:1.00
O B:HOH46 2.1 28.0 1.0
O A:HOH63 2.2 30.3 1.0
O2 A:C55 2.4 33.1 1.0
O A:HOH96 3.0 43.3 1.0
O A:HOH62 3.1 33.7 1.0
C2 A:C55 3.5 29.0 1.0
O A:HOH6 3.9 19.9 1.0
N7 B:A109 4.0 14.8 1.0
O6 B:G110 4.0 20.2 1.0
N6 B:A109 4.1 18.7 1.0
N7 B:G110 4.2 18.8 1.0
N3 A:C55 4.2 24.0 1.0
O B:HOH25 4.2 24.9 1.0
O B:HOH22 4.4 20.6 1.0
N1 A:A54 4.4 16.0 1.0
N4 B:C108 4.5 10.3 1.0
N1 A:C55 4.5 26.1 1.0
C1' A:C55 4.6 25.3 1.0
C5 B:A109 4.7 8.7 1.0
C6 B:G110 4.8 25.4 1.0
C2' A:C55 4.8 26.2 1.0
C5 B:G110 4.8 28.1 1.0
C6 B:A109 4.8 12.8 1.0
C8 B:A109 4.9 17.3 1.0
O2' A:C55 4.9 29.6 1.0
C2 A:A54 5.0 18.6 1.0

Magnesium binding site 2 out of 2 in 3p59

Go back to Magnesium Binding Sites List in 3p59
Magnesium binding site 2 out of 2 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg61

b:33.3
occ:1.00
O E:HOH109 2.4 46.5 1.0
N7 E:G51 3.0 34.6 1.0
O E:HOH64 3.0 34.8 1.0
O6 E:G51 3.1 36.7 1.0
OP2 E:G51 3.6 0.6 1.0
C5 E:G51 3.7 35.0 1.0
C6 E:G51 3.8 29.6 1.0
N7 E:A50 3.8 38.0 1.0
C8 E:G51 4.1 38.1 1.0
C5 E:A50 4.2 36.9 1.0
N6 E:A50 4.4 41.1 1.0
C8 E:A50 4.5 35.3 1.0
C6 E:A50 4.5 36.6 1.0
O6 E:G52 4.6 31.9 1.0
OP2 E:A50 4.6 86.2 1.0
C4 E:A50 5.0 40.7 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: Mon Dec 14 08:38:43 2020

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