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Sodium in PDB 3i31: Hera Helicase Rna Binding Domain Is An Rrm Fold

Protein crystallography data

The structure of Hera Helicase Rna Binding Domain Is An Rrm Fold, PDB code: 3i31 was solved by M.G.Rudolph, D.Klostermeier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.22 / 1.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 37.516, 37.516, 136.890, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.4

Other elements in 3i31:

The structure of Hera Helicase Rna Binding Domain Is An Rrm Fold also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Hera Helicase Rna Binding Domain Is An Rrm Fold (pdb code 3i31). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hera Helicase Rna Binding Domain Is An Rrm Fold, PDB code: 3i31:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3i31

Go back to Sodium Binding Sites List in 3i31
Sodium binding site 1 out of 3 in the Hera Helicase Rna Binding Domain Is An Rrm Fold


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hera Helicase Rna Binding Domain Is An Rrm Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2

b:52.9
occ:1.00
OE1 A:GLU433 2.9 71.8 1.0
O A:HOH37 3.1 60.2 1.0
OE2 A:GLU433 3.3 48.2 1.0
CD A:GLU433 3.3 60.0 1.0
NH2 A:ARG426 3.5 83.9 1.0
CG A:GLU433 4.6 46.6 1.0
CZ A:ARG426 4.7 76.0 1.0

Sodium binding site 2 out of 3 in 3i31

Go back to Sodium Binding Sites List in 3i31
Sodium binding site 2 out of 3 in the Hera Helicase Rna Binding Domain Is An Rrm Fold


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hera Helicase Rna Binding Domain Is An Rrm Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3

b:36.0
occ:1.00
OE2 A:GLU466 2.7 53.0 1.0
OE1 A:GLU466 2.8 35.0 1.0
CD A:GLU466 3.1 47.3 1.0
NA A:NA4 3.6 46.1 1.0
CG A:GLU466 4.5 27.3 1.0
O A:HOH33 4.7 57.1 1.0
O A:HOH25 5.0 53.0 1.0

Sodium binding site 3 out of 3 in 3i31

Go back to Sodium Binding Sites List in 3i31
Sodium binding site 3 out of 3 in the Hera Helicase Rna Binding Domain Is An Rrm Fold


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hera Helicase Rna Binding Domain Is An Rrm Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:46.1
occ:1.00
O A:HOH515 2.1 28.2 1.0
O A:HOH33 3.1 57.1 1.0
O A:HOH25 3.3 53.0 1.0
NA A:NA3 3.6 36.0 1.0
OE2 A:GLU466 4.1 53.0 1.0
ZN A:ZN1 4.2 46.8 1.0
O A:HOH23 4.2 47.8 1.0

Reference:

M.G.Rudolph, D.Klostermeier. The Thermus Thermophilus Dead Box Helicase Hera Contains A Modified Rna Recognition Motif Domain Loosely Connected to the Helicase Core. Rna V. 15 1993 2009.
ISSN: ISSN 1355-8382
PubMed: 19710183
DOI: 10.1261/RNA.1820009
Page generated: Tue Dec 15 06:13:58 2020

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