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Sodium in PDB 2orh: Directing Macromolecular Conformation Through Halogen Bonds

Protein crystallography data

The structure of Directing Macromolecular Conformation Through Halogen Bonds, PDB code: 2orh was solved by A.R.Voth, F.A.Hays, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.610, 24.170, 36.962, 90.00, 110.01, 90.00
R / Rfree (%) 22 / 26.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Directing Macromolecular Conformation Through Halogen Bonds (pdb code 2orh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Directing Macromolecular Conformation Through Halogen Bonds, PDB code: 2orh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2orh

Go back to Sodium Binding Sites List in 2orh
Sodium binding site 1 out of 2 in the Directing Macromolecular Conformation Through Halogen Bonds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Directing Macromolecular Conformation Through Halogen Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na63

b:1.3
occ:0.50
OP2 A:DA6 2.6 9.7 1.0
C8 A:DA6 3.2 10.0 1.0
O5' A:DA6 3.4 9.9 1.0
P A:DA6 3.6 11.7 1.0
C2' A:DA6 3.6 10.1 1.0
N7 A:DA6 4.1 10.2 1.0
N9 A:DA6 4.1 9.2 1.0
O A:HOH35 4.2 7.6 0.5
C1' A:DA6 4.4 9.8 1.0
OP1 A:DA6 4.5 10.6 1.0
C2' A:DT5 4.6 18.0 1.0
C3' A:DA6 4.6 8.9 1.0
C5' A:DA6 4.7 8.3 1.0
O3' A:DT5 4.8 11.0 1.0
O4' A:DA6 4.9 7.8 1.0

Sodium binding site 2 out of 2 in 2orh

Go back to Sodium Binding Sites List in 2orh
Sodium binding site 2 out of 2 in the Directing Macromolecular Conformation Through Halogen Bonds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Directing Macromolecular Conformation Through Halogen Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na28

b:9.6
occ:1.00
O B:HOH21 2.4 1.3 1.0
O B:HOH30 2.4 2.1 1.0
O B:HOH22 2.6 1.3 1.0
O B:HOH43 2.6 11.1 1.0
O B:HOH26 2.8 5.2 1.0
O4' B:DG13 4.2 14.3 1.0
O B:HOH93 4.6 20.9 1.0
C5' B:DG14 4.6 6.2 1.0
O4' B:DG14 4.6 6.5 1.0
C1' B:DG13 4.7 11.4 1.0
N3 B:DG13 4.7 7.8 1.0
O B:HOH86 4.7 14.9 1.0
C4' B:DG13 4.7 15.5 1.0
O2 B:DC12 4.8 5.8 1.0
O3' B:DG13 4.8 14.4 1.0
C4' B:DG14 4.9 6.8 1.0

Reference:

A.R.Voth, F.A.Hays, P.S.Ho. Directing Macromolecular Conformation Through Halogen Bonds. Proc.Natl.Acad.Sci.Usa V. 104 6188 2007.
ISSN: ISSN 0027-8424
PubMed: 17379665
DOI: 10.1073/PNAS.0610531104
Page generated: Tue Dec 15 05:52:45 2020

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