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Sodium in PDB 2c3a: Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry

Protein crystallography data

The structure of Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry, PDB code: 2c3a was solved by C.Krummenacher, V.M.Supekar, J.C.Whitbeck, E.Lazear, S.A.Connolly, R.J.Eisenberg, G.H.Cohen, D.C.Wiley, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.5
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.629, 79.105, 123.563, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 27.5

Other elements in 2c3a:

The structure of Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry (pdb code 2c3a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry, PDB code: 2c3a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2c3a

Go back to Sodium Binding Sites List in 2c3a
Sodium binding site 1 out of 2 in the Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1311

b:44.9
occ:1.00
OE1 B:GLU146 2.0 52.4 1.0
OE2 B:GLU226 2.3 54.2 1.0
OE1 B:GLU226 2.8 53.6 1.0
CD B:GLU226 2.9 48.1 1.0
CD B:GLU146 3.2 48.8 1.0
NE B:ARG229 3.7 29.1 1.0
CG B:GLU146 4.0 39.6 1.0
OE2 B:GLU146 4.2 54.4 1.0
NH2 B:ARG229 4.2 32.3 1.0
CZ B:ARG229 4.4 31.9 1.0
CG B:GLU226 4.4 39.6 1.0
CD B:ARG229 4.5 28.7 1.0

Sodium binding site 2 out of 2 in 2c3a

Go back to Sodium Binding Sites List in 2c3a
Sodium binding site 2 out of 2 in the Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1312

b:26.4
occ:1.00
OG B:SER68 2.7 24.1 1.0
O B:HOH2028 2.7 20.8 1.0
N B:LYS245 2.9 28.9 1.0
O B:LYS245 3.5 29.7 1.0
N B:SER68 3.5 23.4 1.0
CZ2 B:TRP241 3.6 21.8 1.0
CB B:SER68 3.6 22.1 1.0
CA B:PRO244 3.7 26.2 1.0
CH2 B:TRP241 3.8 18.4 1.0
CA B:LYS245 3.8 29.5 1.0
C B:PRO244 3.8 27.3 1.0
CB B:LYS245 3.8 29.9 1.0
C B:ARG67 3.9 24.7 1.0
CA B:ARG67 3.9 24.3 1.0
C B:LYS245 3.9 29.8 1.0
CA B:SER68 4.2 22.8 1.0
O B:CYS66 4.3 24.0 1.0
CG B:LYS245 4.4 30.5 1.0
CB B:PRO244 4.4 25.4 1.0
NE B:ARG67 4.4 27.4 1.0
CA B:GLY243 4.5 27.1 1.0
CB B:ARG67 4.6 24.5 1.0
CE2 B:TRP241 4.7 21.5 1.0
O B:ARG67 4.7 24.4 1.0
CD B:ARG67 4.8 24.8 1.0
ND1 B:HIS154 4.9 25.1 1.0
O B:PRO244 4.9 27.8 1.0
CZ3 B:TRP241 4.9 23.1 1.0
N B:PRO244 5.0 25.7 1.0
N B:ARG67 5.0 23.5 1.0

Reference:

C.Krummenacher, V.M.Supekar, J.C.Whitbeck, E.Lazear, S.A.Connolly, R.J.Eisenberg, G.H.Cohen, D.C.Wiley, A.Carfi. Structure of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation of Virus Entry. Embo J. V. 24 4144 2005.
ISSN: ISSN 0261-4189
PubMed: 16292345
DOI: 10.1038/SJ.EMBOJ.7600875
Page generated: Tue Dec 15 05:46:29 2020

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