Atomistry » Sodium » PDB 3wxt-3zu5 » 3zmo
Atomistry »
  Sodium »
    PDB 3wxt-3zu5 »
      3zmo »

Sodium in PDB 3zmo: VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1)

Protein crystallography data

The structure of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1), PDB code: 3zmo was solved by I.Rissanen, J.M.Grimes, A.Pawlowski, S.Mantynen, K.Harlos, J.K.H.Bamford, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.56 / 1.80
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 61.850, 61.850, 251.220, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 21.5

Other elements in 3zmo:

The structure of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) (pdb code 3zmo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1), PDB code: 3zmo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3zmo

Go back to Sodium Binding Sites List in 3zmo
Sodium binding site 1 out of 2 in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1175

b:37.6
occ:0.50
O A:ARG35 2.7 24.5 1.0
O A:HOH2205 2.9 24.7 0.5
C A:ARG35 3.7 25.9 1.0
CB A:GLN34 3.9 24.1 1.0
CG2 A:VAL36 4.1 27.6 1.0
CA A:VAL36 4.2 21.9 1.0
O A:HOH2056 4.3 27.5 1.0
OE1 A:GLN34 4.3 26.3 1.0
N A:VAL36 4.3 21.1 1.0
N A:ARG35 4.5 24.7 1.0
O A:HOH2014 4.6 32.3 1.0
C A:GLN34 4.7 26.8 1.0
CG A:GLN34 4.7 26.1 1.0
CB A:VAL36 4.7 26.3 1.0
O A:HOH2055 4.7 25.8 1.0
CA A:ARG35 4.8 25.1 1.0
CD A:GLN34 4.9 24.4 1.0
CA A:GLN34 4.9 23.2 1.0

Sodium binding site 2 out of 2 in 3zmo

Go back to Sodium Binding Sites List in 3zmo
Sodium binding site 2 out of 2 in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1176

b:41.6
occ:0.50
OD2 A:ASP63 2.7 36.8 1.0
O A:HOH2100 2.9 28.9 1.0
CG A:ASP63 3.4 34.0 1.0
OD1 A:ASP63 4.0 32.7 1.0
CB A:ASP63 4.1 30.9 1.0
ND2 A:ASN67 4.2 38.0 1.0
CG2 A:VAL149 4.3 28.3 1.0
O A:HOH2098 4.5 30.1 1.0
CA A:VAL149 4.5 24.8 1.0
CG1 A:VAL149 4.6 27.8 1.0
CB A:VAL149 4.7 27.4 1.0
O A:GLY148 4.8 32.5 1.0
N A:GLY65 4.8 33.9 1.0

Reference:

I.Rissanen, J.M.Grimes, A.Pawlowski, S.Mantynen, K.Harlos, J.K.H.Bamford, D.I.Stuart. Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of An Ancient Branch From A Major Virus Lineage. Structure V. 21 718 2013.
ISSN: ISSN 0969-2126
PubMed: 23623731
DOI: 10.1016/J.STR.2013.02.026
Page generated: Tue Dec 15 06:31:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy