Atomistry » Sodium » PDB 7lcz-7lsu » 7loq
Atomistry »
  Sodium »
    PDB 7lcz-7lsu »
      7loq »

Sodium in PDB 7loq: X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2

Enzymatic activity of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2

All present enzymatic activity of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2, PDB code: 7loq was solved by F.Yabukarski, T.Doukov, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.54 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.223, 77.223, 37.188, 90, 90, 90
R / Rfree (%) 13.8 / 16.9

Other elements in 7loq:

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2 (pdb code 7loq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2, PDB code: 7loq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7loq

Go back to Sodium Binding Sites List in 7loq
Sodium binding site 1 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:18.7
occ:0.44
NA A:NA201 0.0 18.7 0.4
HB2 A:SER72 1.2 28.8 0.6
NA A:NA201 1.8 33.7 0.6
O A:SER60 2.1 13.1 0.2
CB A:SER72 2.1 24.0 0.6
HB3 A:SER72 2.4 28.8 0.6
O A:HOH403 2.4 21.4 0.5
O A:CYS64 2.4 14.8 0.4
O A:SER60 2.4 17.1 0.4
O A:SER60 2.4 15.3 0.3
O A:CYS64 2.5 14.1 0.4
O A:HOH325 2.5 20.6 1.0
OG A:SER72 2.5 19.2 0.4
O A:ARG73 2.5 25.2 0.5
HA A:ASN65 2.7 17.1 0.4
O A:CYS64 2.8 13.7 0.3
HB2 A:SER72 2.8 26.4 0.4
HA A:SER72 2.9 25.3 0.6
CA A:SER72 3.0 21.1 0.6
OG A:SER72 3.1 43.2 0.6
HA A:ASN65 3.1 16.5 0.3
CB A:SER72 3.2 22.0 0.4
HG A:SER72 3.2 51.9 0.6
C A:CYS64 3.3 13.9 0.4
HA A:ASN65 3.3 16.8 0.3
C A:SER60 3.3 15.9 0.2
C A:SER60 3.5 14.3 0.3
CA A:ASN65 3.5 14.2 0.4
C A:SER60 3.6 14.4 0.4
H A:ARG73 3.6 20.9 0.6
C A:ARG73 3.6 20.6 0.5
HB2 A:SER60 3.6 15.4 0.4
C A:CYS64 3.6 14.2 0.4
C A:SER72 3.6 20.1 0.6
HA A:ARG61 3.7 22.5 0.5
N A:ASN65 3.7 12.8 0.4
C A:CYS64 3.7 13.9 0.3
HB A:THR69 3.7 17.4 0.3
HB A:THR69 3.8 18.2 0.3
HB2 A:ASN65 3.8 18.8 0.4
N A:ARG73 3.8 17.4 0.5
HA A:SER60 3.8 17.1 0.4
HB3 A:SER72 3.8 26.4 0.4
O A:ARG61 3.9 16.6 0.5
H A:CYS64 3.9 15.8 0.3
HA A:SER60 3.9 15.0 0.3
HB2 A:SER60 3.9 15.1 0.2
HB2 A:ASN74 3.9 20.4 0.6
N A:ASN74 4.0 19.2 0.6
C A:ARG61 4.0 17.5 0.5
HA A:ASN74 4.0 19.8 0.4
H A:CYS64 4.0 14.6 0.4
N A:ARG73 4.0 19.9 0.5
HB2 A:ASN74 4.0 21.7 0.4
CA A:ASN65 4.0 13.7 0.3
H A:ASP66 4.0 16.0 0.3
HA A:SER60 4.0 16.9 0.2
HB2 A:SER60 4.1 14.8 0.3
H A:ARG73 4.1 23.9 0.4
HB A:THR69 4.1 16.8 0.4
HA A:ARG61 4.1 21.5 0.2
CA A:SER60 4.1 14.2 0.4
H A:ASP66 4.1 15.7 0.4
C A:SER72 4.1 21.3 0.4
CA A:ASN65 4.1 13.9 0.3
CA A:ARG61 4.1 18.8 0.5
CB A:ASN65 4.2 15.7 0.4
N A:ARG61 4.2 14.5 0.5
H A:ASP66 4.2 15.3 0.3
CA A:SER60 4.2 14.1 0.2
CA A:SER60 4.2 12.5 0.3
N A:SER72 4.3 18.3 0.6
HA A:ASN74 4.3 23.9 0.6
N A:ASN65 4.3 11.6 0.3
CA A:SER72 4.3 24.6 0.4
N A:ASN65 4.3 14.6 0.3
OD1 A:ASN65 4.3 18.5 0.4
CB A:SER60 4.3 12.9 0.4
C A:ARG61 4.3 18.2 0.2
H A:SER72 4.4 21.9 0.5
N A:ARG61 4.4 14.2 0.2
O A:HOH403 4.4 35.1 0.5
N A:CYS64 4.4 12.1 0.4
CA A:ARG73 4.4 24.8 0.5
N A:ASN74 4.4 23.0 0.4
CA A:CYS64 4.4 12.9 0.4
H A:CYS64 4.5 15.7 0.3
CA A:ARG61 4.5 17.9 0.2
N A:CYS64 4.5 13.2 0.4
O A:SER72 4.5 24.6 0.6
H A:ASN65 4.5 15.4 0.4
CA A:ASN74 4.5 16.5 0.4
HG21 A:THR69 4.5 16.3 0.3
CA A:ASN74 4.5 19.9 0.6
O A:ARG61 4.6 17.3 0.2
HG21 A:THR69 4.6 17.2 0.3
N A:TRP62 4.6 16.9 0.1
CB A:SER60 4.6 12.6 0.2
HA A:ARG61 4.6 19.6 0.3
HB2 A:ASN65 4.6 16.9 0.3
N A:TRP62 4.6 16.5 0.5
O A:ARG61 4.6 14.4 0.3
CB A:THR69 4.6 14.5 0.3
C A:ARG61 4.6 16.1 0.3
CB A:THR69 4.6 15.2 0.3
O A:SER72 4.6 23.4 0.4
O A:HOH334 4.7 22.4 1.0
C A:ASN65 4.7 13.2 0.4
N A:ARG61 4.7 11.9 0.3
H A:TRP63 4.7 15.0 0.5
CB A:SER60 4.7 12.3 0.3
N A:ASP66 4.7 13.1 0.2
HG22 A:THR69 4.7 17.2 0.3
CB A:ASN74 4.7 18.1 0.4
CB A:ASN74 4.7 17.0 0.6
CA A:CYS64 4.7 12.4 0.4
H A:TRP63 4.7 14.9 0.1
N A:CYS64 4.7 13.1 0.3
HG1 A:THR69 4.7 19.0 0.3
N A:ASP66 4.7 13.3 0.5
CG A:ASN65 4.7 18.1 0.4
HG1 A:THR69 4.8 13.7 0.3
H A:TRP62 4.8 19.8 0.2
HA A:ARG73 4.8 29.8 0.5
HA A:CYS64 4.8 15.5 0.4
CB A:ASN65 4.8 14.1 0.3
OD1 A:ASN65 4.8 16.6 0.3
N A:ASP66 4.8 12.7 0.3
CG2 A:THR69 4.9 14.4 0.3
H A:TRP62 4.9 20.3 0.5
C A:ARG73 4.9 27.9 0.5
CA A:ARG61 4.9 16.3 0.3
HA A:SER72 4.9 29.5 0.4
CA A:CYS64 4.9 11.7 0.3
CA A:ARG73 4.9 19.9 0.5
N A:TRP63 4.9 12.5 0.3
HB3 A:SER60 4.9 15.4 0.4
H A:TRP63 4.9 15.6 0.4
OD1 A:ASP66 4.9 14.4 0.2
O A:THR69 4.9 18.2 0.4
HB2 A:ASN65 4.9 16.1 0.3
C A:TRP62 4.9 17.0 0.5
CG2 A:THR69 5.0 13.6 0.3
N A:TRP62 5.0 14.8 0.4
C A:ASN65 5.0 10.8 0.3
HA A:TRP62 5.0 16.2 0.5
C A:ASN65 5.0 12.2 0.3

Sodium binding site 2 out of 2 in 7loq

Go back to Sodium Binding Sites List in 7loq
Sodium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:33.7
occ:0.56
NA A:NA201 0.0 33.7 0.6
O A:ARG73 1.1 25.2 0.5
NA A:NA201 1.8 18.7 0.4
C A:ARG73 2.3 20.6 0.5
HB2 A:SER72 2.4 28.8 0.6
H A:ARG73 2.6 20.9 0.6
N A:ASN74 2.6 19.2 0.6
O A:SER60 2.7 13.1 0.2
HA A:ASN74 2.7 19.8 0.4
O A:CYS64 2.7 14.8 0.4
O A:CYS64 2.7 14.1 0.4
O A:SER60 2.7 17.1 0.4
O A:CYS64 3.0 13.7 0.3
H A:CYS64 3.0 15.8 0.3
HA A:ASN74 3.0 23.9 0.6
N A:ARG73 3.0 17.4 0.5
HB2 A:SER72 3.1 26.4 0.4
N A:ASN74 3.1 23.0 0.4
HA A:SER72 3.2 25.3 0.6
O A:ARG61 3.2 16.6 0.5
H A:CYS64 3.2 14.6 0.4
O A:SER60 3.2 15.3 0.3
CB A:SER72 3.2 24.0 0.6
CA A:ASN74 3.3 16.5 0.4
C A:TRP62 3.3 17.0 0.5
C A:CYS64 3.3 13.9 0.4
C A:ARG61 3.3 17.5 0.5
O A:HOH403 3.3 21.4 0.5
CA A:ASN74 3.3 19.9 0.6
H A:ARG73 3.3 23.9 0.4
H A:TRP63 3.4 15.0 0.5
N A:TRP63 3.4 12.5 0.3
N A:ARG73 3.4 19.9 0.5
N A:CYS64 3.4 12.1 0.4
H A:TRP63 3.4 14.9 0.1
CA A:ARG73 3.5 24.8 0.5
CA A:SER72 3.5 21.1 0.6
C A:TRP62 3.5 17.5 0.1
N A:TRP62 3.5 16.9 0.1
N A:TRP63 3.5 12.4 0.3
C A:SER72 3.5 20.1 0.6
N A:TRP62 3.5 16.5 0.5
C A:SER60 3.5 15.9 0.2
HB2 A:ASN74 3.5 21.7 0.4
N A:CYS64 3.6 13.2 0.4
O A:TRP62 3.6 16.4 0.5
HB2 A:ASN74 3.6 20.4 0.6
HA A:TRP62 3.6 16.2 0.5
C A:TRP62 3.6 14.3 0.4
C A:CYS64 3.6 14.2 0.4
C A:ARG73 3.7 27.9 0.5
N A:TRP63 3.7 13.0 0.4
H A:CYS64 3.7 15.7 0.3
CA A:TRP62 3.7 13.5 0.5
C A:ARG61 3.7 18.2 0.2
OG A:SER72 3.7 19.2 0.4
C A:CYS64 3.7 13.9 0.3
O A:TRP62 3.7 15.7 0.4
H A:TRP63 3.7 15.6 0.4
HA A:TRP62 3.8 18.6 0.1
C A:SER60 3.8 14.4 0.4
HB3 A:SER72 3.8 28.8 0.6
H A:TRP62 3.8 19.8 0.2
CA A:TRP62 3.8 15.5 0.1
HA A:ASN65 3.8 17.1 0.4
N A:CYS64 3.8 13.1 0.3
C A:SER60 3.8 14.3 0.3
CB A:SER72 3.8 22.0 0.4
HA A:SER60 3.8 17.1 0.4
CA A:ARG73 3.9 19.9 0.5
O A:TRP62 3.9 16.9 0.1
H A:TRP62 3.9 20.3 0.5
O A:ARG61 3.9 17.3 0.2
CA A:CYS64 3.9 12.9 0.4
CB A:ASN74 3.9 18.1 0.4
HG A:SER72 3.9 51.9 0.6
H A:ASN74 4.0 27.6 0.5
C A:TRP63 4.0 12.5 0.4
HA A:ARG61 4.0 22.5 0.5
CB A:ASN74 4.0 17.0 0.6
N A:ASN65 4.1 12.8 0.4
O A:ARG61 4.1 14.4 0.3
HA A:ARG73 4.1 29.8 0.5
CA A:ARG61 4.1 18.8 0.5
N A:TRP62 4.1 14.8 0.4
C A:ARG61 4.1 16.1 0.3
C A:SER72 4.1 21.3 0.4
HA A:ASN65 4.1 16.5 0.3
OG A:SER72 4.1 43.2 0.6
HA A:SER60 4.1 16.9 0.2
C A:TRP63 4.1 13.6 0.3
HA A:TRP62 4.1 21.6 0.4
HA A:SER60 4.2 15.0 0.3
HA A:CYS64 4.2 15.5 0.4
CA A:TRP62 4.2 18.0 0.4
HB2 A:ARG73 4.2 34.5 0.5
N A:ARG61 4.2 14.5 0.5
CA A:CYS64 4.2 12.4 0.4
O A:HOH325 4.2 20.6 1.0
HB2 A:ARG73 4.2 32.4 0.5
C A:TRP63 4.3 14.4 0.3
HA A:ASN65 4.3 16.8 0.3
HA A:ARG61 4.3 21.5 0.2
H A:LEU75 4.3 21.5 0.6
CA A:TRP63 4.3 12.7 0.3
CA A:TRP63 4.3 13.0 0.4
N A:ARG61 4.3 14.2 0.2
CA A:CYS64 4.4 11.7 0.3
CA A:ARG61 4.4 17.9 0.2
CA A:SER60 4.4 14.2 0.4
HB2 A:ASN65 4.4 18.8 0.4
CA A:ASN65 4.4 14.2 0.4
CA A:TRP63 4.4 13.1 0.3
H A:TRP62 4.4 17.8 0.3
CA A:SER60 4.5 14.1 0.2
CB A:ARG73 4.5 27.0 0.5
O A:SER72 4.5 24.6 0.6
C A:ASN74 4.5 19.1 0.4
N A:ASN65 4.5 11.6 0.3
CA A:SER72 4.6 24.6 0.4
HB3 A:SER72 4.6 26.4 0.4
HB2 A:SER60 4.6 15.4 0.4
HA A:CYS64 4.6 14.8 0.4
CA A:SER60 4.6 12.5 0.3
HA A:ARG73 4.6 23.9 0.5
N A:ASN65 4.6 14.6 0.3
CB A:ARG73 4.6 28.8 0.5
HA A:TRP63 4.6 15.7 0.4
C A:ASN74 4.6 17.6 0.6
CG A:ASN74 4.7 15.9 0.4
OD1 A:ASN74 4.7 17.3 0.4
HA A:CYS64 4.7 14.1 0.3
H A:ASN65 4.7 15.4 0.4
HB3 A:ASN74 4.7 20.4 0.6
N A:LEU75 4.7 15.7 0.5
N A:ARG61 4.7 11.9 0.3
HA A:TRP63 4.7 15.7 0.3
HA A:TRP63 4.7 15.2 0.3
O A:TRP63 4.7 14.0 0.4
HB3 A:ASN74 4.7 21.7 0.4
O A:SER72 4.8 23.4 0.4
CA A:ASN65 4.8 13.7 0.3
O A:TRP63 4.8 17.8 0.3
N A:LEU75 4.8 17.9 0.2
O A:ARG73 4.8 23.9 0.5
HA A:ARG61 4.8 19.6 0.3
CA A:ARG61 4.8 16.3 0.3
O A:HOH403 4.9 35.1 0.5
N A:SER72 4.9 18.3 0.6
N A:LEU75 4.9 14.3 0.4
CA A:ASN65 4.9 13.9 0.3
HB3 A:ARG73 4.9 32.4 0.5
HB2 A:SER60 4.9 15.1 0.2
CB A:ASN65 5.0 15.7 0.4
HA A:SER72 5.0 29.5 0.4
H A:ARG61 5.0 17.4 0.2

Reference:

F.Yabukarski, T.Doukov, D.A.Mokhtari, S.Du, D.Herschlag. Evaluating the Impact of X-Ray Damage on Conformational Heterogeneity in Room-Temperature (277 K) and Cryo-Cooled Protein Crystals. Acta Crystallogr D Struct V. 78 945 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35916220
DOI: 10.1107/S2059798322005939
Page generated: Tue Oct 8 17:39:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy