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

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

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

Protein crystallography data

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Crystal 2, PDB code: 7lpm 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) 34.62 / 1.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.409, 77.409, 37.418, 90, 90, 90
R / Rfree (%) 13.6 / 15.8

Other elements in 7lpm:

The structure of X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Crystal 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, Crystal 2 (pdb code 7lpm). 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, Crystal 2, PDB code: 7lpm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7lpm

Go back to Sodium Binding Sites List in 7lpm
Sodium binding site 1 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Crystal 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, Crystal 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:21.0
occ:0.59
NA A:NA201 0.0 21.0 0.6
HB2 A:SER72 1.1 25.8 0.6
NA A:NA201 1.7 23.9 0.4
CB A:SER72 2.0 21.5 0.6
O A:SER60 2.0 11.3 0.3
HB3 A:SER72 2.2 25.8 0.6
O A:CYS64 2.4 14.0 0.4
O A:SER60 2.4 13.6 0.4
O A:HOH389 2.4 21.0 0.4
O A:ARG73 2.4 20.0 0.5
O A:SER60 2.5 12.9 0.3
O A:CYS64 2.5 10.3 0.3
O A:HOH345 2.5 19.3 1.0
OG A:SER72 2.5 20.0 0.4
HA A:ASN65 2.7 14.6 0.3
HB2 A:SER72 2.8 22.7 0.4
HG A:SER72 2.8 42.7 0.6
O A:CYS64 2.9 12.4 0.3
OG A:SER72 2.9 35.6 0.6
CA A:SER72 3.0 21.4 0.6
HA A:SER72 3.0 25.7 0.6
CB A:SER72 3.2 18.9 0.4
C A:SER60 3.2 13.1 0.3
HA A:ASN65 3.2 14.3 0.3
HA A:ASN65 3.2 14.5 0.4
C A:CYS64 3.3 12.4 0.4
C A:SER60 3.4 11.7 0.4
CA A:ASN65 3.5 12.1 0.3
C A:ARG73 3.5 18.3 0.5
H A:ARG73 3.5 22.0 0.6
C A:CYS64 3.6 10.6 0.3
C A:SER72 3.6 19.9 0.6
C A:SER60 3.7 14.2 0.3
HA A:ARG61 3.7 17.9 0.4
HB A:THR69 3.7 13.4 0.2
O A:ARG61 3.7 15.7 0.4
N A:ASN65 3.7 10.4 0.3
HB2 A:SER60 3.7 11.4 0.3
HB A:THR69 3.8 16.1 0.3
N A:ARG73 3.8 18.3 0.5
HB2 A:SER60 3.8 12.4 0.3
HB3 A:SER72 3.8 22.7 0.4
HA A:SER60 3.8 13.6 0.4
C A:CYS64 3.8 10.7 0.3
HB2 A:ASN65 3.8 14.5 0.3
HB2 A:ASN74 3.8 20.0 0.5
H A:CYS64 3.9 10.9 0.4
HB2 A:SER60 3.9 13.9 0.4
C A:ARG61 3.9 14.4 0.4
HA A:SER60 3.9 13.4 0.3
H A:CYS64 3.9 15.4 0.3
N A:ARG73 4.0 16.9 0.5
HA A:ASN74 4.0 17.0 0.5
HB A:THR69 4.0 13.2 0.5
N A:ASN74 4.0 16.4 0.5
H A:ARG73 4.0 20.3 0.4
H A:ASP66 4.0 14.8 0.3
CA A:ASN65 4.1 11.9 0.3
CA A:ARG61 4.1 14.9 0.4
CA A:SER60 4.1 11.2 0.3
H A:ASP66 4.1 14.2 0.3
N A:ARG61 4.1 12.4 0.4
HA A:SER60 4.1 12.8 0.3
CA A:ASN65 4.1 12.1 0.4
C A:SER72 4.1 19.4 0.4
HA A:ARG61 4.1 14.1 0.2
HB2 A:ASN74 4.1 18.2 0.5
CA A:SER60 4.1 11.3 0.4
CB A:ASN65 4.2 12.0 0.3
H A:ASP66 4.2 12.9 0.4
N A:SER72 4.2 18.3 0.6
N A:ASN65 4.2 12.5 0.3
CA A:SER72 4.3 17.1 0.4
H A:SER72 4.3 21.9 0.6
N A:CYS64 4.3 9.1 0.4
C A:ARG61 4.3 11.4 0.2
CA A:SER60 4.3 10.7 0.3
N A:ARG61 4.4 11.7 0.2
HA A:ASN74 4.4 18.6 0.5
N A:ASN65 4.4 10.8 0.4
HG21 A:THR69 4.4 13.8 0.3
CA A:ARG73 4.4 22.9 0.5
CB A:SER60 4.4 10.3 0.3
CA A:CYS64 4.4 12.2 0.4
N A:ASN74 4.4 21.9 0.5
OD1 A:ASN65 4.4 17.5 0.3
O A:ARG61 4.4 11.7 0.2
O A:SER72 4.5 22.6 0.6
CA A:ARG61 4.5 11.8 0.2
CB A:SER60 4.5 9.5 0.3
CA A:ASN74 4.5 14.1 0.5
H A:ASN65 4.5 12.5 0.4
OD1 A:ASN65 4.5 16.8 0.4
HA A:ARG61 4.5 14.6 0.3
N A:TRP62 4.5 13.3 0.2
HG21 A:THR69 4.5 14.9 0.2
CB A:SER60 4.5 11.6 0.4
N A:CYS64 4.5 12.8 0.3
O A:ARG61 4.5 15.2 0.3
CB A:THR69 4.6 11.1 0.2
C A:ARG61 4.6 12.9 0.3
CB A:ASN74 4.6 16.6 0.5
HG22 A:THR69 4.6 14.9 0.2
H A:CYS64 4.6 12.6 0.3
CB A:THR69 4.6 13.4 0.3
HG1 A:THR69 4.6 10.9 0.2
C A:ASN65 4.6 9.6 0.3
O A:HOH389 4.6 32.6 0.6
N A:TRP62 4.6 12.6 0.4
N A:ASP66 4.7 11.9 0.2
O A:HOH356 4.7 19.8 1.0
CA A:ASN74 4.7 15.5 0.5
HB2 A:ASN65 4.7 15.2 0.4
O A:SER72 4.7 19.8 0.4
N A:ARG61 4.7 10.8 0.3
CA A:CYS64 4.7 12.4 0.3
H A:TRP63 4.7 13.6 0.4
N A:ASP66 4.7 12.3 0.5
H A:TRP63 4.8 14.4 0.2
HB2 A:ASN65 4.8 16.7 0.3
CG2 A:THR69 4.8 12.4 0.2
HA A:ARG73 4.8 27.5 0.5
HG1 A:THR69 4.8 14.2 0.3
N A:CYS64 4.8 10.5 0.3
O A:THR69 4.8 17.5 0.2
CA A:ARG61 4.8 12.1 0.3
H A:TRP62 4.8 16.0 0.4
CG A:ASN65 4.8 14.9 0.3
HA A:CYS64 4.9 14.6 0.4
HA A:SER72 4.9 20.5 0.4
CB A:ASN74 4.9 15.1 0.5
O A:THR69 4.9 14.9 0.5
CB A:ASN65 4.9 12.7 0.4
H A:TRP63 4.9 13.6 0.4
H A:TRP62 4.9 15.2 0.2
CG2 A:THR69 4.9 11.5 0.3
CA A:ARG73 4.9 21.4 0.5
N A:ASP66 4.9 10.8 0.3
C A:ARG73 4.9 23.9 0.5
H A:ARG61 4.9 14.8 0.3
N A:TRP62 4.9 13.1 0.4
HG A:SER60 4.9 12.6 0.3
C A:TRP62 4.9 12.5 0.4
C A:ASN65 4.9 11.1 0.3
N A:TRP63 4.9 11.3 0.3
CB A:THR69 5.0 11.0 0.5
CA A:CYS64 5.0 10.1 0.3

Sodium binding site 2 out of 2 in 7lpm

Go back to Sodium Binding Sites List in 7lpm
Sodium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Crystal 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, Crystal 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:23.9
occ:0.42
NA A:NA201 0.0 23.9 0.4
O A:ARG73 1.3 20.0 0.5
NA A:NA201 1.7 21.0 0.6
HB2 A:SER72 2.3 25.8 0.6
O A:SER60 2.4 11.3 0.3
C A:ARG73 2.5 18.3 0.5
O A:CYS64 2.5 14.0 0.4
O A:CYS64 2.6 10.3 0.3
O A:SER60 2.6 12.9 0.3
H A:ARG73 2.7 22.0 0.6
HA A:ASN74 2.7 17.0 0.5
H A:CYS64 2.8 10.9 0.4
H A:CYS64 2.9 15.4 0.3
N A:ASN74 2.9 16.4 0.5
O A:CYS64 2.9 12.4 0.3
O A:SER60 2.9 13.6 0.4
O A:ARG61 3.0 15.7 0.4
HB2 A:SER72 3.1 22.7 0.4
C A:ARG61 3.1 14.4 0.4
CB A:SER72 3.2 21.5 0.6
C A:CYS64 3.2 12.4 0.4
N A:ARG73 3.2 18.3 0.5
N A:CYS64 3.2 9.1 0.4
HA A:ASN74 3.2 18.6 0.5
C A:TRP62 3.3 12.5 0.4
C A:SER60 3.3 13.1 0.3
H A:TRP63 3.3 13.6 0.4
N A:ASN74 3.3 21.9 0.5
HA A:SER72 3.3 25.7 0.6
H A:TRP63 3.4 14.4 0.2
N A:TRP63 3.4 11.3 0.3
N A:TRP62 3.4 13.3 0.2
CA A:ASN74 3.4 14.1 0.5
H A:ARG73 3.4 20.3 0.4
C A:TRP62 3.5 13.5 0.2
O A:HOH389 3.5 21.0 0.4
N A:CYS64 3.5 12.8 0.3
N A:TRP63 3.5 12.0 0.3
N A:TRP62 3.5 12.6 0.4
C A:CYS64 3.5 10.6 0.3
H A:TRP63 3.5 13.6 0.4
N A:TRP63 3.5 11.3 0.4
C A:SER60 3.5 11.7 0.4
HB2 A:ASN74 3.5 20.0 0.5
C A:TRP62 3.6 13.3 0.4
N A:ARG73 3.6 16.9 0.5
O A:TRP62 3.6 12.8 0.4
CA A:SER72 3.6 21.4 0.6
C A:ARG61 3.6 11.4 0.2
HB3 A:SER72 3.6 25.8 0.6
HA A:TRP62 3.6 16.4 0.4
CA A:ASN74 3.6 15.5 0.5
C A:SER60 3.6 14.2 0.3
CA A:ARG73 3.6 22.9 0.5
H A:CYS64 3.7 12.6 0.3
CA A:TRP62 3.7 13.7 0.4
C A:SER72 3.7 19.9 0.6
C A:CYS64 3.7 10.7 0.3
HA A:TRP62 3.7 16.7 0.2
CA A:TRP62 3.7 13.9 0.2
OG A:SER72 3.7 20.0 0.4
H A:TRP62 3.7 16.0 0.4
H A:TRP62 3.7 15.2 0.2
HA A:ASN65 3.8 14.6 0.3
CA A:CYS64 3.8 12.2 0.4
HA A:SER60 3.8 13.4 0.3
O A:ARG61 3.8 11.7 0.2
O A:TRP62 3.8 15.1 0.4
N A:CYS64 3.8 10.5 0.3
HA A:SER60 3.8 13.6 0.4
HA A:ARG61 3.9 17.9 0.4
CB A:SER72 3.9 18.9 0.4
C A:TRP63 3.9 10.9 0.4
HA A:SER60 3.9 12.8 0.3
HB2 A:ASN74 3.9 18.2 0.5
CA A:ARG61 3.9 14.9 0.4
C A:ARG73 3.9 23.9 0.5
N A:TRP62 3.9 13.1 0.4
C A:ARG61 3.9 12.9 0.3
O A:TRP62 4.0 10.8 0.2
N A:ARG61 4.0 12.4 0.4
O A:ARG61 4.0 15.2 0.3
N A:ASN65 4.0 10.4 0.3
CB A:ASN74 4.0 16.6 0.5
CA A:ARG73 4.1 21.4 0.5
HA A:ASN65 4.1 14.5 0.4
CA A:CYS64 4.1 12.4 0.3
C A:TRP63 4.1 11.3 0.3
CA A:TRP62 4.1 13.4 0.4
OG A:SER72 4.1 35.6 0.6
CA A:SER60 4.1 11.2 0.3
O A:HOH345 4.1 19.3 1.0
HA A:CYS64 4.1 14.6 0.4
N A:ARG61 4.1 11.7 0.2
H A:ASN74 4.1 26.3 0.5
HA A:TRP62 4.2 16.1 0.4
HA A:ASN65 4.2 14.3 0.3
H A:TRP62 4.2 15.7 0.3
HA A:ARG61 4.2 14.1 0.2
HG A:SER72 4.2 42.7 0.6
CA A:ARG61 4.2 11.8 0.2
CA A:TRP63 4.2 11.2 0.4
C A:SER72 4.2 19.4 0.4
C A:TRP63 4.2 11.7 0.3
HA A:ARG73 4.3 27.5 0.5
CA A:TRP63 4.3 11.8 0.3
CA A:SER60 4.3 11.3 0.4
CA A:SER60 4.3 10.7 0.3
CB A:ASN74 4.3 15.1 0.5
H A:LEU75 4.3 14.9 0.5
HB2 A:ARG73 4.3 30.5 0.5
HB2 A:ARG73 4.3 28.1 0.5
CA A:CYS64 4.3 10.1 0.3
CA A:ASN65 4.4 12.1 0.3
CA A:TRP63 4.4 11.7 0.3
H A:LEU75 4.5 18.9 0.5
N A:ASN65 4.5 12.5 0.3
HB2 A:SER60 4.5 11.4 0.3
HA A:CYS64 4.5 14.9 0.3
HB2 A:ASN65 4.5 14.5 0.3
N A:ASN65 4.5 10.8 0.4
N A:ARG61 4.6 10.8 0.3
HB3 A:SER72 4.6 22.7 0.4
HA A:TRP63 4.6 13.4 0.4
HB2 A:SER60 4.6 12.4 0.3
CB A:ARG73 4.6 23.4 0.5
H A:ASN65 4.6 12.5 0.4
C A:ASN74 4.6 15.0 0.5
HA A:ARG61 4.7 14.6 0.3
CA A:ARG61 4.7 12.1 0.3
O A:SER72 4.7 22.6 0.6
CA A:SER72 4.7 17.1 0.4
O A:TRP63 4.7 11.5 0.4
HA A:CYS64 4.7 12.2 0.3
HA A:TRP63 4.7 14.2 0.3
H A:ARG61 4.7 14.8 0.3
CG A:ASN74 4.8 14.8 0.5
OD1 A:ASN74 4.8 15.2 0.5
O A:ASN59 4.8 13.5 0.5
HA A:TRP63 4.8 14.0 0.3
HB3 A:ASN74 4.8 20.0 0.5
H A:ARG61 4.8 14.1 0.4
CB A:ARG73 4.8 25.4 0.5
O A:TRP63 4.8 14.8 0.3
CA A:ASN65 4.8 12.1 0.4
HB2 A:SER60 4.8 13.9 0.4
N A:LEU75 4.8 12.4 0.5
O A:ASN59 4.8 9.7 0.2
HA A:ARG73 4.8 25.7 0.5
CA A:ASN65 4.8 11.9 0.3
C A:ASN74 4.9 14.4 0.5
O A:SER72 4.9 19.8 0.4
CB A:SER60 5.0 10.3 0.3
N A:LEU75 5.0 15.8 0.1
N A:SER72 5.0 18.3 0.6

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 17:42:34 2024

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