Sodium in PDB 9b7c: High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide

Enzymatic activity of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide

All present enzymatic activity of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide:
3.2.1.17;

Protein crystallography data

The structure of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide, PDB code: 9b7c was solved by H.K.Wang, J.B.Greisman, D.R.Hekstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.15 / 1.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.405, 79.405, 37.837, 90, 90, 90
R / Rfree (%) 11.1 / 12.3

Other elements in 9b7c:

The structure of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide also contains other interesting chemical elements:

Iodine (I) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide (pdb code 9b7c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide, PDB code: 9b7c:

Sodium binding site 1 out of 1 in 9b7c

Go back to Sodium Binding Sites List in 9b7c
Sodium binding site 1 out of 1 in the High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Ambient Temperature Structure of Lysozyme Soaked with Sodium Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:22.4
occ:1.00
 O A:SER60 2.3 16.9 1.0
OG A:SER72 2.3 26.3 1.0
O A:CYS64 2.4 15.2 1.0
O A:HOH374 2.4 28.1 1.0
O A:HOH357 2.5 19.1 1.0
O A:ARG73 2.5 18.2 0.5
HB2 A:SER72 2.8 31.6 1.0
HA A:ASN65 3.0 17.4 1.0
CB A:SER72 3.1 26.3 1.0
H A:ASN74 3.2 23.8 0.5
C A:SER60 3.5 13.9 1.0
H A:ARG73 3.5 26.7 0.5
C A:CYS64 3.5 13.7 1.0
C A:ARG73 3.6 17.6 0.5
HB2 A:ASN74 3.7 22.7 0.5
HB3 A:SER72 3.8 31.6 1.0
HB2 A:SER60 3.8 15.7 1.0
HB A:THR69 3.8 17.7 1.0
N A:ARG73 3.8 22.2 0.5
N A:ASN74 3.9 19.8 0.5
CA A:ASN65 3.9 14.5 1.0
H A:CYS64 3.9 16.3 1.0
HA A:SER60 3.9 15.1 1.0
N A:ARG73 4.0 23.6 0.5
HA A:ASN74 4.0 19.8 0.5
C A:SER72 4.1 25.1 1.0
N A:ASN65 4.1 13.8 1.0
H A:ASP66 4.1 15.5 1.0
HA A:ASN74 4.1 22.1 0.5
HB2 A:ASN74 4.1 19.9 0.5
H A:ARG73 4.1 28.3 0.5
HA A:ARG61 4.2 20.4 1.0
CA A:SER72 4.2 27.4 1.0
CA A:SER60 4.2 12.6 1.0
C A:ARG61 4.3 16.6 1.0
O A:ARG61 4.3 19.3 1.0
CA A:ASN74 4.4 18.4 0.5
N A:ASN74 4.4 17.6 0.5
N A:CYS64 4.4 13.6 1.0
HB2 A:ASN65 4.4 22.2 1.0
N A:ARG61 4.4 14.7 1.0
CA A:ARG73 4.5 22.6 0.5
CB A:ASN74 4.5 18.9 0.5
CB A:SER60 4.5 13.1 1.0
O A:HOH373 4.5 28.9 1.0
CA A:ARG61 4.5 17.0 1.0
CA A:ASN74 4.6 16.5 0.5
CA A:CYS64 4.6 13.3 1.0
O A:SER72 4.7 28.1 1.0
H A:TRP63 4.7 16.8 0.6
HA A:SER72 4.7 32.9 1.0
CB A:THR69 4.7 14.8 1.0
CB A:ASN65 4.7 18.5 1.0
N A:TRP62 4.7 15.9 0.6
C A:ARG73 4.7 22.5 0.5
N A:ASP66 4.8 12.9 1.0
N A:TRP62 4.8 16.0 0.4
OD1 A:ASN65 4.8 28.3 1.0
HG21 A:THR69 4.8 20.5 1.0
CB A:ASN74 4.8 16.6 0.5
CA A:ARG73 4.8 23.9 0.5
H A:TRP63 4.9 16.8 0.4
C A:ASN65 4.9 12.9 1.0
O A:THR69 4.9 18.9 1.0
H A:ASN65 4.9 16.5 1.0
H A:SER72 4.9 35.4 1.0
HA A:ARG73 4.9 27.1 0.5
H A:TRP62 5.0 19.1 0.6
C A:TRP62 5.0 14.7 0.4

Reference:

D.R.Hekstra, H.K.Wang. Bayesian Priors For Comparative Crystallography To Be Published.
Page generated: Wed Oct 9 14:28:09 2024

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