Sodium in PDB 7cjz: Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography

Enzymatic activity of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography

All present enzymatic activity of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography:
3.2.1.17;

Protein crystallography data

The structure of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography, PDB code: 7cjz was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.18 / 1.75
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.450, 79.450, 38.470, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.7

Other elements in 7cjz:

The structure of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography (pdb code 7cjz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography, PDB code: 7cjz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7cjz

Go back to Sodium Binding Sites List in 7cjz
Sodium binding site 1 out of 2 in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:54.4
occ:1.00
H A:ILE106 2.4 41.0 1.0
HG12 A:ILE106 2.7 42.5 1.0
HA A:ASP105 2.9 42.0 1.0
N A:ILE106 3.2 34.2 1.0
HE1 A:HIS33 3.5 54.1 1.0
HG22 A:ILE106 3.6 39.5 1.0
CG1 A:ILE106 3.6 35.3 1.0
O A:HOH318 3.6 54.6 1.0
HZ A:PHE21 3.6 44.8 1.0
HB1 A:ALA29 3.8 43.1 1.0
CA A:ASP105 3.8 35.0 1.0
OD1 A:ASP105 3.9 42.1 1.0
O A:SER104 4.0 41.9 1.0
HG13 A:ILE106 4.0 42.5 1.0
C A:ASP105 4.0 35.9 1.0
HH11 A:ARG32 4.2 67.6 1.0
CB A:ILE106 4.2 33.9 1.0
CA A:ILE106 4.3 31.9 1.0
CE1 A:HIS33 4.3 45.1 1.0
CG2 A:ILE106 4.3 32.9 1.0
HB2 A:ALA29 4.4 43.1 1.0
CZ A:PHE21 4.5 37.3 1.0
CB A:ALA29 4.5 35.9 1.0
H A:THR107 4.5 37.0 1.0
HD11 A:ILE106 4.5 43.8 1.0
CD1 A:ILE106 4.5 36.5 1.0
HD12 A:ILE106 4.6 43.8 1.0
CG A:ASP105 4.6 45.6 1.0
HG1 A:THR107 4.6 47.0 1.0
HE2 A:PHE21 4.6 41.2 1.0
CB A:ASP105 4.6 34.5 1.0
N A:ASP105 4.8 34.7 1.0
HB2 A:ASP105 4.8 41.4 1.0
HG23 A:ILE106 4.8 39.5 1.0
C A:SER104 4.8 35.2 1.0
NH1 A:ARG32 4.9 56.3 1.0
HD1 A:HIS33 4.9 52.8 1.0
HH12 A:ARG32 4.9 67.6 1.0
N A:THR107 4.9 30.8 1.0
ND1 A:HIS33 5.0 43.9 1.0
CE2 A:PHE21 5.0 34.3 1.0
HA A:ILE106 5.0 38.3 1.0

Sodium binding site 2 out of 2 in 7cjz

Go back to Sodium Binding Sites List in 7cjz
Sodium binding site 2 out of 2 in the Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Room Temperature Structure of Lysozyme Delivered in Lard By Serial Millisecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:33.8
occ:1.00
HG A:SER90 2.2 47.5 1.0
O A:ARG91 2.4 38.9 1.0
O A:SER78 2.4 32.2 1.0
O A:CYS82 2.4 27.9 1.0
O A:HOH334 2.5 41.9 1.0
O A:HOH339 2.6 30.3 0.8
OG A:SER90 2.6 39.5 1.0
HA A:ASN83 3.0 33.8 1.0
HB2 A:SER90 3.0 46.0 1.0
CB A:SER90 3.3 38.3 1.0
C A:CYS82 3.5 26.7 1.0
C A:ARG91 3.5 39.2 1.0
C A:SER78 3.6 28.0 1.0
H A:CYS82 3.7 30.8 1.0
HB2 A:SER78 3.8 29.8 1.0
CA A:ASN83 3.9 28.1 1.0
HB A:THR87 3.9 37.1 1.0
HB2 A:ASN92 3.9 40.9 1.0
HA A:SER78 3.9 31.5 1.0
HB3 A:SER90 4.0 46.0 1.0
HA A:ASN92 4.0 40.7 1.0
N A:ARG91 4.0 36.6 1.0
N A:ASN83 4.1 27.5 1.0
H A:ASP84 4.1 32.8 1.0
C A:SER90 4.1 44.1 1.0
H A:ARG91 4.2 43.9 1.0
CA A:SER78 4.2 26.2 1.0
N A:CYS82 4.3 25.7 1.0
CA A:SER90 4.4 41.3 1.0
N A:ASN92 4.4 37.0 1.0
CA A:ARG91 4.4 37.8 1.0
CB A:SER78 4.4 24.8 1.0
HA A:ARG79 4.5 41.6 1.0
HB2 A:ASN83 4.5 36.1 1.0
CA A:ASN92 4.5 33.9 1.0
C A:ARG79 4.5 40.4 1.0
CA A:CYS82 4.6 25.6 1.0
O A:ARG79 4.6 37.5 1.0
N A:ARG79 4.6 28.1 1.0
O A:SER90 4.6 41.5 1.0
OD1 A:ASN83 4.6 39.6 1.0
CB A:ASN92 4.7 34.0 1.0
CB A:ASN83 4.7 30.1 1.0
N A:ASP84 4.7 27.3 1.0
H A:TRP81 4.8 33.8 1.0
CA A:ARG79 4.8 34.7 1.0
HG23 A:THR87 4.8 36.5 1.0
HA A:ARG91 4.8 45.4 1.0
N A:TRP80 4.8 30.8 1.0
CB A:THR87 4.8 30.9 1.0
C A:ASN83 4.9 29.7 1.0
H A:ASN83 4.9 33.0 1.0
O A:HOH357 4.9 34.8 1.0
HA A:SER90 5.0 49.6 1.0
N A:TRP81 5.0 28.1 1.0

Reference:

K.H.Nam, K.H.Nam. N/A N/A.
ISSN: ESSN 1422-0067
PubMed: 32825186
DOI: 10.3390/IJMS21175977
Page generated: Tue Dec 15 17:41:07 2020

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