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Sodium in PDB 6kd1: Room Temperature Structure of Lysozyme Delivered in Agarose By Serial Millisecond Crystallography

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

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

Protein crystallography data

The structure of Room Temperature Structure of Lysozyme Delivered in Agarose By Serial Millisecond Crystallography, PDB code: 6kd1 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) 56.39 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.740, 79.740, 38.560, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.4

Other elements in 6kd1:

The structure of Room Temperature Structure of Lysozyme Delivered in Agarose 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 Agarose By Serial Millisecond Crystallography (pdb code 6kd1). 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 Room Temperature Structure of Lysozyme Delivered in Agarose By Serial Millisecond Crystallography, PDB code: 6kd1:

Sodium binding site 1 out of 1 in 6kd1

Go back to Sodium Binding Sites List in 6kd1
Sodium binding site 1 out of 1 in the Room Temperature Structure of Lysozyme Delivered in Agarose 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 Agarose By Serial Millisecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:59.9
occ:1.00
 O A:ARG91 2.4 53.1 1.0
HB2 A:SER90 2.4 72.4 1.0
OG A:SER90 2.4 64.0 1.0
O A:HOH344 2.7 36.7 1.0
O A:CYS82 2.8 35.4 1.0
O A:SER78 2.8 38.4 1.0
CB A:SER90 2.9 60.3 1.0
HA A:ASN83 3.0 45.1 1.0
C A:ARG91 3.3 64.2 1.0
HB2 A:ASN92 3.5 48.9 1.0
HB3 A:SER90 3.6 72.4 1.0
C A:CYS82 3.7 37.1 1.0
C A:SER90 3.7 66.2 1.0
HA A:ASN92 3.8 45.7 1.0
CA A:ASN83 3.9 37.5 1.0
N A:ARG91 3.9 50.6 1.0
CA A:SER90 3.9 61.7 1.0
O A:SER90 4.0 53.0 1.0
HB2 A:ASN83 4.0 51.7 1.0
C A:SER78 4.0 35.8 1.0
N A:ASN92 4.1 46.3 1.0
H A:CYS82 4.1 36.6 1.0
N A:ASN83 4.2 32.0 1.0
HB A:THR87 4.2 43.2 1.0
H A:ARG91 4.2 60.7 1.0
CA A:ARG91 4.2 45.1 1.0
CA A:ASN92 4.2 38.0 1.0
CB A:ASN92 4.3 40.7 1.0
O A:ARG79 4.3 51.8 1.0
H A:ASP84 4.4 40.3 1.0
HA A:ARG79 4.4 49.5 1.0
CB A:ASN83 4.4 43.1 1.0
HA A:SER90 4.5 74.1 1.0
OD1 A:ASN83 4.5 47.1 1.0
HB2 A:SER78 4.5 38.2 1.0
HA A:SER78 4.5 37.5 1.0
C A:ARG79 4.5 39.9 1.0
N A:CYS82 4.6 30.5 1.0
HA A:ARG91 4.6 54.1 1.0
CA A:CYS82 4.8 32.7 1.0
O A:HOH343 4.8 45.5 1.0
CA A:SER78 4.8 31.2 1.0
CA A:ARG79 4.8 41.2 1.0
H A:SER90 4.9 63.5 1.0
H A:ASN92 4.9 55.6 1.0
N A:ARG79 4.9 36.4 1.0
H A:ASN83 5.0 38.5 1.0
N A:ASP84 5.0 33.5 1.0
O A:THR87 5.0 51.1 1.0
N A:SER90 5.0 52.9 1.0
CG A:ASN83 5.0 44.2 1.0
C A:ASN83 5.0 29.1 1.0
HB3 A:ASN92 5.0 48.9 1.0

Reference:

K.H.Nam, K.H.Nam. N/A N/A.
Page generated: Tue Oct 8 11:33:00 2024

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