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Sodium in PDB 5mjj: Single-Shot Pink Beam Serial Crystallography: Lysozyme

Enzymatic activity of Single-Shot Pink Beam Serial Crystallography: Lysozyme

All present enzymatic activity of Single-Shot Pink Beam Serial Crystallography: Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Single-Shot Pink Beam Serial Crystallography: Lysozyme, PDB code: 5mjj was solved by A.Meents, D.Oberthuer, J.Lieske, V.Srajer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.01 / 1.75
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.100, 79.100, 37.900, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.8

Other elements in 5mjj:

The structure of Single-Shot Pink Beam Serial Crystallography: Lysozyme also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Single-Shot Pink Beam Serial Crystallography: Lysozyme (pdb code 5mjj). 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 Single-Shot Pink Beam Serial Crystallography: Lysozyme, PDB code: 5mjj:

Sodium binding site 1 out of 1 in 5mjj

Go back to Sodium Binding Sites List in 5mjj
Sodium binding site 1 out of 1 in the Single-Shot Pink Beam Serial Crystallography: Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Single-Shot Pink Beam Serial Crystallography: Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:20.4
occ:0.51
HB2 A:SER72 2.0 27.7 1.0
O A:CYS64 2.4 16.3 1.0
O A:HOH301 2.4 23.6 1.0
OG A:SER72 2.4 24.7 1.0
O A:SER60 2.5 19.4 1.0
CB A:SER72 2.6 23.1 1.0
H A:ASN74 2.8 22.8 1.0
O A:HOH340 2.9 18.7 1.0
HA A:ASN65 3.0 19.0 1.0
HB2 A:ASN74 3.2 21.2 1.0
HB3 A:SER72 3.2 27.7 1.0
C A:CYS64 3.3 16.0 1.0
N A:ASN74 3.4 19.0 1.0
H A:ARG73 3.4 27.8 0.5
H A:ARG73 3.4 27.8 0.5
HA A:ASN74 3.6 22.1 1.0
C A:SER60 3.6 18.9 1.0
N A:ARG73 3.6 23.1 1.0
CA A:SER72 3.8 24.0 1.0
C A:SER72 3.8 24.0 1.0
H A:CYS64 3.8 19.1 1.0
CA A:ASN65 3.8 15.9 1.0
CA A:ASN74 3.8 18.4 1.0
N A:ASN65 3.9 14.8 1.0
CB A:ASN74 3.9 17.7 1.0
HB2 A:ASN65 4.1 21.4 1.0
N A:CYS64 4.2 15.9 1.0
HA A:SER60 4.2 19.7 1.0
HA A:SER72 4.2 28.8 1.0
HA A:ARG61 4.2 27.5 1.0
O A:ARG61 4.2 24.1 1.0
C A:ARG61 4.2 24.2 1.0
HB2 A:SER60 4.2 18.7 1.0
C A:ARG73 4.2 21.9 1.0
HB A:THR69 4.3 22.1 1.0
CA A:CYS64 4.3 15.1 1.0
CA A:SER60 4.5 16.4 1.0
O A:SER72 4.5 23.1 1.0
H A:ASP66 4.5 16.5 1.0
CB A:ASN65 4.5 17.9 1.0
CA A:ARG73 4.5 23.0 0.5
CA A:ARG73 4.5 22.9 0.5
HB3 A:ASN74 4.5 21.2 1.0
N A:ARG61 4.5 20.3 1.0
CA A:ARG61 4.6 22.9 1.0
N A:TRP62 4.6 21.9 1.0
H A:TRP63 4.6 22.0 1.0
H A:ASN65 4.7 17.8 1.0
HA A:CYS64 4.7 18.1 1.0
N A:TRP63 4.7 18.3 1.0
C A:TRP62 4.8 20.0 1.0
H A:SER72 4.8 28.9 1.0
H A:TRP62 4.8 26.2 1.0
OD1 A:ASN65 4.8 20.1 1.0
N A:SER72 4.9 24.1 1.0
CB A:SER60 4.9 15.6 1.0
CG A:ASN74 4.9 18.1 1.0
C A:ASN65 5.0 14.3 1.0
HA A:TRP62 5.0 27.0 1.0

Reference:

A.Meents, D.Oberthuer, J.Lieske, V.Srajer. Single-Shot Pink Beam Serial Crystallography: Lysozyme To Be Published.
Page generated: Tue Dec 15 11:18:45 2020

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