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Sodium in PDB 4wm6: High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa

Enzymatic activity of High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa

All present enzymatic activity of High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa:
3.2.1.17;

Protein crystallography data

The structure of High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa, PDB code: 4wm6 was solved by H.Yamada, N.Watanabe, T.Nagae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.76 / 1.85
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 107.269, 107.269, 36.891, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 28.4

Sodium Binding Sites:

The binding sites of Sodium atom in the High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa (pdb code 4wm6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa, PDB code: 4wm6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4wm6

Go back to Sodium Binding Sites List in 4wm6
Sodium binding site 1 out of 4 in the High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:9.6
occ:1.00
 O A:SER60 2.2 12.4 1.0
O A:CYS64 2.3 13.4 1.0
O A:ARG73 2.4 14.4 1.0
O A:HOH386 2.5 13.0 1.0
OG A:SER72 2.5 12.5 1.0
CB A:SER72 3.3 14.2 1.0
C A:CYS64 3.3 13.4 1.0
C A:SER60 3.4 13.9 1.0
C A:ARG73 3.4 14.4 1.0
CA A:ASN65 3.8 13.6 1.0
N A:ARG73 3.9 13.8 1.0
N A:ASN65 4.0 12.6 1.0
CA A:SER60 4.1 13.2 1.0
C A:SER72 4.2 14.4 1.0
N A:ASN74 4.3 13.1 1.0
CA A:ARG73 4.3 14.2 1.0
O A:ARG61 4.3 12.8 1.0
CB A:SER60 4.3 14.0 1.0
N A:CYS64 4.3 12.6 1.0
CA A:SER72 4.4 14.2 1.0
CA A:CYS64 4.4 13.3 1.0
CA A:ASN74 4.4 14.5 1.0
C A:ARG61 4.5 14.8 1.0
N A:ARG61 4.5 14.1 1.0
OD1 A:ASN65 4.6 14.4 1.0
N A:ASP66 4.6 12.8 1.0
O A:HOH347 4.6 8.9 1.0
O A:HOH430 4.7 22.6 1.0
CB A:ASN74 4.7 14.3 1.0
CB A:ASN65 4.7 14.1 1.0
CB A:THR69 4.7 12.9 1.0
C A:ASN65 4.7 13.7 1.0
CA A:ARG61 4.8 15.6 1.0
O A:SER72 4.9 14.8 1.0
N A:TRP62 4.9 13.9 1.0
OG1 A:THR69 4.9 12.8 1.0
OD1 A:ASP66 5.0 13.2 1.0

Sodium binding site 2 out of 4 in 4wm6

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Sodium binding site 2 out of 4 in the High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:31.5
occ:1.00
 O B:CYS64 2.5 15.2 1.0
O B:SER60 2.6 15.8 1.0
OG B:SER72 2.7 22.5 1.0
N B:ASN74 3.0 20.6 1.0
C B:CYS64 3.2 15.8 1.0
C B:SER60 3.3 17.0 1.0
O B:ARG61 3.3 26.4 1.0
CA B:ASN74 3.5 20.1 1.0
C B:ARG61 3.5 23.6 1.0
N B:ARG73 3.5 23.5 1.0
N B:CYS64 3.6 15.0 1.0
O B:HOH383 3.7 13.3 1.0
N B:TRP63 3.7 17.7 1.0
C B:TRP62 3.8 19.8 1.0
N B:TRP62 3.9 23.3 1.0
CB B:SER72 3.9 23.0 1.0
N B:ARG61 4.0 18.5 1.0
CA B:CYS64 4.0 14.9 1.0
C B:TRP63 4.0 15.8 1.0
CA B:SER60 4.1 14.3 1.0
N B:ASN65 4.1 15.9 1.0
C B:ARG73 4.1 22.9 1.0
CA B:ARG61 4.1 22.5 1.0
CB B:ASN74 4.1 21.1 1.0
CA B:SER72 4.1 22.6 1.0
C B:SER72 4.1 22.4 1.0
CA B:TRP62 4.2 23.1 1.0
O B:TRP62 4.2 18.5 1.0
CA B:ASN65 4.3 16.5 1.0
CA B:ARG73 4.3 24.6 1.0
CA B:TRP63 4.4 15.7 1.0
O B:HOH347 4.5 22.0 1.0
O B:TRP63 4.7 14.8 1.0
O B:ASN59 4.7 11.6 1.0
C B:ASN74 4.8 19.6 1.0
OD1 B:ASN74 4.9 24.6 1.0
CG B:ASN74 4.9 23.2 1.0
CB B:SER60 4.9 13.6 1.0
N B:LEU75 5.0 19.3 1.0

Sodium binding site 3 out of 4 in 4wm6

Go back to Sodium Binding Sites List in 4wm6
Sodium binding site 3 out of 4 in the High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:38.9
occ:1.00
 O C:CYS64 2.2 13.6 1.0
O C:SER60 2.3 15.4 1.0
OG C:SER72 2.3 27.7 1.0
O C:ARG73 2.4 24.0 1.0
O C:HOH383 2.5 10.1 1.0
CB C:SER72 3.1 27.4 1.0
C C:CYS64 3.2 14.3 1.0
C C:SER60 3.3 16.3 1.0
C C:ARG73 3.5 29.6 1.0
CA C:ASN65 3.6 15.9 1.0
N C:ASN65 3.8 14.4 1.0
N C:ARG73 3.9 33.2 1.0
CA C:SER60 3.9 14.8 1.0
C C:SER72 4.2 31.8 1.0
O C:ARG61 4.2 25.2 1.0
CA C:ARG73 4.3 32.0 1.0
CA C:SER72 4.3 29.0 1.0
N C:CYS64 4.3 14.1 1.0
CB C:SER60 4.3 13.2 1.0
N C:ARG61 4.3 19.0 1.0
C C:ARG61 4.3 22.0 1.0
CB C:ASN65 4.3 17.3 1.0
CB C:ASN74 4.4 21.4 1.0
N C:ASN74 4.4 26.8 1.0
CA C:CYS64 4.4 14.2 1.0
CA C:ASN74 4.5 23.8 1.0
CA C:ARG61 4.5 21.8 1.0
N C:ASP66 4.6 13.3 1.0
C C:ASN65 4.6 14.1 1.0
ND2 C:ASN65 4.7 20.1 1.0
O C:HOH384 4.7 22.3 1.0
CB C:THR69 4.8 16.7 1.0
N C:TRP62 4.8 20.7 1.0
O C:SER72 4.9 31.3 1.0
O C:HOH427 4.9 21.9 1.0
N C:TRP63 5.0 15.9 1.0

Sodium binding site 4 out of 4 in 4wm6

Go back to Sodium Binding Sites List in 4wm6
Sodium binding site 4 out of 4 in the High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High Pressure Protein Crystallography of Hen Egg White Lysozyme at 950 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:38.2
occ:1.00
 O D:ARG73 2.3 39.5 1.0
O D:SER60 2.7 19.6 1.0
O D:CYS64 2.8 15.0 1.0
O D:HOH449 3.0 36.4 1.0
C D:ARG73 3.2 35.9 1.0
O D:ARG61 3.2 30.8 1.0
C D:ARG61 3.3 30.4 1.0
C D:TRP62 3.3 27.6 1.0
OG D:SER72 3.3 34.2 1.0
C D:SER60 3.3 19.9 1.0
N D:TRP63 3.4 22.0 1.0
N D:TRP62 3.5 30.1 1.0
O D:TRP62 3.6 27.1 1.0
CA D:ASN74 3.6 27.1 1.0
N D:CYS64 3.7 15.6 1.0
CA D:TRP62 3.7 31.0 1.0
C D:CYS64 3.7 14.8 1.0
CB D:SER72 3.7 31.2 1.0
N D:ASN74 3.7 31.1 1.0
N D:ARG73 3.8 36.5 1.0
N D:ARG61 3.9 24.1 1.0
CA D:ARG61 4.0 29.7 1.0
CA D:SER72 4.1 32.7 1.0
O D:HOH383 4.1 11.8 1.0
C D:SER72 4.1 33.5 1.0
C D:TRP63 4.1 17.8 1.0
CA D:SER60 4.2 18.2 1.0
CA D:ARG73 4.2 36.1 1.0
CA D:TRP63 4.2 19.5 1.0
CB D:ASN74 4.2 25.9 1.0
CA D:CYS64 4.3 14.6 1.0
O D:ASN59 4.4 16.8 1.0
N D:ASN65 4.6 14.8 1.0
CA D:ASN65 4.7 14.1 1.0
O D:SER72 4.9 31.2 1.0
C D:ASN74 4.9 26.5 1.0
O D:TRP63 5.0 16.6 1.0
N D:LEU75 5.0 24.1 1.0

Reference:

H.Yamada, T.Nagae, N.Watanabe. High Pressure Protein Crystallography of Hen Egg White Lysozyme Acta Crystallogr.,Sect.D V. 71 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715000292
Page generated: Tue Dec 15 09:38:31 2020

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