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Sodium in PDB 2hu1: Crystal Structure Analysis of Hen Egg White Lyszoyme

Enzymatic activity of Crystal Structure Analysis of Hen Egg White Lyszoyme

All present enzymatic activity of Crystal Structure Analysis of Hen Egg White Lyszoyme:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure Analysis of Hen Egg White Lyszoyme, PDB code: 2hu1 was solved by Y.Wine, N.Cohen-Hadar, A.Freeman, S.Lagziel-Simis, F.Frolow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.73 / 1.63
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.827, 78.827, 37.053, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 22

Other elements in 2hu1:

The structure of Crystal Structure Analysis of Hen Egg White Lyszoyme also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of Hen Egg White Lyszoyme (pdb code 2hu1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure Analysis of Hen Egg White Lyszoyme, PDB code: 2hu1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2hu1

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Sodium binding site 1 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9501

b:35.6
occ:1.00
 O A:HOH9706 2.8 24.2 1.0
O A:HOH9763 3.0 45.3 1.0
O A:HOH9707 3.2 41.5 1.0
O1 A:EDO9701 3.5 57.5 1.0
CG2 A:VAL2 3.8 27.4 1.0
N A:VAL2 4.1 29.2 1.0
CA A:LYS1 4.3 30.1 0.5
CA A:LYS1 4.4 29.7 0.5
N A:LYS1 4.5 30.2 1.0
C A:LYS1 4.5 28.6 1.0
NE2 A:GLN41 4.6 23.0 1.0
CB A:VAL2 4.6 28.2 1.0
C1 A:EDO9701 4.9 56.5 1.0
CA A:VAL2 4.9 27.4 1.0
OD1 A:ASN39 5.0 21.3 1.0

Sodium binding site 2 out of 8 in 2hu1

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Sodium binding site 2 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9502

b:36.8
occ:1.00
 O A:LEU83 2.4 24.9 1.0
O A:HOH9711 2.4 27.5 1.0
N A:ILE55 2.9 19.5 1.0
OG A:SER91 3.2 20.8 1.0
CA A:GLY54 3.4 18.2 1.0
O A:THR40 3.4 20.6 1.0
C A:LEU83 3.6 24.0 1.0
CG2 A:ILE55 3.6 24.8 1.0
C A:GLY54 3.6 17.3 1.0
CB A:ILE55 3.6 24.8 1.0
CA A:THR40 3.7 20.6 1.0
CB A:THR40 3.7 21.6 1.0
CA A:ILE55 3.8 20.1 1.0
NA A:NA9506 4.0 28.7 1.0
C A:THR40 4.0 18.6 1.0
CB A:SER91 4.1 20.8 1.0
CG2 A:THR40 4.1 24.5 1.0
O A:HOH9710 4.2 27.6 1.0
CA A:LEU84 4.2 21.2 1.0
O A:SER85 4.3 30.1 1.0
N A:LEU84 4.3 21.9 1.0
C A:LEU84 4.5 24.7 1.0
CA A:LEU83 4.6 23.3 1.0
N A:GLY54 4.7 16.9 1.0
N A:SER85 4.8 24.0 1.0
O A:GLY54 4.8 18.5 1.0
N A:THR40 5.0 20.4 1.0
C A:ILE55 5.0 19.8 1.0
N A:LEU56 5.0 20.2 1.0
OG1 A:THR40 5.0 23.9 1.0

Sodium binding site 3 out of 8 in 2hu1

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Sodium binding site 3 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9503

b:34.4
occ:1.00
 O A:HOH9716 2.8 28.5 1.0
ND2 A:ASN44 3.6 27.6 1.0
CB A:ALA42 3.6 19.4 1.0
CA A:ALA42 4.2 16.3 1.0
OD1 A:ASN44 4.4 26.3 1.0
CG A:ASN44 4.4 24.6 1.0
O A:THR43 4.6 23.4 1.0
O A:SER36 4.7 21.8 1.0
N A:THR43 4.7 16.4 1.0
C A:ALA42 4.9 16.1 1.0
CA A:SER36 4.9 18.3 1.0
O A:GLU35 5.0 19.8 1.0
C A:SER36 5.0 20.2 1.0

Sodium binding site 4 out of 8 in 2hu1

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Sodium binding site 4 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9504

b:36.6
occ:1.00
 O A:ARG21 2.8 28.5 1.0
CL A:CL9601 3.3 29.0 1.0
CE2 A:TYR23 3.6 20.6 1.0
CZ A:TYR23 3.9 18.5 1.0
CA A:GLY22 3.9 27.8 1.0
C A:ARG21 3.9 28.6 1.0
C A:GLY22 4.0 27.0 1.0
CD2 A:TYR23 4.0 20.9 1.0
O A:GLY22 4.1 27.4 1.0
OH A:TYR23 4.2 22.2 1.0
N A:GLY22 4.4 27.8 1.0
CE1 A:TYR23 4.5 21.1 1.0
N A:TYR23 4.5 26.2 1.0
CG A:TYR23 4.6 19.1 1.0
CD1 A:TYR23 4.8 19.2 1.0

Sodium binding site 5 out of 8 in 2hu1

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Sodium binding site 5 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9505

b:27.9
occ:1.00
 OG1 A:THR51 2.6 19.7 1.0
OD2 A:ASP66 2.7 18.6 1.0
NE A:ARG68 2.7 23.3 0.5
O A:GLY49 2.9 27.4 1.0
OG1 A:THR69 3.0 23.8 1.0
NE A:ARG68 3.0 16.3 0.5
N A:THR51 3.4 17.0 1.0
CB A:THR51 3.5 16.5 1.0
CD A:ARG68 3.5 26.8 0.5
CG A:ARG68 3.5 14.3 0.5
C A:SER50 3.5 17.5 1.0
CG A:ASP66 3.6 19.7 1.0
CZ A:ARG68 3.6 27.8 0.5
CG A:ARG68 3.6 23.9 0.5
NE A:ARG45 3.7 27.4 0.5
NH2 A:ARG68 3.7 26.3 0.5
OG A:SER60 3.7 18.4 1.0
CA A:SER50 3.7 19.9 1.0
OD1 A:ASP66 3.8 20.8 1.0
CD A:ARG68 3.8 22.8 0.5
CZ A:ARG68 3.9 18.4 0.5
NH2 A:ARG68 3.9 12.2 0.5
C A:GLY49 4.0 26.4 1.0
O A:ARG68 4.0 29.3 1.0
NH2 A:ARG45 4.1 27.1 0.5
CA A:THR51 4.1 15.9 1.0
CZ A:ARG45 4.1 28.9 0.5
O A:SER50 4.1 20.1 1.0
OH A:TYR53 4.3 18.8 1.0
C A:ARG68 4.3 25.0 1.0
CB A:THR69 4.3 24.0 1.0
N A:SER50 4.3 23.7 1.0
CD A:ARG45 4.4 34.9 0.5
NE A:ARG45 4.4 44.6 0.5
CD A:ARG45 4.4 21.5 0.5
CB A:ARG68 4.6 29.0 0.5
N A:THR69 4.7 23.6 1.0
CB A:SER60 4.7 17.7 1.0
CB A:ARG68 4.7 23.6 0.5
CA A:THR69 4.8 25.4 1.0
CG2 A:THR51 4.8 17.5 1.0
NH1 A:ARG68 4.9 31.2 0.5
CG2 A:THR69 4.9 23.7 1.0
CB A:ASP66 4.9 21.1 1.0
CA A:ARG68 5.0 25.2 0.5

Sodium binding site 6 out of 8 in 2hu1

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Sodium binding site 6 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9506

b:28.7
occ:1.00
 OG A:SER91 2.8 20.8 1.0
O A:TYR53 2.8 17.8 1.0
N A:LEU56 2.9 20.2 1.0
N A:ILE55 3.3 19.5 1.0
C A:GLY54 3.4 17.3 1.0
CB A:SER91 3.5 20.8 1.0
N A:GLN57 3.6 18.2 1.0
CA A:GLY54 3.6 18.2 1.0
CA A:LEU56 3.6 20.0 1.0
CD1 A:ILE58 3.7 27.8 1.0
C A:LEU56 3.7 19.6 1.0
CB A:LEU56 3.8 21.9 1.0
CG1 A:ILE58 3.9 20.6 1.0
C A:TYR53 3.9 19.6 1.0
C A:ILE55 4.0 19.8 1.0
NA A:NA9502 4.0 36.8 1.0
O A:GLY54 4.0 18.5 1.0
CG2 A:ILE55 4.1 24.8 1.0
N A:ILE58 4.1 16.6 1.0
CA A:ILE55 4.1 20.1 1.0
O A:LEU83 4.2 24.9 1.0
N A:GLY54 4.2 16.9 1.0
CB A:ILE58 4.3 19.3 1.0
CB A:LEU83 4.4 25.0 1.0
CA A:SER91 4.4 22.8 1.0
CD2 A:LEU83 4.5 31.7 1.0
O A:LEU56 4.6 20.4 1.0
CA A:GLN57 4.6 16.5 1.0
CB A:ILE55 4.7 24.8 1.0
CG A:LEU56 4.8 22.2 1.0
CA A:ILE58 4.9 17.6 1.0
C A:GLN57 4.9 17.5 1.0
CG A:LEU83 4.9 23.6 1.0

Sodium binding site 7 out of 8 in 2hu1

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Sodium binding site 7 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9507

b:38.6
occ:1.00
 O A:HOH9717 2.4 19.0 1.0
O A:HOH9718 3.0 24.9 1.0
OD1 A:ASN65 3.1 29.9 1.0
OG A:SER72 3.2 30.9 1.0
O A:ARG73 3.4 31.8 1.0
CA A:ASN65 3.5 24.4 1.0
CB A:ASN65 3.6 24.0 1.0
O A:CYS64 3.7 22.9 1.0
C A:ARG73 3.7 30.8 1.0
CG A:ASN65 3.8 25.0 1.0
CB A:ASN74 3.8 25.7 1.0
CL A:CL9602 4.0 32.7 1.0
N A:ASN74 4.2 29.0 1.0
N A:ASN65 4.2 22.7 1.0
C A:CYS64 4.2 22.7 1.0
O A:SER72 4.2 33.8 1.0
C A:SER72 4.3 32.5 1.0
CA A:ASN74 4.4 26.9 1.0
CB A:SER72 4.4 29.4 1.0
CA A:ARG73 4.4 30.6 1.0
N A:ARG73 4.5 30.7 1.0
O A:HOH9742 4.6 39.7 1.0
O A:HOH9743 4.6 40.0 1.0
C A:ASN65 4.7 22.5 1.0
N A:ASP66 4.7 19.9 1.0
O A:SER60 4.7 27.0 1.0
CG A:ASN74 4.8 29.6 1.0
CA A:SER72 4.9 30.5 1.0

Sodium binding site 8 out of 8 in 2hu1

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Sodium binding site 8 out of 8 in the Crystal Structure Analysis of Hen Egg White Lyszoyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure Analysis of Hen Egg White Lyszoyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9508

b:26.8
occ:1.00
 O A:GLN41 2.7 20.8 1.0
OG1 A:THR43 2.8 18.8 1.0
N A:THR43 3.1 16.4 1.0
CB A:THR43 3.6 17.6 1.0
CG2 A:THR43 3.7 18.9 1.0
C A:ALA42 3.7 16.1 1.0
C A:GLN41 3.8 18.7 1.0
CA A:THR43 3.9 17.0 1.0
CA A:ALA42 3.9 16.3 1.0
O A:THR43 4.3 23.4 1.0
N A:ALA42 4.3 18.1 1.0
C A:THR43 4.6 20.3 1.0
O A:ALA42 4.6 17.5 1.0
CA A:GLN41 5.0 17.4 1.0
CB A:GLN41 5.0 17.8 1.0

Reference:

Y.Wine, N.Cohen-Hadar, A.Freeman, F.Frolow. Elucidation of the Mechanism and End Products of Glutaraldehyde Crosslinking Reaction By X-Ray Structure Analysis Biotechnol.Bioeng. V. 98 711 2007.
ISSN: ISSN 0006-3592
PubMed: 17461426
DOI: 10.1002/BIT.21459
Page generated: Mon Oct 7 02:48:24 2024

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