Sodium in PDB 9b7e: S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422

Enzymatic activity of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422

All present enzymatic activity of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422:
3.2.1.17;

Protein crystallography data

The structure of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422, PDB code: 9b7e was solved by J.Jakoncic, H.J.Bernstein, A.S.Soares, K.Horvat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 1.65
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.893, 78.893, 36.952, 90, 90, 90
R / Rfree (%) 16.1 / 20

Other elements in 9b7e:

The structure of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 (pdb code 9b7e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422, PDB code: 9b7e:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 9b7e

Go back to Sodium Binding Sites List in 9b7e
Sodium binding site 1 out of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na213

b:7.7
occ:1.00
 O A:SER60 2.3 8.3 1.0
O A:ARG73 2.3 7.8 1.0
O A:CYS64 2.4 6.0 1.0
O A:HOH378 2.4 7.6 1.0
OG A:SER72 2.5 8.9 1.0
O A:HOH362 2.6 2.8 1.0
CB A:SER72 3.2 8.6 1.0
C A:CYS64 3.4 5.2 1.0
C A:ARG73 3.4 8.0 1.0
C A:SER60 3.4 7.4 1.0
N A:ARG73 3.9 8.3 1.0
CA A:ASN65 3.9 5.2 1.0
CA A:SER60 4.1 6.7 1.0
N A:ASN65 4.1 5.1 1.0
C A:SER72 4.1 9.3 1.0
CB A:SER60 4.2 6.5 1.0
CA A:ARG73 4.3 8.5 1.0
CA A:SER72 4.3 9.0 1.0
N A:ASN74 4.4 7.5 1.0
N A:CYS64 4.4 5.2 1.0
O A:ARG61 4.4 8.8 1.0
C A:ARG61 4.5 9.6 1.0
N A:ARG61 4.5 8.7 1.0
CA A:ASN74 4.5 7.2 1.0
CA A:CYS64 4.6 5.2 1.0
OD1 A:ASN65 4.7 5.9 1.0
N A:ASP66 4.7 5.1 1.0
O A:HOH398 4.7 25.1 1.0
CB A:ASN74 4.7 7.1 1.0
O A:SER72 4.7 9.5 1.0
CL A:CL205 4.7 8.6 1.0
CA A:ARG61 4.7 9.5 0.5
CB A:THR69 4.8 7.5 1.0
CA A:ARG61 4.8 9.7 0.5
CB A:ASN65 4.8 5.2 1.0
C A:ASN65 4.8 5.1 1.0
N A:TRP62 4.9 8.8 1.0
N A:TRP63 5.0 6.3 1.0

Sodium binding site 2 out of 4 in 9b7e

Go back to Sodium Binding Sites List in 9b7e
Sodium binding site 2 out of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na214

b:13.0
occ:1.00
 O A:ALA82 2.6 8.2 1.0
O A:ASP87 2.6 12.3 1.0
N A:SER91 2.8 8.0 1.0
O A:HOH321 3.1 6.9 1.0
O A:HOH329 3.3 8.8 1.0
N A:ALA90 3.4 7.7 1.0
CB A:ALA90 3.5 7.6 1.0
C A:ALA90 3.6 7.6 1.0
CA A:ALA90 3.7 7.6 1.0
C A:ILE88 3.7 8.6 1.0
CA A:ILE88 3.7 8.7 1.0
C A:ASP87 3.7 9.3 1.0
C A:ALA82 3.8 6.3 1.0
O A:ILE88 3.8 7.9 1.0
CB A:SER91 3.8 7.6 1.0
CA A:SER91 3.8 7.2 1.0
CA A:LEU83 3.9 5.8 1.0
OG A:SER91 3.9 8.5 1.0
N A:THR89 4.1 8.6 1.0
C A:LEU83 4.1 5.7 1.0
CB A:SER85 4.2 7.4 1.0
N A:ILE88 4.2 9.3 1.0
O A:HOH386 4.2 17.0 1.0
N A:LEU83 4.3 5.7 1.0
O A:LEU83 4.3 5.5 1.0
C A:THR89 4.4 8.4 1.0
O A:HOH313 4.4 10.9 1.0
O A:SER85 4.5 7.3 1.0
N A:SER85 4.5 6.7 1.0
N A:LEU84 4.8 6.0 1.0
CD2 A:LEU83 4.8 6.2 1.0
O A:ALA90 4.8 7.4 1.0
CA A:SER85 4.8 7.2 1.0
CA A:THR89 4.9 8.6 1.0
CB A:ILE88 5.0 8.2 1.0

Sodium binding site 3 out of 4 in 9b7e

Go back to Sodium Binding Sites List in 9b7e
Sodium binding site 3 out of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na215

b:9.3
occ:1.00
 O A:TYR53 2.6 5.6 1.0
N A:LEU56 2.7 6.4 1.0
OG A:SER91 2.7 8.5 1.0
N A:ILE55 3.2 5.3 1.0
C A:GLY54 3.3 5.2 1.0
N A:GLN57 3.4 4.2 1.0
CA A:LEU56 3.4 5.3 1.0
CA A:GLY54 3.5 4.7 1.0
C A:LEU56 3.6 4.8 1.0
C A:TYR53 3.6 4.6 1.0
CB A:SER91 3.7 7.6 1.0
CB A:LEU56 3.8 5.5 1.0
C A:ILE55 3.8 6.4 1.0
CD1 A:ILE58 3.8 5.1 1.0
O A:GLY54 3.8 4.9 1.0
O A:HOH313 3.9 10.9 1.0
CG1 A:ILE58 3.9 4.7 1.0
N A:ILE58 4.0 4.5 1.0
N A:GLY54 4.0 4.6 1.0
CA A:ILE55 4.1 6.5 1.0
CG1 A:ILE55 4.2 8.3 1.0
CB A:ILE58 4.3 4.8 1.0
O A:LEU83 4.4 5.5 1.0
CA A:GLN57 4.4 4.2 1.0
CB A:LEU83 4.5 5.7 1.0
O A:LEU56 4.5 4.5 1.0
CD2 A:LEU83 4.6 6.2 1.0
CA A:SER91 4.6 7.2 1.0
C A:GLN57 4.7 4.3 1.0
CB A:ILE55 4.7 7.6 1.0
CG A:LEU56 4.8 5.6 1.0
CA A:ILE58 4.8 4.8 1.0
O A:ILE55 4.9 6.5 1.0
CG A:LEU83 5.0 5.7 1.0

Sodium binding site 4 out of 4 in 9b7e

Go back to Sodium Binding Sites List in 9b7e
Sodium binding site 4 out of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na216

b:12.6
occ:1.00
 NE A:ARG114 2.5 7.3 1.0
O A:HOH332 3.1 10.7 1.0
NH2 A:ARG114 3.3 6.1 1.0
CZ A:ARG114 3.3 6.5 1.0
CB A:ARG114 3.6 6.1 1.0
CD A:ARG114 3.6 6.5 1.0
CG A:ARG114 3.6 6.4 1.0
CZ A:PHE34 3.9 6.0 1.0
CE1 A:PHE34 4.2 6.0 1.0
CE2 A:PHE34 4.2 5.9 1.0
CA A:ARG114 4.3 6.0 1.0
O A:ARG114 4.4 6.7 1.0
NH1 A:ARG114 4.6 6.4 1.0
CD1 A:PHE34 4.7 5.6 1.0
CD2 A:PHE34 4.7 5.7 1.0
C A:ARG114 4.9 6.2 1.0
CG A:PHE34 5.0 5.3 1.0

Reference:

J.Jakoncic, H.J.Bernstein, A.S.Soares, K.Horvat. Investigation of Fast and Efficient Lossless Compression Algorithms For Macromolecular Crystallography Experiments To Be Published.
Page generated: Wed Oct 9 14:28:10 2024

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