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Sodium in PDB 3txd: Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant

Enzymatic activity of Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant

All present enzymatic activity of Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant:
3.2.1.17;

Protein crystallography data

The structure of Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant, PDB code: 3txd was solved by S.W.M.Tanley, A.M.M.Schreurs, J.R.Helliwell, L.M.J.Kroon-Batenburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.77 / 1.53
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.870, 78.870, 36.980, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.8

Other elements in 3txd:

The structure of Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant (pdb code 3txd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant, PDB code: 3txd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3txd

Go back to Sodium Binding Sites List in 3txd
Sodium binding site 1 out of 3 in the Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1138

b:35.2
occ:1.00
 O A:SER60 2.2 32.5 1.0
O3 A:GOL130 2.3 45.7 1.0
NA A:NA131 2.3 34.1 1.0
OG A:SER72 2.4 42.9 1.0
O A:ARG73 2.5 36.1 1.0
O A:CYS64 2.6 28.3 1.0
CB A:SER72 3.2 41.2 1.0
C A:SER60 3.4 30.5 1.0
C A:ARG73 3.5 35.5 1.0
C3 A:GOL130 3.6 55.5 1.0
C A:CYS64 3.7 27.3 1.0
N A:ARG73 3.9 38.0 1.0
CA A:ASN65 4.0 27.0 1.0
CA A:SER60 4.1 28.5 1.0
C A:SER72 4.2 40.9 1.0
O2 A:GOL130 4.2 61.0 1.0
O A:ARG61 4.2 34.2 1.0
N A:ASN65 4.3 27.1 1.0
CA A:SER72 4.3 41.6 1.0
CA A:ARG73 4.3 36.2 1.0
C A:ARG61 4.3 33.1 1.0
CB A:SER60 4.3 27.4 1.0
N A:ARG61 4.4 31.4 1.0
N A:ASN74 4.4 33.8 1.0
CA A:ARG61 4.5 34.1 1.0
OD1 A:ASN65 4.5 29.3 1.0
CB A:THR69 4.5 30.6 1.0
C2 A:GOL130 4.6 58.5 1.0
N A:CYS64 4.6 27.2 1.0
CA A:ASN74 4.6 31.1 1.0
N A:ASP66 4.7 25.2 1.0
CL A:CL1132 4.7 30.2 1.0
CA A:CYS64 4.8 27.8 1.0
O A:SER72 4.8 41.9 1.0
CB A:ASN65 4.8 27.3 1.0
CB A:ASN74 4.8 31.7 1.0
O A:THR69 4.9 32.1 1.0
N A:TRP62 4.9 30.2 1.0
C A:ASN65 4.9 25.5 1.0
CG2 A:THR69 5.0 31.8 1.0

Sodium binding site 2 out of 3 in 3txd

Go back to Sodium Binding Sites List in 3txd
Sodium binding site 2 out of 3 in the Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na131

b:34.1
occ:1.00
 NA A:NA1138 2.3 35.2 1.0
N A:ASP66 2.9 25.2 1.0
O3 A:GOL130 2.9 45.7 1.0
OD1 A:ASP66 3.1 25.2 1.0
CL A:CL1132 3.2 30.2 1.0
OG A:SER72 3.2 42.9 1.0
O A:CYS64 3.3 28.3 1.0
O A:SER60 3.3 32.5 1.0
OD1 A:ASN65 3.3 29.3 1.0
CA A:ASN65 3.5 27.0 1.0
CB A:THR69 3.6 30.6 1.0
C A:ASN65 3.7 25.5 1.0
OG1 A:THR69 3.8 26.2 1.0
N A:GLY67 3.8 26.2 1.0
CG A:ASP66 3.8 24.8 1.0
CB A:SER60 3.9 27.4 1.0
CA A:ASP66 3.9 25.4 1.0
C3 A:GOL130 4.2 55.5 1.0
CG A:ASN65 4.2 30.5 1.0
C A:CYS64 4.2 27.3 1.0
C A:SER60 4.3 30.5 1.0
N A:THR69 4.3 30.6 1.0
C A:ASP66 4.3 26.2 1.0
CB A:ASN65 4.3 27.3 1.0
CB A:ASP66 4.3 22.8 1.0
N A:ASN65 4.4 27.1 1.0
CB A:SER72 4.4 41.2 1.0
CA A:THR69 4.4 30.9 1.0
O A:THR69 4.5 32.1 1.0
CA A:SER60 4.5 28.5 1.0
OG A:SER60 4.5 27.2 1.0
OD2 A:ASP66 4.6 24.5 1.0
CG2 A:THR69 4.7 31.8 1.0
O A:ARG73 4.8 36.1 1.0
N A:ARG68 4.8 28.4 1.0
O A:ASN65 4.9 25.2 1.0
SG A:CYS80 4.9 24.8 1.0
CA A:GLY67 4.9 28.6 1.0
C A:THR69 5.0 33.5 1.0

Sodium binding site 3 out of 3 in 3txd

Go back to Sodium Binding Sites List in 3txd
Sodium binding site 3 out of 3 in the Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hewl Co-Crystallization with Carboplatin in Aqueous Media with Glycerol As the Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na137

b:52.3
occ:1.00
 CL A:CL1132 3.5 30.2 1.0
N A:PRO70 3.6 36.5 1.0
C A:THR69 3.8 33.5 1.0
N A:THR69 3.8 30.6 1.0
CA A:PRO70 3.8 39.0 1.0
CD A:PRO70 3.8 37.1 1.0
O A:HOH2081 3.9 22.0 0.5
CG A:PRO70 4.0 39.6 1.0
O A:THR69 4.0 32.1 1.0
O A:GLY67 4.1 31.5 1.0
C A:ARG68 4.1 30.6 1.0
CA A:ARG68 4.3 29.4 1.0
O A:HOH2079 4.3 30.0 1.0
CA A:THR69 4.4 30.9 1.0
C A:GLY67 4.4 29.4 1.0
N A:ARG68 4.5 28.4 1.0
CB A:PRO70 4.5 41.2 1.0
O A:ARG68 4.8 33.2 1.0
C A:PRO70 5.0 40.0 1.0

Reference:

S.W.Tanley, A.M.Schreurs, J.R.Helliwell, L.M.Kroon-Batenburg. Experience with Exchange and Archiving of Raw Data: Comparison of Data From Two Diffractometers and Four Software Packages on A Series of Lysozyme Crystals. J.Appl.Crystallogr. V. 46 108 2013.
ISSN: ISSN 0021-8898
PubMed: 23396873
DOI: 10.1107/S0021889812044172
Page generated: Mon Oct 7 13:22:02 2024

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