Atomistry » Sodium » PDB 3tkj-3tzl » 3txd
Atomistry »
  Sodium »
    PDB 3tkj-3tzl »
      3txd »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy