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Sodium in PDB 5idd: Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted.

Enzymatic activity of Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted.

All present enzymatic activity of Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted.:
3.2.1.17;

Protein crystallography data

The structure of Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted., PDB code: 5idd was solved by S.W.M.Tanley, J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.21 / 1.13
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 26.957, 31.794, 34.055, 88.76, 71.99, 68.33
R / Rfree (%) 17.8 / 22

Other elements in 5idd:

The structure of Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted. also contains other interesting chemical elements:

Platinum (Pt) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted. (pdb code 5idd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted., PDB code: 5idd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5idd

Go back to Sodium Binding Sites List in 5idd
Sodium binding site 1 out of 2 in the Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:12.6
occ:1.00
 O A:TYR53 2.9 6.0 1.0
OG A:SER91 2.9 7.9 1.0
N A:LEU56 2.9 7.5 1.0
N A:ILE55 3.3 6.2 1.0
C A:GLY54 3.4 7.0 1.0
CA A:LEU56 3.6 7.1 1.0
CB A:SER91 3.6 6.8 1.0
CA A:GLY54 3.6 6.9 1.0
N A:GLN57 3.6 6.1 1.0
CB A:LEU56 3.7 7.5 1.0
C A:LEU56 3.8 6.4 1.0
CD1 A:ILE58 3.8 8.6 1.0
C A:TYR53 3.9 6.7 1.0
C A:ILE55 4.0 7.5 1.0
O A:GLY54 4.0 7.1 1.0
CG1 A:ILE58 4.0 7.5 1.0
CA A:ILE55 4.1 7.1 1.0
O A:LEU83 4.1 8.9 1.0
N A:GLY54 4.2 6.5 1.0
CG2 A:ILE55 4.2 10.3 1.0
N A:ILE58 4.2 6.1 1.0
O A:HOH306 4.3 8.5 1.0
CB A:LEU83 4.4 8.0 1.0
CB A:ILE58 4.4 7.4 1.0
CA A:SER91 4.5 6.6 1.0
O A:LEU56 4.6 7.4 1.0
CA A:GLN57 4.7 6.6 1.0
CG A:LEU56 4.7 9.7 1.0
CD2 A:LEU83 4.7 16.0 1.0
CB A:ILE55 4.7 8.6 1.0
CD1 A:LEU83 4.8 14.3 1.0
CG A:LEU83 4.9 9.8 1.0
C A:GLN57 4.9 6.1 1.0
CA A:ILE58 5.0 6.9 1.0

Sodium binding site 2 out of 2 in 5idd

Go back to Sodium Binding Sites List in 5idd
Sodium binding site 2 out of 2 in the Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Comment on S. W. M. Tanley and J. R. Helliwell Structural Dynamics of Cisplatin Binding to Histidine in A Protein Struct. Dyn. 1, 034701 (2014) Regarding the Refinement of 4MWK, 4MWM, 4MWN and 4OXE and the Method We Have Adopted. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na210

b:13.8
occ:1.00
 O A:CYS64 2.7 8.1 1.0
OG A:SER72 2.8 12.3 1.0
O A:ARG61 2.8 9.5 1.0
O A:SER60 2.9 7.2 1.0
N A:ASN74 2.9 6.2 1.0
N A:ARG73 3.3 6.4 1.0
CA A:ASN74 3.4 6.8 1.0
C A:CYS64 3.5 7.5 1.0
CB A:SER72 3.5 9.3 1.0
CA A:SER72 3.5 7.7 1.0
O A:HOH333 3.6 8.9 1.0
C A:ARG61 3.6 6.1 1.0
C A:SER60 3.8 5.5 1.0
C A:SER72 3.8 7.0 1.0
CB A:ASN74 3.9 7.0 1.0
C A:TRP62 3.9 7.4 1.0
N A:CYS64 3.9 8.4 1.0
C A:ARG73 4.0 6.6 1.0
N A:TRP63 4.0 5.1 1.0
N A:ASN65 4.1 7.9 1.0
O A:TRP62 4.1 6.7 1.0
CA A:ASN65 4.2 8.9 1.0
CA A:ARG73 4.2 6.5 1.0
N A:TRP62 4.3 6.5 1.0
CA A:CYS64 4.3 6.7 1.0
CA A:ARG61 4.3 6.0 1.0
CA A:TRP62 4.4 6.4 1.0
C A:TRP63 4.4 5.4 1.0
N A:ARG61 4.5 6.6 1.0
CA A:SER60 4.6 5.9 1.0
CA A:TRP63 4.8 6.1 1.0
CG A:ASN74 4.8 6.8 1.0
C A:ASN74 4.8 6.3 1.0
CB A:ASN65 4.9 10.1 1.0
O A:SER72 4.9 9.7 1.0
N A:SER72 5.0 8.7 1.0
OD1 A:ASN74 5.0 6.9 1.0

Reference:

S.W.Tanley, J.R.Helliwell. Comment on "Structural Dynamics of Cisplatin Binding to Histidine in A Protein" [Struct. Dyn. 1, 034701 (2014)]. Struct Dyn. V. 3 37101 2016.
ISSN: ESSN 2329-7778
PubMed: 27226979
DOI: 10.1063/1.4948613
Page generated: Mon Oct 7 21:34:57 2024

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