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Zinc in PDB 4dih: X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions, PDB code: 4dih was solved by I.Russo Krauss, A.Merlino, L.Mazzarella, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.018, 44.716, 52.689, 65.22, 85.33, 69.97
R / Rfree (%) 16.7 / 21.3

Other elements in 4dih:

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions (pdb code 4dih). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions, PDB code: 4dih:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4dih

Go back to Zinc Binding Sites List in 4dih
Zinc binding site 1 out of 3 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:23.8
occ:1.00
 OD1 L:ASP1A 1.8 27.5 1.0
NE2 H:HIS119 2.1 21.8 1.0
O L:HOH203 2.1 25.2 1.0
CG L:ASP1A 2.7 30.8 1.0
OD2 L:ASP1A 3.0 26.4 1.0
CE1 H:HIS119 3.0 20.9 1.0
CD2 H:HIS119 3.0 21.2 1.0
O L:HOH208 3.7 34.7 1.0
CB L:ASP1A 4.1 30.8 1.0
ND1 H:HIS119 4.1 19.8 1.0
CG H:HIS119 4.2 19.9 1.0
NZ L:LYS9 4.2 45.2 1.0
CD2 H:PHE114 4.5 19.4 1.0
CB H:PHE114 4.9 17.3 1.0

Zinc binding site 2 out of 3 in 4dih

Go back to Zinc Binding Sites List in 4dih
Zinc binding site 2 out of 3 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn304

b:39.3
occ:1.00
 OD1 H:ASP60E 2.0 33.3 1.0
CG H:ASP60E 2.7 31.9 1.0
OD2 H:ASP60E 2.7 31.6 1.0
CL H:CL307 2.9 37.2 1.0
CL H:CL306 3.1 27.4 1.0
CB H:ASP60E 4.1 32.6 1.0
O H:HOH413 4.5 27.6 1.0
O H:ASP60E 4.5 27.7 1.0

Zinc binding site 3 out of 3 in 4dih

Go back to Zinc Binding Sites List in 4dih
Zinc binding site 3 out of 3 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn305

b:48.8
occ:1.00
 OE2 H:GLU86 2.1 42.6 1.0
O H:HOH402 2.3 46.0 1.0
O H:HOH403 2.4 57.9 1.0
O H:HOH523 2.5 48.4 1.0
CD H:GLU86 2.8 37.8 1.0
OE1 H:GLU86 2.9 38.2 1.0
NH2 H:ARG50 3.9 38.6 1.0
NZ H:LYS107 4.0 32.2 1.0
O H:HOH565 4.1 46.6 1.0
CG H:GLU86 4.2 35.6 1.0
O H:HOH511 4.6 45.7 1.0
CE H:LYS107 4.6 29.5 1.0

Reference:

I.Russo Krauss, A.Merlino, A.Randazzo, E.Novellino, L.Mazzarella, F.Sica. High-Resolution Structures of Two Complexes Between Thrombin and Thrombin-Binding Aptamer Shed Light on the Role of Cations in the Aptamer Inhibitory Activity. Nucleic Acids Res. V. 40 8119 2012.
ISSN: ISSN 0305-1048
PubMed: 22669903
DOI: 10.1093/NAR/GKS512
Page generated: Sat Oct 26 21:27:20 2024

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