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Sodium in PDB 3qlp: X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba)

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba)

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba):
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba), PDB code: 3qlp 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) 25.10 / 2.14
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.208, 110.574, 120.916, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.7

Other elements in 3qlp:

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba) also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba) (pdb code 3qlp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba), PDB code: 3qlp:

Sodium binding site 1 out of 1 in 3qlp

Go back to Sodium Binding Sites List in 3qlp
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Modified Thrombin Binding Aptamer (Mtba) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na601

b:20.0
occ:1.00
 O H:HOH1085 2.2 12.8 1.0
O H:ARG221 2.3 15.3 1.0
O H:HOH1232 2.3 26.2 1.0
O H:HOH1042 2.5 10.2 1.0
O H:LYS224 2.7 15.8 1.0
O H:HOH1053 3.1 25.3 1.0
C H:ARG221 3.2 17.9 1.0
C H:LYS224 3.7 14.8 1.0
N H:ARG221 3.7 15.7 1.0
C H:ASP221A 3.8 16.3 1.0
O H:HOH1127 4.0 15.7 1.0
N H:ASP222 4.1 18.0 1.0
N H:LYS224 4.1 15.6 1.0
CA H:ARG221 4.1 15.8 1.0
O H:HOH1202 4.1 39.3 1.0
CA H:ASP222 4.1 19.3 1.0
O H:TYR184A 4.1 18.6 1.0
CA H:ASP221A 4.2 15.3 1.0
O H:HOH1079 4.2 11.6 1.0
O H:ASP221A 4.2 15.7 1.0
CA H:LYS224 4.3 15.8 1.0
O H:HOH1184 4.4 13.2 1.0
N H:GLY223 4.4 16.8 1.0
OD1 H:ASP221A 4.5 18.5 1.0
C H:ASP222 4.5 17.3 1.0
CB H:LYS224 4.5 16.7 1.0
N H:TYR225 4.7 14.3 1.0
N H:ASP221A 5.0 16.6 1.0
CA H:TYR225 5.0 13.7 1.0

Reference:

I.Russo Krauss, A.Merlino, C.Giancola, A.Randazzo, L.Mazzarella, F.Sica. Thrombin-Aptamer Recognition: A Revealed Ambiguity. Nucleic Acids Res. V. 39 7858 2011.
ISSN: ISSN 0305-1048
PubMed: 21715374
DOI: 10.1093/NAR/GKR522
Page generated: Tue Dec 15 06:22:54 2020

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