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Sodium in PDB 2ody: Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop

Enzymatic activity of Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop

All present enzymatic activity of Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop:
3.4.21.5;

Protein crystallography data

The structure of Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop, PDB code: 2ody was solved by S.Macedo-Ribeiro, P.Fuentes-Prior, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.19 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.500, 104.200, 129.100, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop (pdb code 2ody). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop, PDB code: 2ody:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2ody

Go back to Sodium Binding Sites List in 2ody
Sodium binding site 1 out of 2 in the Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na900

b:38.0
occ:1.00
O B:HOH1024 2.3 30.2 1.0
O B:HOH990 2.4 32.9 1.0
O B:ARG221A 2.5 25.4 1.0
O B:HOH991 2.7 21.2 1.0
O B:LYS224 2.7 23.1 1.0
O B:HOH989 3.3 29.5 1.0
C B:ARG221A 3.5 25.0 1.0
C B:LYS224 3.7 23.0 1.0
N B:ARG221A 3.7 23.9 1.0
O B:HOH903 3.8 23.1 1.0
C B:ASP221 3.8 23.6 1.0
O B:HOH935 4.0 23.5 1.0
CA B:ASP221 4.0 23.6 1.0
OD1 B:ASP221 4.2 24.1 1.0
N B:LYS224 4.2 23.5 1.0
CA B:ARG221A 4.3 24.6 1.0
O B:TYR184A 4.3 23.6 1.0
O B:ASP221 4.3 23.8 1.0
N B:ASP222 4.4 25.3 1.0
CA B:LYS224 4.4 23.1 1.0
CA B:ASP222 4.6 25.9 1.0
N B:TYR225 4.7 23.1 1.0
CB B:LYS224 4.7 23.5 1.0
O B:HOH912 4.8 17.7 1.0
N B:GLY223 4.8 24.5 1.0
N B:ASP221 4.8 23.6 1.0
CA B:TYR225 4.9 23.6 1.0
C B:ASP222 4.9 25.4 1.0
CG B:ASP221 5.0 23.6 1.0

Sodium binding site 2 out of 2 in 2ody

Go back to Sodium Binding Sites List in 2ody
Sodium binding site 2 out of 2 in the Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin-Bound Boophilin Displays A Functional and Accessible Reactive-Site Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na901

b:26.9
occ:1.00
O D:HOH993 2.4 23.7 1.0
O D:HOH952 2.5 19.0 1.0
O D:ARG221A 2.5 29.2 1.0
O D:LYS224 2.7 26.9 1.0
O D:HOH992 2.8 34.4 1.0
C D:ARG221A 3.5 28.9 1.0
C D:LYS224 3.7 26.6 1.0
O D:HOH953 3.7 28.2 1.0
O D:HOH970 3.9 19.9 1.0
C D:ASP221 4.0 27.4 1.0
N D:ARG221A 4.0 27.6 1.0
O D:TYR184A 4.0 30.1 1.0
O D:HOH971 4.1 26.0 1.0
N D:LYS224 4.1 27.6 1.0
CA D:ASP221 4.2 27.0 1.0
O D:ASP221 4.3 27.7 1.0
CA D:LYS224 4.3 27.5 1.0
N D:ASP222 4.3 29.4 1.0
CA D:ASP222 4.4 29.8 1.0
CA D:ARG221A 4.4 28.3 1.0
OD1 D:ASP221 4.5 26.5 1.0
CB D:LYS224 4.5 27.7 1.0
N D:GLY223 4.6 28.4 1.0
N D:TYR225 4.7 25.6 1.0
O D:HOH954 4.7 30.1 1.0
C D:ASP222 4.8 29.0 1.0
CA D:TYR225 5.0 25.0 1.0

Reference:

S.Macedo-Ribeiro, C.Almeida, B.M.Calisto, T.Friedrich, R.Mentele, J.Sturzebecher, P.Fuentes-Prior, P.J.Pereira. Isolation, Cloning and Structural Characterisation of Boophilin, A Multifunctional Kunitz-Type Proteinase Inhibitor From the Cattle Tick. Plos One V. 3 E1624 2008.
ISSN: ESSN 1932-6203
PubMed: 18286181
DOI: 10.1371/JOURNAL.PONE.0001624
Page generated: Tue Dec 15 05:52:20 2020

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