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Sodium in PDB 3sw2: X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide

Enzymatic activity of X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide

All present enzymatic activity of X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide:
3.4.21.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide, PDB code: 3sw2 was solved by H.E.Klei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.88 / 2.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.018, 72.515, 77.956, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 26.2

Other elements in 3sw2:

The structure of X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide (pdb code 3sw2). 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 Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide, PDB code: 3sw2:

Sodium binding site 1 out of 1 in 3sw2

Go back to Sodium Binding Sites List in 3sw2
Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Human Fxa in Complex with 6-Chloro-N-((3S)- 2-Oxo-1-(2-Oxo-2-((5S)-8-Oxo-5,6-Dihydro-1H-1,5-Methanopyrido[1,2- A][1,5]Diazocin-3(2H,4H,8H)-Yl)Ethyl)Piperidin-3-Yl)Naphthalene-2- Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na249

b:47.3
occ:1.00
 O B:TYR185 1.9 35.0 1.0
O B:LYS224 2.4 36.0 1.0
O B:ARG222 2.9 39.0 1.0
C B:TYR185 3.2 35.3 1.0
O B:ASP185A 3.2 41.9 1.0
C B:LYS224 3.6 39.1 1.0
C B:ASP185A 3.6 43.9 1.0
O B:ALA221 3.9 37.3 1.0
CA B:ASP185A 4.0 42.6 1.0
N B:ASP185A 4.0 42.1 1.0
C B:ARG222 4.0 39.2 1.0
N B:LYS224 4.0 35.9 1.0
C B:ALA221 4.0 38.8 1.0
CA B:TYR185 4.2 33.1 1.0
N B:TYR185 4.2 36.0 1.0
CA B:LYS224 4.3 39.0 1.0
CA B:ALA221 4.4 38.1 1.0
O B:LYS186 4.4 40.5 1.0
N B:THR185B 4.4 40.3 1.0
N B:ARG222 4.5 41.9 1.0
CB B:TYR185 4.5 37.4 1.0
N B:TYR225 4.5 34.9 1.0
N B:GLY223A 4.6 37.6 1.0
CA B:TYR225 4.7 32.3 1.0
CA B:LYS223 4.8 51.1 1.0
N B:LYS223 4.8 46.8 1.0
CD1 B:TYR225 4.9 33.9 1.0
CA B:ARG222 4.9 39.9 1.0
CA B:THR185B 4.9 41.5 1.0
CB B:LYS224 4.9 38.2 1.0
C B:GLY223A 5.0 43.6 1.0
C B:LYS223 5.0 42.7 1.0
C B:THR185B 5.0 44.0 1.0

Reference:

Y.Shi, S.P.O'connor, D.Sitkoff, J.Zhang, M.Shi, S.N.Bisaha, Y.Wang, C.Li, Z.Ruan, R.Michael Lawrence, H.E.Klei, K.Kish, E.C.Liu, S.M.Seiler, L.Schweizer, T.E.Steinbacher, W.A.Schumacher, J.A.Robl, J.E.Macor, K.S.Atwal, P.D.Stein. Arylsulfonamidopiperidone Derivatives As A Novel Class of Factor Xa Inhibitors. Bioorg.Med.Chem.Lett. V. 21 7516 2011.
ISSN: ISSN 0960-894X
PubMed: 22041058
DOI: 10.1016/J.BMCL.2011.06.098
Page generated: Mon Oct 7 13:01:19 2024

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