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Calcium 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
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium 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:

Calcium binding site 1 out of 1 in 3sw2

Go back to Calcium Binding Sites List in 3sw2
Calcium 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 Calcium with other atoms in the Ca 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:Ca2

b:72.8
occ:1.00
 O B:ASN72 2.4 53.3 1.0
OD1 B:ASP70 2.5 53.8 1.0
O B:GLN75 2.5 67.5 1.0
OE1 B:GLU80 2.5 60.3 1.0
C B:ASN72 3.2 45.7 1.0
O B:HOH290 3.2 43.6 1.0
N B:GLU77 3.5 65.1 1.0
C B:GLN75 3.5 63.1 1.0
N B:ASN72 3.5 42.2 1.0
O B:HOH294 3.5 51.2 1.0
CD B:GLU80 3.6 60.4 1.0
CG B:ASP70 3.6 51.2 1.0
CA B:ASN72 3.8 42.6 1.0
CB B:GLU77 3.8 59.4 1.0
OE2 B:GLU80 3.9 63.1 1.0
CA B:GLU77 4.0 68.0 1.0
N B:ARG71 4.1 36.5 1.0
N B:THR73 4.1 46.1 1.0
CB B:ASN72 4.2 44.7 1.0
C B:GLU76 4.2 70.8 1.0
CA B:GLU76 4.3 68.2 1.0
N B:GLU76 4.3 67.3 1.0
N B:GLN75 4.3 62.6 1.0
CA B:GLN75 4.4 59.4 1.0
OD2 B:ASP70 4.4 55.3 1.0
CA B:ASP70 4.4 38.7 1.0
CA B:THR73 4.5 50.2 1.0
CB B:ASP70 4.6 43.6 1.0
C B:ARG71 4.7 36.5 1.0
C B:THR73 4.7 53.1 1.0
CB B:GLN75 4.7 52.9 1.0
C B:ASP70 4.7 38.1 1.0
CG B:GLU80 4.9 47.6 1.0
CA B:ARG71 4.9 35.5 1.0
N B:GLU74 5.0 48.1 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: Sat Jul 13 19:27:53 2024

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