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Sodium in PDB 2p3f: Crystal Structure of the Factor Xa/NAP5 Complex

Enzymatic activity of Crystal Structure of the Factor Xa/NAP5 Complex

All present enzymatic activity of Crystal Structure of the Factor Xa/NAP5 Complex:
3.4.21.6;

Protein crystallography data

The structure of Crystal Structure of the Factor Xa/NAP5 Complex, PDB code: 2p3f was solved by J.L.Rios-Steiner, M.T.Murakami, A.Tulinsky, R.K.Arni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 3.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 137.170, 137.170, 167.670, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 28

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Factor Xa/NAP5 Complex (pdb code 2p3f). 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 Crystal Structure of the Factor Xa/NAP5 Complex, PDB code: 2p3f:

Sodium binding site 1 out of 1 in 2p3f

Go back to Sodium Binding Sites List in 2p3f
Sodium binding site 1 out of 1 in the Crystal Structure of the Factor Xa/NAP5 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Factor Xa/NAP5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1

b:21.6
occ:1.00
O H:TYR185 2.4 21.9 1.0
O H:ASP185A 2.5 19.8 1.0
O H:LYS224 2.7 16.0 1.0
O H:ARG222 2.8 10.0 1.0
C H:ASP185A 3.2 24.0 1.0
O H:ALA221 3.3 14.4 1.0
C H:TYR185 3.4 20.4 1.0
C H:ALA221 3.6 13.0 1.0
C H:ARG222 3.7 11.2 1.0
N H:THR185B 3.9 25.8 1.0
C H:LYS224 3.9 16.6 1.0
CA H:ASP185A 4.0 22.9 1.0
N H:LYS224 4.0 10.0 1.0
CA H:THR185B 4.1 25.6 1.0
N H:ASP185A 4.1 24.5 1.0
O H:LYS186 4.1 20.6 1.0
CA H:ALA221 4.2 13.2 1.0
C H:THR185B 4.2 23.9 1.0
CA H:LYS223 4.2 21.0 1.0
N H:ARG222 4.2 13.3 1.0
N H:GLY223A 4.3 16.6 1.0
O H:THR185B 4.3 23.4 1.0
N H:LYS223 4.3 15.2 1.0
CA H:TYR185 4.4 18.5 1.0
C H:LYS223 4.5 18.8 1.0
CA H:LYS224 4.5 10.8 1.0
CB H:TYR185 4.6 17.5 1.0
O H:HOH256 4.6 11.8 1.0
CA H:ARG222 4.6 12.6 1.0
N H:TYR185 4.7 17.9 1.0
N H:LYS186 4.8 22.5 1.0

Reference:

J.L.Rios-Steiner, M.T.Murakami, A.Tulinsky, R.K.Arni. Active and Exo-Site Inhibition of Human Factor Xa: Structure of Des-Gla Factor Xa Inhibited By NAP5, A Potent Nematode Anticoagulant Protein From Ancylostoma Caninum J.Mol.Biol. V. 371 774 2007.
ISSN: ISSN 0022-2836
PubMed: 17588602
DOI: 10.1016/J.JMB.2007.05.042
Page generated: Tue Dec 15 05:53:35 2020

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