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Sodium in PDB 2b8o: Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex

Enzymatic activity of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex

All present enzymatic activity of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex, PDB code: 2b8o was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.280, 81.110, 126.860, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 28.5

Other elements in 2b8o:

The structure of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Calcium (Ca) 6 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex (pdb code 2b8o). 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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex, PDB code: 2b8o:

Sodium binding site 1 out of 1 in 2b8o

Go back to Sodium Binding Sites List in 2b8o
Sodium binding site 1 out of 1 in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor 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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na511

b:49.3
occ:1.00
O H:HIS224 2.5 2.0 1.0
O H:TYR184 2.8 13.2 1.0
O H:HOH574 2.8 18.9 1.0
O H:THR221 3.0 6.9 1.0
N H:THR221 3.3 11.9 1.0
C H:TYR184 3.6 8.3 1.0
CA H:ALA221A 3.6 12.2 1.0
C H:ALA221A 3.7 13.5 1.0
C H:THR221 3.7 8.2 1.0
CA H:SER185 3.8 6.8 1.0
C H:HIS224 3.8 4.5 1.0
OD2 H:ASP189 4.0 9.4 1.0
O H:LYS188 4.0 18.5 1.0
N H:SER185 4.1 8.6 1.0
CA H:THR221 4.1 10.7 1.0
N H:GLY187 4.2 19.8 1.0
N H:ALA221A 4.3 13.6 1.0
C H:SER185 4.3 7.6 1.0
CA H:GLY187 4.3 18.6 1.0
O H:ALA221A 4.5 17.4 1.0
CG H:ASP189 4.6 13.6 1.0
CA H:PHE225 4.6 8.9 1.0
N H:PHE225 4.7 6.2 1.0
CB H:ASP189 4.7 11.8 1.0
CA H:HIS224 4.7 2.1 1.0
N H:VAL222 4.7 8.4 1.0
N H:HIS224 4.8 2.7 1.0
CA H:TYR184 4.8 8.0 1.0
N H:ASP186 4.8 9.1 1.0
O H:SER185 4.8 5.7 1.0
CB H:ALA221A 4.9 11.2 1.0
CB H:SER185 4.9 6.2 1.0
N H:TYR184 4.9 8.1 1.0

Reference:

S.P.Bajaj, A.E.Schmidt, K.Padmanabhan. Crystal Structure of Factor Viia/Soluble Tissue Factor Complexed with Glu-Gly-Arg-Chloromethyl Ketone To Be Published.
Page generated: Tue Dec 15 05:45:40 2020

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