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Sodium in PDB 1gj5: Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design

Enzymatic activity of Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design

All present enzymatic activity of Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design:
3.4.21.5;

Protein crystallography data

The structure of Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design, PDB code: 1gj5 was solved by B.A.Katz, P.A.Sprengeler, C.Luong, E.Verner, J.R.Spencer, J.G.Breitenbucher, H.Hui, D.Mcgee, D.Allen, A.Martelli, R.L.Mackman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.73
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.330, 71.960, 72.960, 90.00, 101.05, 90.00
R / Rfree (%) 19.3 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design (pdb code 1gj5). 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 Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design, PDB code: 1gj5:

Sodium binding site 1 out of 1 in 1gj5

Go back to Sodium Binding Sites List in 1gj5
Sodium binding site 1 out of 1 in the Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Selectivity at S1, H2O Displacement, Upa, Tpa, SER190/ALA190 Protease, Structure-Based Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na409

b:35.0
occ:1.00
 O H:LYS224 2.4 24.8 1.0
O H:ARG221A 2.4 34.3 1.0
O H:HOH453 2.5 45.6 1.0
O H:HOH455 2.7 36.6 1.0
O H:HOH431 2.7 29.9 1.0
O H:HOH428 2.7 32.4 1.0
H1 H:HOH428 2.9 34.2 1.0
H2 H:HOH431 3.0 32.5 1.0
H1 H:HOH455 3.0 37.4 1.0
H H:LYS224 3.1 24.9 1.0
H1 H:HOH453 3.1 46.5 1.0
H1 H:HOH431 3.1 33.0 1.0
HA H:ASP222 3.1 37.9 1.0
H2 H:HOH428 3.2 33.9 1.0
H2 H:HOH453 3.2 46.6 1.0
H2 H:HOH439 3.4 29.5 1.0
H2 H:HOH455 3.4 37.2 1.0
C H:LYS224 3.5 24.0 1.0
C H:ARG221A 3.5 34.9 1.0
H H:GLY223 3.6 31.4 1.0
H1 H:HOH422 3.7 25.5 1.0
N H:LYS224 3.7 24.9 1.0
HA H:ASP221 3.7 32.9 1.0
O H:HOH441 3.8 31.3 1.0
HB2 H:LYS224 3.9 29.6 1.0
O H:HOH439 3.9 27.8 1.0
CA H:ASP222 3.9 38.2 1.0
HA H:TYR225 3.9 21.3 1.0
N H:GLY223 4.0 32.6 1.0
N H:ARG221A 4.1 31.8 1.0
N H:ASP222 4.1 35.9 1.0
CA H:LYS224 4.1 24.7 1.0
O H:TYR184A 4.1 28.9 1.0
C H:ASP221 4.2 32.4 1.0
H H:ARG221A 4.2 33.8 1.0
C H:ASP222 4.3 36.3 1.0
H1 H:HOH435 4.4 37.7 1.0
N H:TYR225 4.5 21.2 1.0
O H:HOH422 4.5 24.0 1.0
CA H:ARG221A 4.5 34.3 1.0
CA H:ASP221 4.5 32.0 1.0
O H:ASP221 4.5 30.3 1.0
H2 H:HOH441 4.5 31.6 1.0
H1 H:HOH439 4.5 30.1 1.0
H1 H:HOH441 4.5 31.2 1.0
CB H:LYS224 4.6 29.6 1.0
C H:GLY223 4.7 27.6 1.0
CA H:TYR225 4.7 20.7 1.0
H2 H:HOH422 4.8 24.3 1.0
OD1 H:ASP221 4.9 35.4 1.0
O H:HOH435 4.9 37.6 1.0
HB2 H:ARG221A 4.9 34.6 1.0
CA H:GLY223 5.0 29.9 1.0
HB2 H:ASP189 5.0 26.1 1.0

Reference:

B.A.Katz, P.A.Sprengeler, C.Luong, E.Verner, K.Elrod, M.Kirtley, J.Janc, J.R.Spencer, J.G.Breitenbucher, H.Hui, D.Mcgee, D.Allen, A.Martelli, R.L.Mackman. Engineering Inhibitors Highly Selective For the S1 Sites of SER190 Trypsin-Like Serine Protease Drug Targets. Chem.Biol. V. 8 1107 2001.
ISSN: ISSN 1074-5521
PubMed: 11731301
DOI: 10.1016/S1074-5521(01)00084-9
Page generated: Sun Aug 17 05:06:06 2025

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