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Sodium in PDB 1ghv: A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site

Enzymatic activity of A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site

All present enzymatic activity of A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site:
3.4.21.5;

Protein crystallography data

The structure of A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site, PDB code: 1ghv was solved by B.A.Katz, K.Elrod, C.Luong, M.Rice, R.L.Mackman, P.A.Sprengeler, J.Spencer, J.Hatayte, J.Janc, J.Link, J.Litvak, R.Rai, K.Rice, S.Sideris, E.Verner, W.Young, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.620, 72.070, 73.200, 90.00, 101.14, 90.00
R / Rfree (%) 18.8 / 23.5

Sodium Binding Sites:

The binding sites of Sodium atom in the A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site (pdb code 1ghv). 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 A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site, PDB code: 1ghv:

Sodium binding site 1 out of 1 in 1ghv

Go back to Sodium Binding Sites List in 1ghv
Sodium binding site 1 out of 1 in the A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na409

b:31.9
occ:1.00
O H:ARG221A 2.4 27.0 1.0
O H:LYS224 2.4 15.9 1.0
O H:HOH445 2.6 14.9 1.0
O H:HOH447 2.6 23.7 1.0
O H:HOH416 2.7 39.0 1.0
O H:HOH419 2.7 36.9 1.0
H1 H:HOH416 2.9 42.3 1.0
H2 H:HOH445 2.9 15.2 1.0
H2 H:HOH419 3.1 38.4 1.0
H1 H:HOH419 3.1 38.0 1.0
H H:LYS224 3.1 23.0 1.0
H1 H:HOH447 3.1 22.0 1.0
H2 H:HOH416 3.2 40.0 1.0
H1 H:HOH445 3.2 14.2 1.0
HA H:ASP222 3.3 32.1 1.0
H2 H:HOH447 3.4 23.2 1.0
H2 H:HOH427 3.4 28.2 1.0
C H:LYS224 3.5 21.3 1.0
C H:ARG221A 3.5 27.4 1.0
H1 H:HOH410 3.6 15.6 1.0
H H:GLY223 3.7 26.9 1.0
N H:LYS224 3.7 27.4 1.0
HA H:ASP221 3.8 23.2 1.0
HB2 H:LYS224 3.8 25.5 1.0
O H:HOH427 4.0 28.8 1.0
O H:HOH430 4.0 27.8 1.0
CA H:ASP222 4.0 31.9 1.0
HA H:TYR225 4.0 10.8 1.0
N H:ARG221A 4.0 21.4 1.0
H H:ARG221A 4.1 22.1 1.0
N H:GLY223 4.1 27.9 1.0
CA H:LYS224 4.1 21.9 1.0
N H:ASP222 4.2 31.2 1.0
C H:ASP221 4.2 22.6 1.0
O H:TYR184A 4.3 21.3 1.0
C H:ASP222 4.3 29.8 1.0
O H:HOH410 4.4 12.6 1.0
H1 H:HOH427 4.5 27.1 1.0
CA H:ARG221A 4.5 27.0 1.0
CB H:LYS224 4.5 28.3 1.0
N H:TYR225 4.5 16.0 1.0
CA H:ASP221 4.6 23.2 1.0
C H:GLY223 4.7 24.4 1.0
H1 H:HOH430 4.7 24.8 1.0
O H:ASP221 4.7 24.6 1.0
H2 H:HOH410 4.7 15.6 1.0
HH21 H:ARG187 4.7 32.5 1.0
H2 H:HOH430 4.7 27.1 1.0
H1 H:HOH423 4.8 17.1 1.0
O H:HOH423 4.8 17.4 1.0
CA H:TYR225 4.8 11.4 1.0
OD1 H:ASP221 4.9 29.4 1.0
HB2 H:ARG221A 4.9 28.8 1.0

Reference:

B.A.Katz, K.Elrod, C.Luong, M.J.Rice, R.L.Mackman, P.A.Sprengeler, J.Spencer, J.Hataye, J.Janc, J.Link, J.Litvak, R.Rai, K.Rice, S.Sideris, E.Verner, W.Young. A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site. J.Mol.Biol. V. 307 1451 2001.
ISSN: ISSN 0022-2836
PubMed: 11292354
DOI: 10.1006/JMBI.2001.4516
Page generated: Tue Dec 15 05:24:41 2020

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