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Zinc in PDB 1ghy: 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: 1ghy 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 (°) 71.890, 72.220, 72.740, 90.00, 100.97, 90.00
R / Rfree (%) 19.5 / 22

Other elements in 1ghy:

The structure of A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site (pdb code 1ghy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network at the Active Site, PDB code: 1ghy:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1ghy

Go back to Zinc Binding Sites List in 1ghy
Zinc binding site 1 out of 3 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 Zinc with other atoms in the Zn 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
L:Zn580

b:86.5
occ:0.85
H1 L:HOH1029 2.9 61.3 1.0
O L:HOH1029 3.5 61.0 1.0
HB2 L:ASP14L 3.7 74.3 0.0
H1 L:HOH718 3.8 62.4 1.0
OD2 L:ASP14L 3.9 72.7 0.0
H2 L:HOH1029 4.2 60.4 1.0
H2 L:HOH582 4.3 62.0 1.0
O L:HOH718 4.3 66.1 1.0
O L:HOH582 4.3 64.5 1.0
CB L:ASP14L 4.4 72.8 0.0
CG L:ASP14L 4.5 72.8 0.0
H1 L:HOH582 4.5 62.8 1.0
HB3 L:ASP14L 4.6 73.2 0.0
H2 L:HOH718 4.8 61.8 1.0

Zinc binding site 2 out of 3 in 1ghy

Go back to Zinc Binding Sites List in 1ghy
Zinc binding site 2 out of 3 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 Zinc with other atoms in the Zn binding site number 2 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:Zn247

b:25.3
occ:1.00
O6' H:121246 1.9 59.9 1.0
NE2 H:HIS57 2.0 10.5 1.0
N3 H:121246 2.1 29.5 1.0
C6' H:121246 2.3 51.4 1.0
H1 H:HOH477 2.4 17.6 1.0
OG H:SER195 2.4 17.9 1.0
O H:HOH477 2.5 14.7 1.0
C1' H:121246 2.6 47.0 1.0
C8 H:121246 2.7 36.2 1.0
H2 H:HOH477 3.0 9.1 1.0
CE1 H:HIS57 3.0 9.8 1.0
CD2 H:HIS57 3.0 11.6 1.0
HB2 H:SER195 3.1 14.5 1.0
HE1 H:HIS57 3.2 9.2 1.0
CB H:SER195 3.2 11.1 1.0
HD2 H:HIS57 3.2 12.1 1.0
C4 H:121246 3.3 24.0 1.0
C5' H:121246 3.4 54.3 1.0
HB3 H:SER195 3.5 11.3 1.0
N2' H:121246 3.8 52.0 1.0
HC5' H:121246 3.8 53.0 1.0
HC3 H:121246 3.9 20.7 1.0
N4 H:121246 4.0 29.9 1.0
H1 H:HOH1230 4.0 53.9 1.0
C3 H:121246 4.1 18.7 1.0
O H:SER214 4.1 28.2 1.0
ND1 H:HIS57 4.1 11.8 1.0
HA H:GLU192 4.1 25.7 1.0
CG H:HIS57 4.1 11.6 1.0
OE2 H:GLU192 4.3 38.2 0.4
C5 H:121246 4.3 19.9 1.0
H H:SER195 4.3 15.8 1.0
O H:HOH1230 4.3 59.6 1.0
H H:GLY193 4.3 17.2 1.0
C4' H:121246 4.4 54.1 1.0
C3' H:121246 4.5 54.0 1.0
CA H:SER195 4.5 13.6 1.0
HZ2 H:LYS60F 4.7 40.1 1.0
HA H:TRP215 4.7 26.8 1.0
N H:SER195 4.8 16.3 1.0
HA H:SER195 4.9 15.2 1.0
CD H:GLU192 4.9 35.4 0.4
HD1 H:HIS57 5.0 13.2 1.0

Zinc binding site 3 out of 3 in 1ghy

Go back to Zinc Binding Sites List in 1ghy
Zinc binding site 3 out of 3 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 Zinc with other atoms in the Zn binding site number 3 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:Zn248

b:55.5
occ:1.00
N4 H:121246 2.4 29.9 1.0
H2 H:HOH620 2.6 41.8 1.0
O H:HOH1184 2.8 57.2 1.0
O H:GLY216 2.8 24.9 1.0
N2' H:121246 3.0 52.0 1.0
O H:HOH610 3.0 60.1 1.0
O H:HOH620 3.1 45.8 1.0
H H:GLY216 3.2 16.1 1.0
H2 H:HOH1184 3.2 55.2 1.0
H2 H:HOH610 3.4 59.2 1.0
HC6 H:121246 3.4 19.4 1.0
C8 H:121246 3.4 36.2 1.0
C5 H:121246 3.4 19.9 1.0
H1 H:HOH1184 3.6 55.3 1.0
C1' H:121246 3.6 47.0 1.0
HB2 H:TRP215 3.6 36.1 1.0
C6 H:121246 3.8 20.5 1.0
C3' H:121246 3.8 54.0 1.0
H1 H:HOH610 3.9 58.6 1.0
HC3' H:121246 3.9 54.0 1.0
H H:GLY219 3.9 18.6 1.0
H1 H:HOH620 4.0 44.1 1.0
C H:GLY216 4.0 22.1 1.0
HA H:GLU217 4.1 24.5 1.0
N H:GLY216 4.1 14.8 1.0
HA H:TRP215 4.2 26.8 1.0
OE1 H:GLU192 4.3 37.9 0.4
CB H:TRP215 4.5 36.2 1.0
N3 H:121246 4.5 29.5 1.0
C4 H:121246 4.5 24.0 1.0
HB3 H:TRP215 4.7 37.1 1.0
CA H:TRP215 4.8 26.6 1.0
CA H:GLY216 4.8 17.6 1.0
N H:GLY219 4.8 17.5 1.0
HE3 H:TRP215 4.9 45.2 1.0
C6' H:121246 4.9 51.4 1.0
CA H:GLU217 4.9 25.7 1.0
N H:GLU217 4.9 25.0 1.0
C H:TRP215 5.0 20.2 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: Sun Oct 13 01:31:21 2024

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