Zinc in PDB 1iau: Human Granzyme B in Complex with Ac-Iepd-Cho

All present enzymatic activity of Human Granzyme B in Complex with Ac-Iepd-Cho:
3.4.21.79;

The structure of Human Granzyme B in Complex with Ac-Iepd-Cho, PDB code: 1iau was solved by J.Rotonda, M.Garcia-Calvo, H.G.Bull, W.M.Geissler, B.M.Mckeever, C.A.Willoughby, N.A.Thornberry, J.W.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.873, 75.081, 80.261, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Human Granzyme B in Complex with Ac-Iepd-Cho (pdb code 1iau). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Human Granzyme B in Complex with Ac-Iepd-Cho, PDB code: 1iau:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Human Granzyme B in Complex with Ac-Iepd-Cho


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Granzyme B in Complex with Ac-Iepd-Cho within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:59.9 occ:1.00 NE2 A:HIS153 1.9 50.8 1.0 NE2 A:HIS151 2.4 90.3 1.0 CE1 A:HIS153 2.6 53.0 1.0 CD2 A:HIS153 3.0 53.4 1.0 CE1 A:HIS151 3.0 91.3 1.0 CD2 A:HIS151 3.4 89.1 1.0 ND1 A:HIS153 3.8 54.5 1.0 CG A:HIS153 4.0 49.1 1.0 ND1 A:HIS151 4.1 92.0 1.0 CG A:HIS151 4.3 83.9 1.0 CE A:LYS74 4.9 78.9 1.0 CG A:LYS74 4.9 65.8 1.0

Zinc binding site 2 out of 5 in the Human Granzyme B in Complex with Ac-Iepd-Cho


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Granzyme B in Complex with Ac-Iepd-Cho within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:38.4 occ:1.00 NE2 A:HIS25 2.0 33.8 1.0 O A:HOH605 2.1 23.6 1.0 OE2 A:GLU77 2.1 44.4 1.0 CE1 A:HIS25 2.9 31.0 1.0 CD A:GLU77 3.1 68.5 1.0 CD2 A:HIS25 3.2 32.4 1.0 OE1 A:GLU77 4.0 96.8 1.0 ND1 A:HIS25 4.1 31.4 1.0 CG A:GLU77 4.1 61.5 1.0 CG A:HIS25 4.2 35.1 1.0 OG1 A:THR79 4.3 27.0 1.0 CB A:PRO24 4.7 38.5 1.0 CG2 A:THR79 4.7 33.5 1.0

Zinc binding site 3 out of 5 in the Human Granzyme B in Complex with Ac-Iepd-Cho


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Granzyme B in Complex with Ac-Iepd-Cho within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:66.6 occ:1.00 OE2 A:GLU169 1.9 46.0 1.0 CD A:GLU169 2.5 39.6 1.0 OE1 A:GLU169 2.6 52.2 1.0 CG A:GLU169 4.0 37.3 1.0 O A:HOH624 4.7 50.5 1.0 CB A:ASP165 4.8 25.8 1.0 OG A:SER177 4.9 30.7 1.0 CB A:GLU169 5.0 36.5 1.0

Zinc binding site 4 out of 5 in the Human Granzyme B in Complex with Ac-Iepd-Cho


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Granzyme B in Complex with Ac-Iepd-Cho within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:53.2 occ:1.00 NE2 A:HIS20 1.8 29.1 1.0 O A:HOH655 2.1 44.6 1.0 OE2 A:GLU157 2.2 28.0 1.0 O A:HOH653 2.5 36.5 1.0 CE1 A:HIS20 2.7 33.2 1.0 CD2 A:HIS20 2.9 37.7 1.0 CD A:GLU157 3.0 28.4 1.0 CG A:GLU157 3.3 24.9 1.0 ND1 A:HIS20 3.8 35.6 1.0 CG A:HIS20 4.0 34.7 1.0 OE1 A:GLU157 4.1 33.1 1.0 CB A:GLU157 4.6 25.5 1.0 O A:GLU157 4.7 33.4 1.0 O A:HOH639 4.9 60.4 1.0 C A:GLU157 5.0 36.6 1.0

Zinc binding site 5 out of 5 in the Human Granzyme B in Complex with Ac-Iepd-Cho


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Granzyme B in Complex with Ac-Iepd-Cho within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:59.2 occ:1.00 O A:HOH649 1.7 35.4 1.0 CG A:GLU186 1.9 42.0 1.0 OD1 A:ASP184 2.3 30.3 1.0 CB A:GLU186 3.0 48.4 1.0 CD A:GLU186 3.1 46.4 1.0 CG A:ASP184 3.2 46.3 1.0 OE2 A:GLU186 3.3 42.1 1.0 OD2 A:ASP184 3.5 56.8 1.0 N A:GLU186 3.6 48.5 1.0 CA A:GLU186 4.0 54.0 1.0 OE1 A:GLU186 4.2 64.7 1.0 CD A:PRO185 4.2 34.6 1.0 N A:PRO185 4.4 30.2 1.0 CB A:ASP184 4.6 43.0 1.0 C A:PRO185 4.7 45.4 1.0 C A:ASP184 4.8 36.5 1.0 CB A:PRO185 4.8 32.3 1.0 CG A:PRO185 4.9 32.4 1.0 CA A:ASP184 4.9 40.3 1.0 CA A:PRO185 5.0 32.4 1.0 C A:GLU186 5.0 58.5 1.0

J.Rotonda, M.Garcia-Calvo, H.G.Bull, W.M.Geissler, B.M.Mckeever, C.A.Willoughby, N.A.Thornberry, J.W.Becker. The Three-Dimensional Structure of Human Granzyme B Compared to Caspase-3, Key Mediators of Cell Death with Cleavage Specificity For Aspartic Acid in P1. Chem.Biol. V. 8 357 2001.
ISSN: ISSN 1074-5521
PubMed: 11325591
DOI: 10.1016/S1074-5521(01)00018-7