Zinc in PDB 1z8i: Crystal Structure of the Thrombin Mutant G193A Bound to Ppack

All present enzymatic activity of Crystal Structure of the Thrombin Mutant G193A Bound to Ppack:
3.4.21.5;

The structure of Crystal Structure of the Thrombin Mutant G193A Bound to Ppack, PDB code: 1z8i was solved by K.M.Bobofchak, A.O.Pineda, F.S.Mathews, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.820, 73.650, 89.770, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.2

The structure of Crystal Structure of the Thrombin Mutant G193A Bound to Ppack also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Thrombin Mutant G193A Bound to Ppack (pdb code 1z8i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Thrombin Mutant G193A Bound to Ppack, PDB code: 1z8i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Thrombin Mutant G193A Bound to Ppack


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Thrombin Mutant G193A Bound to Ppack within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:25.4 occ:1.00 OD2 A:ASP1A 2.0 33.7 1.0 O A:HOH710 2.0 40.3 1.0 NE2 B:HIS119 2.1 28.1 1.0 CE1 B:HIS119 2.9 24.0 1.0 CG A:ASP1A 3.0 28.7 1.0 CD2 B:HIS119 3.2 21.5 1.0 OD1 A:ASP1A 3.4 38.2 1.0 O A:HOH765 4.1 47.4 1.0 ND1 B:HIS119 4.1 24.1 1.0 CG B:HIS119 4.2 24.5 1.0 O A:HOH735 4.3 68.0 1.0 CB A:ASP1A 4.3 30.2 1.0 CD2 B:PHE114 4.3 28.1 1.0 CB B:PHE114 4.5 25.7 1.0 O B:HOH715 4.6 78.9 1.0 NZ A:LYS9 4.7 50.1 1.0 CG B:PHE114 4.9 23.3 1.0 O A:ASP1A 5.0 37.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Thrombin Mutant G193A Bound to Ppack


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Thrombin Mutant G193A Bound to Ppack within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:40.6 occ:1.00 O B:HOH756 2.2 24.1 1.0 O B:HOH752 2.4 21.9 1.0 CA B:PRO60C 4.5 29.9 1.0 CG B:PRO60C 4.7 29.6 1.0 CB B:PRO60C 4.8 28.6 1.0 N B:PRO60C 5.0 28.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Thrombin Mutant G193A Bound to Ppack


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Thrombin Mutant G193A Bound to Ppack within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:34.1 occ:1.00 ND1 B:HIS71 2.0 73.5 1.0 O B:HOH746 2.1 36.5 1.0 OE2 B:GLU77 2.3 88.2 1.0 O B:HOH834 2.4 49.8 1.0 CE1 B:HIS71 2.9 73.9 1.0 CG B:HIS71 3.0 76.6 1.0 CD B:GLU77 3.3 90.1 1.0 O B:HOH865 3.5 79.7 1.0 CB B:HIS71 3.5 74.0 1.0 CG B:GLU77 3.7 88.1 1.0 NE2 B:HIS71 4.0 75.6 1.0 CD2 B:HIS71 4.1 76.6 1.0 O B:HOH761 4.2 47.0 1.0 OE1 B:GLU77 4.4 93.1 1.0 CG2 B:ILE79 4.6 63.2 1.0 CB B:GLU77 4.7 86.5 1.0 CA B:HIS71 4.9 74.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Thrombin Mutant G193A Bound to Ppack


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Thrombin Mutant G193A Bound to Ppack within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn704 b:61.5 occ:1.00 O B:HOH759 2.3 44.6 1.0 O B:HOH737 2.4 41.1 1.0 OD2 B:ASP21 3.7 46.0 1.0 O B:HOH919 3.9 38.5 1.0 OD1 B:ASP21 4.2 36.4 1.0 CG B:ASP21 4.3 45.0 1.0 O B:HOH850 4.6 66.3 1.0

K.M.Bobofchak, A.O.Pineda, F.S.Mathews, E.Di Cera. Energetic and Structural Consequences of Perturbing Gly-193 in the Oxyanion Hole of Serine Proteases J.Biol.Chem. V. 280 25644 2005.
ISSN: ISSN 0021-9258
PubMed: 15890651
DOI: 10.1074/JBC.M503499200