Zinc in PDB 3b4r: Site-2 Protease From Methanocaldococcus Jannaschii

The structure of Site-2 Protease From Methanocaldococcus Jannaschii, PDB code: 3b4r was solved by P.D.Jeffrey, L.Feng, H.Yan, Z.Wu, N.Yan, Z.Wang, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.99 / 3.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	124.420, 124.420, 136.720, 90.00, 90.00, 120.00
R / Rfree (%)	25.1 / 31.8

The binding sites of Zinc atom in the Site-2 Protease From Methanocaldococcus Jannaschii (pdb code 3b4r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Site-2 Protease From Methanocaldococcus Jannaschii, PDB code: 3b4r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Site-2 Protease From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Site-2 Protease From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn225 b:77.3 occ:1.00 OD2 A:ASP148 2.2 79.0 1.0 OD1 A:ASP148 2.2 80.3 1.0 NE2 A:HIS54 2.3 80.8 1.0 NE2 A:HIS58 2.3 89.5 1.0 CE1 A:HIS54 2.4 83.4 1.0 CG A:ASP148 2.5 78.3 1.0 CD2 A:HIS58 2.9 91.2 1.0 OE2 A:GLU55 3.3 89.3 1.0 CE1 A:HIS58 3.6 91.7 1.0 OD1 A:ASN140 3.6 49.2 1.0 CD2 A:HIS54 3.7 79.2 1.0 ND1 A:HIS54 3.8 84.1 1.0 CB A:ASP148 4.0 75.9 1.0 CG A:ASN140 4.2 49.6 1.0 CG A:HIS58 4.2 91.3 1.0 CG A:HIS54 4.4 81.5 1.0 ND1 A:HIS58 4.5 92.2 1.0 CD A:GLU55 4.5 87.8 1.0 ND2 A:ASN140 4.6 49.8 1.0 N A:ASP148 4.8 72.2 1.0 CA A:ASP148 4.8 74.1 1.0 CD A:PRO99 4.9 61.1 1.0 CB A:ASN140 4.9 50.0 1.0

Zinc binding site 2 out of 2 in the Site-2 Protease From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Site-2 Protease From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn225 b:77.6 occ:1.00 OD1 B:ASP148 2.2 81.3 1.0 NE2 B:HIS58 2.2 96.7 1.0 NE2 B:HIS54 2.3 87.1 1.0 OD2 B:ASP148 2.5 85.5 1.0 CG B:ASP148 2.7 83.2 1.0 CD2 B:HIS58 2.7 0.9 1.0 CD2 B:HIS54 2.9 91.2 1.0 OE2 B:GLU55 3.4 91.8 1.0 CE1 B:HIS54 3.5 87.6 1.0 CE1 B:HIS58 3.5 0.8 1.0 OD1 B:ASN140 3.8 66.2 1.0 N B:GLY79 4.0 91.5 1.0 CG B:HIS58 4.0 0.0 1.0 O B:GLY79 4.0 1.0 1.0 CB B:ASP148 4.2 79.9 1.0 CG B:HIS54 4.2 92.7 1.0 ND1 B:HIS58 4.3 0.3 1.0 ND1 B:HIS54 4.4 90.3 1.0 CD B:GLU55 4.5 95.1 1.0 N B:ASP148 4.6 81.2 1.0 CA B:GLY78 4.7 89.8 1.0 CA B:GLY79 4.8 96.2 1.0 CA B:ASP148 4.8 79.7 1.0 C B:GLY79 4.8 99.5 1.0 C B:GLY78 4.9 89.8 1.0 CG B:ASN140 4.9 68.6 1.0

L.Feng, H.Yan, Z.Wu, N.Yan, Z.Wang, P.D.Jeffrey, Y.Shi. Structure of A Site-2 Protease Family Intramembrane Metalloprotease. Science V. 318 1608 2007.
ISSN: ISSN 0036-8075
PubMed: 18063795
DOI: 10.1126/SCIENCE.1150755