Zinc in PDB 1cvr: Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)

All present enzymatic activity of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb):
3.4.22.37;

The structure of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb), PDB code: 1cvr was solved by A.Eichinger, H.-G.Beisel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.930, 79.920, 99.820, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.7

The structure of Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb) (pdb code 1cvr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb), PDB code: 1cvr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


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 Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:60.4 occ:1.00 OE1 A:GLU152 2.3 33.0 1.0 NE2 A:HIS211 2.4 23.8 1.0 O A:HOH920 2.8 39.9 1.0 O A:HOH724 3.0 39.5 1.0 CD A:GLU152 3.1 29.6 1.0 CE1 A:HIS211 3.2 25.3 1.0 OE2 A:GLU152 3.3 30.1 1.0 CD2 A:HIS211 3.5 23.7 1.0 CZ3 A:TRP284 3.5 17.1 1.0 O A:HOH771 3.6 35.6 1.0 CH2 A:TRP284 4.0 17.4 1.0 ND1 A:HIS211 4.4 25.0 1.0 CE3 A:TRP284 4.5 17.4 1.0 CG A:GLU152 4.5 27.3 1.0 CG A:HIS211 4.6 23.4 1.0 O1 A:H37501 4.7 19.3 1.0 CB A:GLU152 4.8 22.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Arg Specific Cysteine Proteinase Gingipain R (Rgpb)


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 Arg Specific Cysteine Proteinase Gingipain R (Rgpb) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:39.6 occ:1.00 ND1 A:HIS130 2.3 18.4 1.0 O A:HOH921 2.6 39.9 1.0 CG A:HIS130 3.2 16.5 1.0 CE1 A:HIS130 3.3 17.0 1.0 OD1 A:ASN134 3.3 32.0 1.0 CB A:HIS130 3.5 14.3 1.0 CG A:ASN134 4.1 27.3 1.0 CB A:ASN134 4.1 23.1 1.0 CA A:HIS130 4.2 15.5 1.0 CD2 A:HIS130 4.4 16.9 1.0 NE2 A:HIS130 4.4 18.6 1.0 ND2 A:ASN234 4.5 18.9 1.0

A.Eichinger, H.G.Beisel, U.Jacob, R.Huber, F.J.Medrano, A.Banbula, J.Potempa, J.Travis, W.Bode. Crystal Structure of Gingipain R: An Arg-Specific Bacterial Cysteine Proteinase with A Caspase-Like Fold. Embo J. V. 18 5453 1999.
ISSN: ISSN 0261-4189
PubMed: 10523290
DOI: 10.1093/EMBOJ/18.20.5453