Zinc in PDB 2x5r: Crystal Structure of the Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus

The structure of Crystal Structure of the Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus, PDB code: 2x5r was solved by M.Oke, L.G.Carter, K.A.Johnson, H.Liu, S.A.Mcmahon, M.F.White, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.63 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	39.041, 39.041, 143.733, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 24.6

The binding sites of Zinc atom in the Crystal Structure of the Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus (pdb code 2x5r). 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 Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus, PDB code: 2x5r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus


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 Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1125 b:50.1 occ:1.00 O A:HOH2084 1.7 2.0 1.0 NE2 A:HIS14 2.3 59.1 1.0 O A:HOH2085 2.4 12.0 1.0 CD2 A:HIS14 3.0 58.8 1.0 CE1 A:HIS14 3.3 59.0 1.0 O A:HOH2016 4.0 4.9 1.0 OD1 A:ASP75 4.1 53.7 1.0 CG A:HIS14 4.3 57.9 1.0 CE A:LYS71 4.3 57.4 1.0 ND1 A:HIS14 4.4 58.0 1.0 NZ A:LYS71 4.5 58.9 1.0 OD2 A:ASP75 4.6 57.2 1.0 CG A:ASP75 4.8 53.1 1.0 CG A:LYS71 5.0 49.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus


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 Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1126 b:40.6 occ:1.00 SG A:CYS83 2.3 44.6 1.0 SG A:CYS112 2.4 44.7 1.0 SG A:CYS109 2.4 46.4 1.0 SG A:CYS80 2.5 37.1 1.0 CB A:CYS83 3.2 44.8 1.0 CB A:CYS80 3.2 36.2 1.0 CB A:CYS112 3.3 42.9 1.0 CB A:CYS109 3.6 42.8 1.0 N A:CYS83 3.8 42.8 1.0 CA A:CYS83 4.0 44.6 1.0 N A:CYS109 4.1 38.2 1.0 N A:CYS112 4.2 44.2 1.0 CG A:LYS111 4.2 54.1 1.0 CA A:CYS109 4.3 39.0 1.0 CA A:CYS112 4.3 44.2 1.0 CE A:LYS111 4.4 61.1 1.0 NZ A:LYS111 4.5 62.1 1.0 C A:LYS82 4.6 43.1 1.0 O A:CYS109 4.6 37.0 1.0 CB A:ALA85 4.7 45.2 1.0 CA A:CYS80 4.7 35.5 1.0 C A:CYS83 4.7 44.9 1.0 C A:CYS109 4.7 37.7 1.0 O A:HOH2070 4.8 22.8 1.0 CB A:LYS82 4.8 41.7 1.0 N A:GLY84 4.9 43.1 1.0 CD A:LYS111 4.9 60.9 1.0 N A:ALA85 4.9 44.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus


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 Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1127 b:61.4 occ:1.00 ND1 A:HIS92 2.0 39.1 1.0 OD2 A:ASP110 2.2 49.5 1.0 O A:HOH2086 2.3 23.5 1.0 CE1 A:HIS92 2.9 40.3 1.0 CG A:HIS92 3.1 37.5 1.0 CG A:ASP110 3.1 44.8 1.0 N A:HIS92 3.4 39.3 1.0 CB A:HIS92 3.5 36.6 1.0 OD1 A:ASP110 3.6 46.6 1.0 OG1 A:THR117 3.8 46.5 1.0 NE2 A:HIS92 4.0 39.6 1.0 CA A:HIS92 4.0 37.0 1.0 CD2 A:HIS92 4.1 37.0 1.0 C A:ASN91 4.1 41.4 1.0 CB A:ASP110 4.3 39.3 1.0 CA A:ASN91 4.5 44.0 1.0 CD A:PRO45 4.6 42.4 1.0 CG2 A:THR117 4.7 50.1 1.0 CG A:PRO45 4.8 45.8 1.0 O A:LYS90 4.9 49.2 1.0 CB A:THR117 4.9 46.2 1.0 O A:ASN91 5.0 41.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus


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 Hypothetical Protein ORF126 From Pyrobaculum Spherical Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1128 b:33.8 occ:0.50 ND1 A:HIS27 1.9 37.5 1.0 OE2 A:GLU37 2.0 49.1 1.0 CD A:GLU37 2.6 46.8 1.0 OE1 A:GLU37 2.6 47.0 1.0 CG A:HIS27 2.9 38.4 1.0 CE1 A:HIS27 3.0 41.0 1.0 CB A:HIS27 3.2 38.5 1.0 CD2 A:HIS27 4.0 40.1 1.0 NE2 A:HIS27 4.0 41.2 1.0 CG A:GLU37 4.1 44.0 1.0 CA A:HIS27 4.1 36.4 1.0 NH1 A:ARG31 4.4 43.8 0.5 O A:HIS27 4.5 37.0 1.0 CB A:PRO58 4.5 48.5 1.0 O A:HOH2034 4.6 19.2 1.0 C A:HIS27 4.8 36.8 1.0 CB A:GLU37 5.0 44.6 1.0

M.Oke, L.G.Carter, K.A.Johnson, H.Liu, S.A.Mcmahon, X.Yan, M.Kerou, N.D.Weikart, N.Kadi, M.A.Sheikh, S.Schmelz, M.Dorward, M.Zawadzki, C.Cozens, H.Falconer, H.Powers, I.M.Overton, C.A.J.Van Niekerk, X.Peng, P.Patel, R.A.Garrett, D.Prangishvili, C.H.Botting, P.J.Coote, D.T.F.Dryden, G.J.Barton, U.Schwarz-Linek, G.L.Challis, G.L.Taylor, M.F.White, J.H.Naismith. The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. J.Struct.Funct.Genomics V. 11 167 2010.
ISSN: ISSN 1345-711X
PubMed: 20419351
DOI: 10.1007/S10969-010-9090-Y