Zinc in PDB 2pve: uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin

The structure of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin, PDB code: 2pve was solved by D.M.Lemaster, J.S.Anderson, L.Wang, Y.Guo, H.Li, G.Hernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 0.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.169, 56.860, 38.170, 90.00, 112.92, 90.00
R / Rfree (%)	11.2 / 12.5

The binding sites of Zinc atom in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin (pdb code 2pve). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin, PDB code: 2pve:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:5.5 occ:1.00 SG A:CYS9 2.3 5.5 1.0 SG A:CYS42 2.3 6.2 1.0 SG A:CYS6 2.3 5.7 1.0 SG A:CYS39 2.4 5.5 1.0 HB3 A:CYS9 3.1 6.4 1.0 HB3 A:CYS6 3.1 7.0 1.0 H A:CYS42 3.1 8.0 1.0 CB A:CYS6 3.2 5.8 1.0 HB3 A:CYS39 3.2 6.7 1.0 CB A:CYS39 3.2 5.6 1.0 H A:CYS9 3.2 6.6 1.0 HB2 A:CYS39 3.2 6.7 1.0 HB3 A:CYS42 3.2 8.2 1.0 HB2 A:CYS6 3.2 7.0 1.0 CB A:CYS9 3.3 5.3 1.0 CB A:CYS42 3.4 6.8 1.0 HB A:ILE8 3.6 6.5 1.0 HB3 A:TYR11 3.7 7.3 1.0 HB A:ILE41 3.7 8.4 0.7 HB1 A:ALA44 3.8 10.6 1.0 N A:CYS42 3.8 6.7 1.0 HB A:ILE41 3.8 8.7 0.3 N A:CYS9 3.8 5.5 1.0 H A:ALA44 3.9 8.0 1.0 HB2 A:ALA44 4.0 10.6 1.0 CA A:CYS9 4.1 5.2 1.0 HB2 A:CYS9 4.1 6.4 1.0 H A:TYR11 4.1 6.6 1.0 CA A:CYS42 4.1 6.7 1.0 HB2 A:TYR11 4.2 7.3 1.0 HB2 A:CYS42 4.2 8.2 1.0 CB A:ALA44 4.3 7.1 1.0 CB A:TYR11 4.4 6.1 1.0 H A:GLY43 4.5 8.6 1.0 H A:GLY10 4.5 6.7 1.0 H A:ILE41 4.5 8.1 1.0 H A:ILE8 4.6 6.7 1.0 CB A:ILE8 4.6 5.5 1.0 CA A:CYS6 4.6 5.9 1.0 CB A:ILE41 4.6 7.0 0.7 CA A:CYS39 4.7 5.5 1.0 CB A:ILE41 4.7 7.3 0.3 HZ A:PHE49 4.7 9.0 1.0 C A:CYS42 4.7 7.3 1.0 HG23 A:ILE41 4.7 10.7 0.3 N A:ALA44 4.7 6.7 1.0 C A:ILE8 4.8 5.2 1.0 C A:CYS9 4.8 5.2 1.0 N A:GLY43 4.8 7.2 1.0 C A:ILE41 4.8 7.3 1.0 N A:GLY10 4.8 5.6 1.0 N A:TYR11 4.8 5.5 1.0 HA A:CYS9 4.9 6.3 1.0 HG23 A:ILE8 4.9 9.4 1.0 HA A:CYS42 4.9 8.1 1.0 HG21 A:ILE41 4.9 14.4 0.7 HA A:CYS6 5.0 7.0 1.0 HA A:CYS39 5.0 6.6 1.0

Zinc binding site 2 out of 3 in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:5.3 occ:1.00 SG B:CYS142 2.3 5.3 1.0 SG B:CYS109 2.3 6.0 1.0 SG B:CYS106 2.3 5.9 1.0 SG B:CYS139 2.4 4.8 1.0 HB3 B:CYS142 3.1 6.2 1.0 HB3 B:CYS106 3.2 7.4 1.0 HB3 B:CYS139 3.2 5.8 1.0 CB B:CYS106 3.2 6.2 1.0 CB B:CYS139 3.2 4.8 1.0 H B:CYS142 3.2 5.6 1.0 HB2 B:CYS139 3.2 5.8 1.0 H B:CYS109 3.3 8.1 1.0 HB2 B:CYS106 3.3 7.4 1.0 HB3 B:CYS109 3.3 7.7 1.0 CB B:CYS142 3.3 5.2 1.0 CB B:CYS109 3.4 6.4 1.0 HB B:ILE108 3.6 9.5 1.0 HB3 B:TYR111 3.6 8.1 1.0 HB B:ILE141 3.7 6.6 1.0 N B:CYS142 3.8 4.7 1.0 N B:CYS109 3.8 6.7 1.0 HB1 B:ALA144 3.9 9.3 1.0 H B:TYR111 4.0 9.0 1.0 H B:ALA144 4.0 5.9 1.0 HB2 B:ALA144 4.1 9.3 1.0 CA B:CYS142 4.1 4.9 1.0 HB2 B:CYS142 4.1 6.2 1.0 HB2 B:TYR111 4.1 8.1 1.0 CA B:CYS109 4.1 6.9 1.0 HB2 B:CYS109 4.2 7.7 1.0 CB B:TYR111 4.3 6.7 1.0 CB B:ALA144 4.4 6.2 1.0 H B:GLY110 4.5 8.9 1.0 HZ B:PHE149 4.5 7.4 1.0 CB B:ILE108 4.5 7.9 1.0 H B:ILE141 4.5 5.4 1.0 H B:ILE108 4.6 9.0 1.0 CB B:ILE141 4.6 5.5 1.0 H B:GLY143 4.6 5.5 1.0 CA B:CYS139 4.6 4.4 1.0 CA B:CYS106 4.7 6.2 1.0 HG23 B:ILE108 4.7 13.3 1.0 C B:CYS142 4.7 4.5 1.0 C B:CYS109 4.7 7.0 1.0 N B:TYR111 4.8 7.5 1.0 HG21 B:ILE141 4.8 10.8 1.0 C B:ILE108 4.8 7.8 1.0 N B:GLY110 4.8 7.5 1.0 N B:ALA144 4.8 4.9 1.0 C B:ILE141 4.9 4.5 1.0 N B:GLY143 4.9 4.6 1.0 HA B:CYS142 4.9 5.8 1.0 HA B:CYS109 5.0 8.3 1.0 CZ B:PHE149 5.0 6.2 1.0 HA B:CYS139 5.0 5.3 1.0 HA B:CYS106 5.0 7.4 1.0

Zinc binding site 3 out of 3 in the uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:5.4 occ:1.00 SG C:CYS209 2.3 5.7 1.0 SG C:CYS242 2.3 5.9 1.0 SG C:CYS206 2.3 5.2 1.0 SG C:CYS239 2.4 5.5 1.0 HB3 C:CYS209 3.1 6.7 1.0 HB3 C:CYS206 3.1 6.4 1.0 CB C:CYS206 3.1 5.3 1.0 CB C:CYS239 3.2 5.2 1.0 HB3 C:CYS239 3.2 6.2 1.0 HB2 C:CYS239 3.2 6.2 1.0 HB2 C:CYS206 3.2 6.4 1.0 H C:CYS242 3.2 7.7 1.0 H C:CYS209 3.2 6.2 1.0 HB3 C:CYS242 3.2 8.1 1.0 CB C:CYS209 3.3 5.6 1.0 CB C:CYS242 3.4 6.8 1.0 HB3 C:TYR211 3.6 8.4 1.0 HB C:ILE241 3.7 8.7 1.0 HB1 C:ALA244 3.7 9.7 1.0 HB C:ILE208 3.8 6.3 1.0 N C:CYS209 3.8 5.2 1.0 N C:CYS242 3.8 6.4 1.0 H C:ALA244 4.0 7.0 1.0 H C:TYR211 4.0 7.8 1.0 HB2 C:ALA244 4.0 9.7 1.0 HB2 C:CYS209 4.0 6.7 1.0 CA C:CYS209 4.0 5.4 1.0 HB2 C:TYR211 4.0 8.4 1.0 CA C:CYS242 4.1 6.9 1.0 HB2 C:CYS242 4.2 8.1 1.0 CB C:TYR211 4.3 7.0 1.0 CB C:ALA244 4.3 6.5 1.0 H C:GLY210 4.4 7.2 1.0 H C:GLY243 4.5 7.2 1.0 HZ C:PHE249 4.5 7.8 1.0 H C:ILE241 4.5 8.6 1.0 CA C:CYS206 4.6 4.7 1.0 CB C:ILE241 4.6 7.2 1.0 CA C:CYS239 4.6 5.3 1.0 H C:ILE208 4.6 6.2 1.0 CB C:ILE208 4.7 5.3 1.0 C C:CYS209 4.7 5.3 1.0 N C:ALA244 4.7 5.8 1.0 C C:CYS242 4.7 6.2 1.0 N C:TYR211 4.8 6.5 1.0 N C:GLY210 4.8 6.0 1.0 N C:GLY243 4.8 6.0 1.0 C C:ILE208 4.8 5.5 1.0 C C:ILE241 4.9 7.2 1.0 HA C:CYS209 4.9 6.4 1.0 HG23 C:ILE208 4.9 9.3 1.0 HA C:CYS206 4.9 5.6 1.0 HA C:CYS242 4.9 8.3 1.0 HA C:CYS239 4.9 6.3 1.0 HG21 C:ILE241 5.0 12.6 1.0

D.M.Lemaster, J.S.Anderson, L.Wang, Y.Guo, H.Li, G.Hernandez. uc(Nmr) and X-Ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin. Bmc Struct.Biol. V. 7 81 2007.
ISSN: ESSN 1472-6807
PubMed: 18053245
DOI: 10.1186/1472-6807-7-81