Zinc in PDB 3p2a: Crystal Structure of Thioredoxin 2 From Yersinia Pestis

The structure of Crystal Structure of Thioredoxin 2 From Yersinia Pestis, PDB code: 3p2a was solved by Y.Kim, M.Zhou, S.Grimshaw, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.28 / 2.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.970, 75.582, 81.512, 90.00, 90.85, 90.00
R / Rfree (%)	18.4 / 23.4

The binding sites of Zinc atom in the Crystal Structure of Thioredoxin 2 From Yersinia Pestis (pdb code 3p2a). 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 Thioredoxin 2 From Yersinia Pestis, PDB code: 3p2a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Thioredoxin 2 From Yersinia Pestis


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 Thioredoxin 2 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn151 b:28.5 occ:1.00 SG A:CYS25 2.3 25.6 1.0 SG A:CYS8 2.3 26.8 1.0 SG A:CYS5 2.4 25.2 1.0 SG A:CYS28 2.4 27.0 1.0 CB A:CYS25 3.0 22.1 1.0 CB A:CYS5 3.0 18.2 1.0 CB A:CYS8 3.3 16.1 1.0 CB A:CYS28 3.4 20.6 1.0 N A:CYS8 3.7 22.9 1.0 N A:CYS28 3.8 25.0 1.0 CA A:CYS8 4.0 23.2 1.0 CA A:CYS28 4.1 24.9 1.0 CB A:HIS30 4.4 28.2 1.0 CB A:ALA10 4.4 26.0 1.0 CA A:CYS25 4.5 23.6 1.0 CA A:CYS5 4.5 18.6 1.0 C A:CYS8 4.6 26.0 1.0 CB A:ARG27 4.6 30.9 1.0 N A:ALA10 4.7 27.8 1.0 C A:ARG27 4.8 30.0 1.0 N A:MSE9 4.8 33.5 1.0 C A:CYS28 4.8 27.4 1.0 C A:ALA7 4.9 22.6 1.0 N A:HIS30 5.0 29.5 1.0 N A:GLY29 5.0 27.0 1.0 N A:ARG27 5.0 31.0 1.0 CB A:ALA7 5.0 27.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Thioredoxin 2 From Yersinia Pestis


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 Thioredoxin 2 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn151 b:35.6 occ:1.00 SG B:CYS28 2.3 34.3 1.0 SG B:CYS25 2.4 35.7 1.0 SG B:CYS8 2.4 36.3 1.0 SG B:CYS5 2.4 29.6 1.0 CB B:CYS5 3.0 26.3 1.0 CB B:CYS25 3.0 32.9 1.0 CB B:CYS28 3.3 40.8 1.0 CB B:CYS8 3.4 36.9 1.0 N B:CYS28 3.8 43.4 1.0 N B:CYS8 3.9 37.4 1.0 CA B:CYS28 4.1 40.5 1.0 CA B:CYS8 4.2 39.4 1.0 CB B:HIS30 4.3 44.5 1.0 CA B:CYS25 4.5 32.9 1.0 CA B:CYS5 4.5 29.1 1.0 C B:CYS28 4.6 41.7 1.0 N B:HIS30 4.7 41.8 1.0 CB B:ALA10 4.7 36.4 1.0 CB B:ARG27 4.7 54.0 1.0 C B:ARG27 4.8 46.9 1.0 C B:CYS8 4.8 40.2 1.0 CB B:ALA7 4.9 21.1 1.0 N B:MSE9 4.9 39.4 1.0 N B:GLY29 4.9 39.5 1.0 N B:ALA10 4.9 34.0 1.0 N B:ARG27 5.0 45.1 1.0 C B:ALA7 5.0 38.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Thioredoxin 2 From Yersinia Pestis


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 Thioredoxin 2 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn151 b:49.3 occ:1.00 SG C:CYS5 2.3 49.6 1.0 SG C:CYS8 2.3 52.7 1.0 SG C:CYS25 2.4 44.5 1.0 SG C:CYS28 2.5 61.5 1.0 CB C:CYS25 3.1 53.0 1.0 CB C:CYS5 3.2 46.4 1.0 CB C:CYS8 3.5 45.9 1.0 CB C:CYS28 3.5 58.6 1.0 N C:CYS8 3.8 45.9 1.0 N C:CYS28 4.0 63.7 1.0 CA C:CYS8 4.1 44.9 1.0 CA C:CYS28 4.3 62.0 1.0 CB C:HIS30 4.4 61.7 1.0 CA C:CYS25 4.5 58.8 1.0 CB C:ALA10 4.6 43.4 1.0 CA C:CYS5 4.6 43.5 1.0 CB C:ARG27 4.7 69.3 1.0 C C:CYS8 4.7 46.8 1.0 C C:ARG27 4.8 67.8 1.0 C C:CYS28 4.8 63.5 1.0 CB C:ALA7 4.9 42.6 1.0 C C:ALA7 4.9 43.8 1.0 N C:ALA10 4.9 36.9 1.0 N C:ARG27 4.9 69.9 1.0 N C:HIS30 4.9 61.0 1.0 N C:GLY29 5.0 63.4 1.0 N C:MSE9 5.0 42.0 1.0 C C:CYS5 5.0 41.7 1.0 C C:CYS25 5.0 63.5 1.0 CA C:ARG27 5.0 69.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Thioredoxin 2 From Yersinia Pestis


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 Thioredoxin 2 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn151 b:31.4 occ:1.00 SG D:CYS8 2.3 30.3 1.0 SG D:CYS28 2.3 31.8 1.0 SG D:CYS5 2.5 32.2 1.0 SG D:CYS25 2.5 35.2 1.0 CB D:CYS25 3.1 27.9 1.0 CB D:CYS5 3.2 26.6 1.0 CB D:CYS8 3.3 38.8 1.0 CB D:CYS28 3.3 33.6 1.0 N D:CYS8 3.7 35.0 1.0 N D:CYS28 3.8 34.5 1.0 CA D:CYS8 4.0 35.6 1.0 CA D:CYS28 4.1 34.0 1.0 CB D:ALA10 4.4 32.9 1.0 CB D:HIS30 4.5 27.8 1.0 CA D:CYS25 4.6 30.3 1.0 C D:CYS8 4.6 35.0 1.0 CA D:CYS5 4.7 30.8 1.0 CB D:ARG27 4.7 36.4 1.0 C D:CYS28 4.8 34.6 1.0 C D:ARG27 4.8 34.0 1.0 C D:ALA7 4.8 33.3 1.0 N D:MSE9 4.8 33.9 1.0 N D:ALA10 4.8 34.3 1.0 N D:HIS30 4.9 30.9 1.0 CB D:ALA7 4.9 26.8 1.0

Y.Kim, M.Zhou, S.Grimshaw, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Thioredoxin 2 From Yersinia Pestis To Be Published.