Zinc in PDB 4rvp: Crystal Structure of Superoxide Dismutase From Sedum Alfredii

All present enzymatic activity of Crystal Structure of Superoxide Dismutase From Sedum Alfredii:
1.15.1.1;

The structure of Crystal Structure of Superoxide Dismutase From Sedum Alfredii, PDB code: 4rvp was solved by R.Qiu, C.Li, J.Zhai, L.Tang, H.Zhang, M.Yuan, X.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.07 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.979, 85.781, 105.312, 90.00, 99.84, 90.00
R / Rfree (%)	22.4 / 29

The binding sites of Zinc atom in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii (pdb code 4rvp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii, PDB code: 4rvp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii


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 Superoxide Dismutase From Sedum Alfredii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:40.9 occ:1.00 OD1 A:ASP95 1.9 38.3 1.0 ND1 A:HIS83 2.1 41.3 1.0 ND1 A:HIS75 2.2 45.7 1.0 ND1 A:HIS92 2.2 51.4 1.0 CG A:ASP95 2.6 44.0 1.0 OD2 A:ASP95 2.7 47.8 1.0 CE1 A:HIS92 2.9 49.0 1.0 CE1 A:HIS83 3.0 44.9 1.0 CG A:HIS75 3.1 35.1 1.0 CG A:HIS83 3.2 44.2 1.0 CE1 A:HIS75 3.2 39.5 1.0 CG A:HIS92 3.3 42.1 1.0 CB A:HIS75 3.4 36.5 1.0 O A:SER148 3.5 46.0 1.0 CB A:HIS83 3.6 41.1 1.0 CB A:HIS92 3.8 39.5 1.0 CA A:HIS83 4.0 45.5 1.0 CB A:ASP95 4.0 40.0 1.0 NE2 A:HIS92 4.0 55.4 1.0 NE2 A:HIS83 4.1 46.6 1.0 CD2 A:HIS83 4.2 47.2 1.0 CD2 A:HIS92 4.2 48.8 1.0 NE2 A:HIS75 4.3 37.5 1.0 CD2 A:HIS75 4.3 24.8 1.0 C A:SER148 4.5 47.1 1.0 CA A:ASP95 4.6 34.3 1.0 N A:HIS92 4.8 42.9 1.0 N A:HIS83 4.9 49.4 1.0 CA A:HIS92 4.9 42.3 1.0 CA A:HIS75 4.9 30.7 1.0 N A:GLY84 4.9 40.5 1.0 C A:HIS83 4.9 44.9 1.0 CD2 A:HIS58 4.9 38.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii


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 Superoxide Dismutase From Sedum Alfredii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:29.2 occ:1.00 CD2 B:HIS92 1.9 31.3 1.0 OD1 B:ASP95 2.0 29.5 1.0 ND1 B:HIS75 2.2 28.1 1.0 ND1 B:HIS83 2.3 31.3 1.0 CG B:ASP95 2.7 34.2 1.0 NE2 B:HIS92 2.8 37.7 1.0 OD2 B:ASP95 2.8 30.2 1.0 CG B:HIS92 3.0 32.3 1.0 CE1 B:HIS83 3.0 35.2 1.0 CG B:HIS75 3.1 28.5 1.0 CE1 B:HIS75 3.2 26.3 1.0 CB B:HIS75 3.3 26.6 1.0 CG B:HIS83 3.5 30.5 1.0 CB B:HIS92 3.7 34.5 1.0 O B:SER148 3.7 33.3 1.0 CE1 B:HIS92 3.9 34.7 1.0 CB B:HIS83 4.0 35.3 1.0 ND1 B:HIS92 4.0 35.8 1.0 CB B:ASP95 4.1 31.6 1.0 CA B:HIS83 4.2 32.2 1.0 NE2 B:HIS83 4.2 28.2 1.0 CD2 B:HIS75 4.3 25.9 1.0 NE2 B:HIS75 4.3 25.0 1.0 CD2 B:HIS83 4.5 33.7 1.0 CA B:ASP95 4.6 28.8 1.0 N B:HIS92 4.7 33.7 1.0 N B:ASP95 4.8 23.7 1.0 CA B:HIS92 4.8 29.0 1.0 C B:SER148 4.8 39.0 1.0 CA B:HIS75 4.8 22.4 1.0 N B:GLY84 4.9 35.4 1.0 CD2 B:HIS58 5.0 25.6 1.0 O B:THR149 5.0 32.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii


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 Superoxide Dismutase From Sedum Alfredii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:67.7 occ:1.00 OD1 C:ASP95 1.8 66.9 1.0 CD2 C:HIS92 2.0 71.6 1.0 ND1 C:HIS75 2.5 63.3 1.0 ND1 C:HIS83 2.6 67.8 1.0 CG C:ASP95 2.7 69.3 1.0 CG C:HIS92 2.8 64.8 1.0 OD2 C:ASP95 3.0 76.2 1.0 CB C:HIS92 3.1 55.6 1.0 NE2 C:HIS92 3.2 75.8 1.0 CG C:HIS75 3.3 46.5 1.0 CB C:HIS75 3.4 47.9 1.0 CE1 C:HIS83 3.4 65.8 1.0 CE1 C:HIS75 3.6 52.4 1.0 CG C:HIS83 3.6 69.5 1.0 CB C:HIS83 4.0 73.0 1.0 ND1 C:HIS92 4.0 61.7 1.0 CA C:HIS83 4.1 73.0 1.0 CB C:ASP95 4.1 61.7 1.0 O C:SER148 4.1 68.2 1.0 CE1 C:HIS92 4.2 64.0 1.0 CA C:HIS92 4.3 55.9 1.0 N C:HIS92 4.3 57.1 1.0 CA C:ASP95 4.5 62.8 1.0 CD2 C:HIS75 4.5 51.6 1.0 NE2 C:HIS83 4.6 68.1 1.0 NE2 C:HIS75 4.6 48.9 1.0 CD2 C:HIS83 4.7 66.0 1.0 N C:ASP95 4.7 59.3 1.0 N C:GLY84 4.8 75.0 1.0 O C:THR149 4.8 66.4 1.0 CA C:HIS75 4.9 49.7 1.0 CD2 C:HIS58 4.9 53.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii


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 Superoxide Dismutase From Sedum Alfredii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:54.0 occ:1.00 OD1 D:ASP95 1.9 52.4 1.0 ND1 D:HIS83 2.0 45.9 1.0 ND1 D:HIS92 2.0 53.7 1.0 ND1 D:HIS75 2.2 42.1 1.0 CE1 D:HIS92 2.7 48.5 1.0 CG D:ASP95 2.7 52.4 1.0 OD2 D:ASP95 2.8 54.6 1.0 CE1 D:HIS83 2.9 47.3 1.0 CG D:HIS83 3.0 49.6 1.0 CE1 D:HIS75 3.0 38.5 1.0 CG D:HIS92 3.1 55.1 1.0 CG D:HIS75 3.2 34.6 1.0 CB D:HIS83 3.5 50.4 1.0 CB D:HIS75 3.6 33.3 1.0 CB D:HIS92 3.7 43.9 1.0 CA D:HIS83 3.7 54.0 1.0 NE2 D:HIS92 3.8 52.0 1.0 O D:SER148 4.0 48.0 1.0 CD2 D:HIS92 4.0 58.0 1.0 NE2 D:HIS83 4.0 46.2 1.0 CD2 D:HIS83 4.1 53.7 1.0 CB D:ASP95 4.1 48.3 1.0 NE2 D:HIS75 4.2 38.5 1.0 CD2 D:HIS75 4.3 31.3 1.0 CA D:ASP95 4.6 43.6 1.0 N D:GLY84 4.6 48.4 1.0 C D:HIS83 4.7 52.5 1.0 N D:HIS83 4.7 54.2 1.0 N D:HIS92 4.8 51.9 1.0 CA D:HIS92 4.8 46.4 1.0 CD2 D:HIS58 4.9 38.0 1.0 C D:SER148 4.9 51.0 1.0 N D:ASP95 5.0 39.3 1.0 O D:GLY84 5.0 61.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Superoxide Dismutase From Sedum Alfredii within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:35.3 occ:1.00 ND1 E:HIS92 1.9 38.4 1.0 OD1 E:ASP95 2.0 38.9 1.0 ND1 E:HIS75 2.3 31.4 1.0 ND1 E:HIS83 2.3 45.3 1.0 CE1 E:HIS92 2.6 39.1 1.0 CG E:ASP95 2.9 36.0 1.0 CG E:HIS92 3.1 37.2 1.0 CE1 E:HIS83 3.1 45.2 1.0 OD2 E:ASP95 3.2 43.2 1.0 CG E:HIS75 3.2 29.4 1.0 CE1 E:HIS75 3.2 34.5 1.0 CG E:HIS83 3.3 46.3 1.0 CB E:HIS75 3.5 31.9 1.0 CB E:HIS83 3.6 45.0 1.0 CB E:HIS92 3.7 36.8 1.0 NE2 E:HIS92 3.8 39.6 1.0 O E:SER148 3.9 44.4 1.0 CA E:HIS83 3.9 40.5 1.0 CD2 E:HIS92 4.0 34.4 1.0 NE2 E:HIS83 4.3 42.3 1.0 CB E:ASP95 4.3 42.0 1.0 NE2 E:HIS75 4.3 29.9 1.0 CD2 E:HIS75 4.4 30.0 1.0 CD2 E:HIS83 4.4 43.9 1.0 CA E:ASP95 4.7 36.7 1.0 N E:GLY84 4.7 46.6 1.0 C E:SER148 4.7 39.7 1.0 N E:HIS92 4.8 43.2 1.0 C E:HIS83 4.9 44.6 1.0 CA E:HIS92 4.9 34.8 1.0 N E:HIS83 4.9 37.3 1.0 CD2 E:HIS58 4.9 32.6 1.0 O E:THR149 5.0 43.6 1.0 CA E:HIS75 5.0 25.8 1.0 N E:ASP95 5.0 36.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Superoxide Dismutase From Sedum Alfredii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Superoxide Dismutase From Sedum Alfredii within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:41.8 occ:1.00 OD1 F:ASP95 1.9 41.9 1.0 ND1 F:HIS92 2.1 43.4 1.0 ND1 F:HIS75 2.1 47.0 1.0 ND1 F:HIS83 2.2 48.4 1.0 CG F:ASP95 2.6 44.3 1.0 OD2 F:ASP95 2.7 47.5 1.0 CE1 F:HIS92 2.8 43.2 1.0 CE1 F:HIS75 3.0 41.6 1.0 CE1 F:HIS83 3.0 47.1 1.0 CG F:HIS75 3.1 41.5 1.0 CG F:HIS92 3.1 40.5 1.0 CG F:HIS83 3.1 49.5 1.0 CB F:HIS75 3.5 34.1 1.0 CB F:HIS83 3.5 44.3 1.0 CB F:HIS92 3.6 38.3 1.0 O F:SER148 3.8 52.2 1.0 NE2 F:HIS92 3.9 38.7 1.0 CA F:HIS83 4.0 48.7 1.0 CB F:ASP95 4.0 37.5 1.0 CD2 F:HIS92 4.1 36.7 1.0 NE2 F:HIS83 4.1 48.3 1.0 NE2 F:HIS75 4.2 35.9 1.0 CD2 F:HIS83 4.2 50.1 1.0 CD2 F:HIS75 4.2 42.1 1.0 CA F:ASP95 4.6 39.8 1.0 C F:SER148 4.7 44.9 1.0 N F:HIS92 4.8 45.4 1.0 CA F:HIS92 4.8 42.0 1.0 CD2 F:HIS58 4.9 47.2 1.0 N F:GLY84 4.9 51.7 1.0 N F:HIS83 5.0 44.6 1.0 O F:THR149 5.0 49.8 1.0 CA F:HIS75 5.0 32.7 1.0 N F:ASP95 5.0 40.9 1.0

R.Qiu, C.Li, J.Zhai, L.Tang, H.Zhang, M.Yuan, X.Hu. The Positive Effects of Cd and Cd-Zn Relationship in the Zn-Related Physiological Processes Involved in Growth in the Zn/Cd Hyperaccumulator Sedum Alfredii To Be Published.