Zinc in PDB 3ngj: Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica

The structure of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica, PDB code: 3ngj was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.38 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.260, 70.780, 126.750, 90.00, 92.46, 90.00
R / Rfree (%)	14.6 / 17.5

The structure of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica (pdb code 3ngj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica, PDB code: 3ngj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn250 b:13.1 occ:1.00 OD2 A:ASP192 2.0 11.3 1.0 ND1 B:HIS162 2.1 10.7 1.0 NE2 A:HIS218 2.1 13.3 1.0 O B:HOH711 2.2 10.9 1.0 CG A:ASP192 2.8 12.5 1.0 OD1 A:ASP192 2.9 11.9 1.0 CE1 B:HIS162 2.9 12.4 1.0 CE1 A:HIS218 3.0 15.5 1.0 CG B:HIS162 3.2 10.0 1.0 CD2 A:HIS218 3.2 14.9 1.0 CB B:HIS162 3.6 10.2 1.0 OG1 B:THR161 4.0 12.0 1.0 O A:HOH253 4.1 13.8 1.0 NE2 B:HIS162 4.1 11.2 1.0 ND1 A:HIS218 4.2 14.6 1.0 CB A:ASP192 4.2 11.5 1.0 CD2 B:HIS162 4.3 10.1 1.0 CG A:HIS218 4.3 16.3 1.0 CB B:THR161 4.4 11.8 1.0 N B:HIS162 4.4 10.1 1.0 C B:THR161 4.5 10.3 1.0 O A:HOH262 4.6 12.3 1.0 O B:THR161 4.6 11.2 1.0 CA B:HIS162 4.7 9.8 1.0 O B:HOH257 4.7 33.4 1.0 CB B:CYS131 4.9 9.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn251 b:49.2 occ:0.50 SG A:CYS61 1.7 11.9 0.5 SG A:CYS40 2.1 10.6 0.6 SG A:CYS61 2.3 11.1 0.5 SG A:CYS40 2.5 11.1 0.4 OD2 A:ASP92 3.1 16.0 1.0 CB A:CYS40 3.2 8.6 0.6 CB A:CYS40 3.3 8.5 0.4 CG A:ASP92 3.3 10.5 1.0 CB A:CYS61 3.4 9.2 0.5 CB A:CYS61 3.4 9.3 0.5 O A:THR62 3.4 10.8 1.0 OD1 A:ASP92 3.7 13.9 1.0 C A:CYS61 3.7 8.3 1.0 N A:THR62 3.8 8.4 1.0 C A:THR62 3.8 8.3 1.0 CA A:CYS40 4.0 7.8 0.4 CA A:CYS40 4.0 7.6 0.6 CB A:ASP92 4.0 9.9 1.0 CG1 A:VAL63 4.0 7.5 1.0 O A:CYS61 4.0 9.3 1.0 NZ A:LYS183 4.1 11.1 1.0 CA A:THR62 4.1 7.9 1.0 CA A:CYS61 4.1 9.1 0.5 CA A:CYS61 4.2 9.0 0.5 NZ A:LYS125 4.3 14.0 1.0 NZ A:LYS154 4.3 16.3 1.0 N A:VAL63 4.6 7.4 1.0 C A:CYS40 4.8 7.6 1.0 N A:ASP92 4.8 10.2 1.0 O A:HOH472 4.9 20.7 1.0 N A:VAL41 4.9 7.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn250 b:16.5 occ:1.00 OD2 B:ASP192 2.1 12.7 1.0 O B:HOH853 2.1 15.7 1.0 NE2 B:HIS218 2.1 17.7 1.0 O B:HOH989 2.2 13.1 1.0 CE1 B:HIS218 2.9 17.1 1.0 CG B:ASP192 3.0 14.2 1.0 OD1 B:ASP192 3.2 16.0 1.0 CD2 B:HIS218 3.2 18.5 1.0 O B:HOH854 3.9 34.8 1.0 ND1 B:HIS218 4.1 16.3 1.0 CG B:HIS218 4.3 17.5 1.0 CB B:ASP192 4.4 12.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn251 b:45.2 occ:0.50 SG B:CYS61 1.8 22.4 1.0 SG B:CYS40 2.3 13.8 0.6 SG B:CYS40 2.6 14.7 0.4 CB B:CYS61 3.2 14.6 1.0 CB B:CYS40 3.2 11.2 0.6 CB B:CYS40 3.2 11.3 0.4 OD2 B:ASP92 3.3 21.8 1.0 CG B:ASP92 3.4 17.2 1.0 O B:THR62 3.5 12.9 1.0 N B:THR62 3.6 13.0 1.0 C B:CYS61 3.6 13.6 1.0 OD1 B:ASP92 3.7 18.5 1.0 C B:THR62 3.8 12.0 1.0 CA B:CYS61 4.0 14.4 1.0 CA B:CYS40 4.0 11.4 0.4 CB B:ASP92 4.0 14.1 1.0 CA B:CYS40 4.0 11.4 0.6 CA B:THR62 4.0 12.0 1.0 O B:CYS61 4.0 13.2 1.0 CG1 B:VAL63 4.1 10.8 1.0 NZ B:LYS183 4.2 15.2 1.0 NZ B:LYS125 4.3 13.8 1.0 N B:VAL63 4.6 10.6 1.0 N B:ASP92 4.8 12.8 1.0 NZ B:LYS154 4.8 18.1 1.0 C B:CYS40 4.9 10.7 1.0 O B:HOH614 4.9 21.6 1.0 OD2 B:ASP11 4.9 16.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn250 b:11.2 occ:1.00 OD2 C:ASP192 1.9 12.1 1.0 ND1 D:HIS162 2.0 7.0 1.0 NE2 C:HIS218 2.1 10.2 1.0 O D:HOH222 2.3 8.2 1.0 CG C:ASP192 2.8 10.7 1.0 CE1 D:HIS162 2.9 10.0 1.0 OD1 C:ASP192 2.9 10.8 1.0 CE1 C:HIS218 2.9 10.6 1.0 CG D:HIS162 3.2 8.2 1.0 CD2 C:HIS218 3.2 13.3 1.0 CB D:HIS162 3.7 6.5 1.0 O C:HOH744 4.0 32.6 1.0 OG1 D:THR161 4.0 8.8 1.0 NE2 D:HIS162 4.0 9.2 1.0 O C:HOH260 4.1 14.2 1.0 ND1 C:HIS218 4.1 11.5 1.0 CD2 D:HIS162 4.2 9.2 1.0 CB C:ASP192 4.2 9.5 1.0 CG C:HIS218 4.3 13.1 1.0 CB D:THR161 4.3 9.2 1.0 N D:HIS162 4.4 7.3 1.0 C D:THR161 4.5 8.2 1.0 O D:HOH560 4.6 30.0 1.0 O1 C:EDO252 4.6 14.0 1.0 O D:THR161 4.6 9.2 1.0 CA D:HIS162 4.7 6.6 1.0 CB D:CYS131 4.9 6.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn251 b:41.2 occ:0.50 SG C:CYS61 1.8 18.0 1.0 SG C:CYS40 2.3 11.7 0.6 SG C:CYS40 2.7 13.8 0.4 OD2 C:ASP92 3.1 16.9 1.0 CB C:CYS61 3.2 11.0 1.0 CB C:CYS40 3.3 10.1 0.6 O C:THR62 3.3 12.7 1.0 CG C:ASP92 3.3 13.8 1.0 CB C:CYS40 3.3 10.2 0.4 C C:CYS61 3.6 10.7 1.0 N C:THR62 3.6 10.3 1.0 OD1 C:ASP92 3.7 14.3 1.0 C C:THR62 3.7 10.4 1.0 CA C:CYS61 3.9 10.8 1.0 CB C:ASP92 3.9 11.7 1.0 CA C:THR62 4.0 9.6 1.0 CA C:CYS40 4.0 9.7 0.6 CA C:CYS40 4.0 10.0 0.4 O C:CYS61 4.0 9.9 1.0 CG1 C:VAL63 4.0 9.5 1.0 NZ C:LYS183 4.1 11.0 1.0 NZ C:LYS125 4.3 15.1 1.0 N C:VAL63 4.6 9.8 1.0 NZ C:LYS154 4.6 15.2 1.0 C C:CYS40 4.8 9.4 1.0 N C:ASP92 4.9 11.6 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn250 b:9.1 occ:1.00 NE2 D:HIS218 2.0 8.9 1.0 OD1 D:ASP192 2.0 7.8 1.0 O D:HOH918 2.1 9.2 1.0 OD2 D:ASP192 2.6 11.3 1.0 CG D:ASP192 2.7 8.8 1.0 CE1 D:HIS218 3.0 10.9 1.0 CD2 D:HIS218 3.1 7.4 1.0 O D:HOH667 4.0 32.2 1.0 ND1 D:HIS218 4.1 10.2 1.0 CG D:HIS218 4.2 8.8 1.0 CB D:ASP192 4.2 8.8 1.0 O D:HOH764 4.2 41.2 1.0 CD2 D:PHE191 4.4 6.9 1.0 CE2 D:PHE191 4.6 6.2 1.0 O D:HOH257 4.7 11.5 1.0 CA D:ASP192 4.9 7.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn251 b:28.1 occ:0.50 SG D:CYS61 2.0 18.1 1.0 SG D:CYS40 2.2 8.8 0.6 SG D:CYS40 2.6 11.5 0.4 CB D:CYS61 3.2 8.6 1.0 O D:THR62 3.2 9.8 1.0 OD2 D:ASP92 3.2 16.4 1.0 CB D:CYS40 3.2 7.6 0.6 CG D:ASP92 3.3 13.2 1.0 CB D:CYS40 3.4 8.0 0.4 N D:THR62 3.5 6.2 1.0 OD1 D:ASP92 3.5 14.4 1.0 C D:CYS61 3.6 7.2 1.0 C D:THR62 3.6 6.9 1.0 CA D:THR62 3.9 5.9 1.0 CB D:ASP92 3.9 9.7 1.0 CA D:CYS61 3.9 7.5 1.0 CA D:CYS40 4.0 7.4 0.4 CA D:CYS40 4.1 7.0 0.6 O D:CYS61 4.1 7.5 1.0 CG1 D:VAL63 4.1 4.0 1.0 NZ D:LYS183 4.3 11.0 1.0 NZ D:LYS125 4.4 9.7 1.0 N D:VAL63 4.5 6.0 1.0 N D:ASP92 4.6 9.2 1.0 O D:HOH551 4.7 22.8 1.0 NZ D:LYS154 4.8 14.3 1.0 C D:CYS40 4.9 6.9 1.0 CA D:ASP92 4.9 9.5 1.0 OD2 D:ASP11 5.0 12.1 1.0

J.Abendroth, A.Gardberg, B.Staker. Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica To Be Published.