Manganese in PDB 3pzl: The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium

The structure of The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium, PDB code: 3pzl was solved by Z.Zhang, S.K.Burley, S.Swaminathan, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.39 / 2.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.139, 95.139, 198.375, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 27.1

The binding sites of Manganese atom in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium (pdb code 3pzl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium, PDB code: 3pzl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn314 b:47.7 occ:1.00 OD2 A:ASP229 2.1 43.1 1.0 ND1 A:HIS124 2.3 45.9 1.0 OD2 A:ASP148 2.3 49.5 1.0 OD2 A:ASP144 2.4 48.1 1.0 OD1 A:ASP148 2.9 46.7 1.0 CG A:ASP148 2.9 47.4 1.0 CE1 A:HIS124 3.2 49.3 1.0 MN A:MN315 3.3 64.2 1.0 CG A:HIS124 3.3 45.6 1.0 CG A:ASP229 3.4 46.0 1.0 CG A:ASP144 3.5 45.1 1.0 CB A:HIS124 3.5 44.7 1.0 O A:HIS160 3.9 50.4 1.0 OD1 A:ASP144 4.0 43.6 1.0 CB A:ASP229 4.1 44.4 1.0 CG1 A:VAL163 4.2 50.9 1.0 CB A:ASP148 4.3 48.3 1.0 OD1 A:ASP229 4.3 44.0 1.0 NE2 A:HIS124 4.4 47.2 1.0 CD2 A:HIS124 4.4 45.2 1.0 CG A:GLU272 4.6 45.1 1.0 CB A:ASP144 4.8 44.6 1.0

Manganese binding site 2 out of 6 in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn315 b:64.2 occ:1.00 OD2 A:ASP231 2.3 51.5 1.0 OD1 A:ASP144 2.6 43.6 1.0 OD1 A:ASP231 2.6 45.6 1.0 OD2 A:ASP229 2.6 43.1 1.0 CD2 A:HIS146 2.7 42.8 1.0 CG A:ASP231 2.8 46.9 1.0 CG A:ASP229 3.0 46.0 1.0 CG A:ASP144 3.1 45.1 1.0 OD2 A:ASP144 3.2 48.1 1.0 OD1 A:ASP229 3.2 44.0 1.0 MN A:MN314 3.3 47.7 1.0 NE2 A:HIS146 3.6 44.5 1.0 CG A:HIS146 3.7 43.2 1.0 N A:HIS146 3.9 44.8 1.0 N A:ALA145 4.1 45.4 1.0 CB A:HIS146 4.2 45.0 1.0 CB A:ASP229 4.2 44.4 1.0 OD1 A:ASP148 4.3 46.7 1.0 CB A:ASP231 4.3 44.3 1.0 OG1 A:THR243 4.4 51.0 1.0 CB A:ASP144 4.4 44.6 1.0 O A:HOH325 4.5 41.4 1.0 CA A:HIS146 4.6 45.5 1.0 CA A:ASP144 4.7 44.2 1.0 O A:HIS146 4.7 46.9 1.0 C A:ALA145 4.8 45.1 1.0 CE1 A:HIS146 4.8 46.8 1.0 CA A:ALA145 4.8 45.1 1.0 OD2 A:ASP148 4.8 49.5 1.0 C A:ASP144 4.8 44.8 1.0 ND1 A:HIS146 4.8 43.9 1.0 CB A:ALA145 4.9 45.0 1.0 CG A:ASP148 5.0 47.4 1.0

Manganese binding site 3 out of 6 in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn314 b:56.3 occ:1.00 OD2 B:ASP229 2.1 47.6 1.0 OD2 B:ASP148 2.2 66.9 1.0 ND1 B:HIS124 2.4 51.8 1.0 OD2 B:ASP144 2.6 55.6 1.0 CG B:ASP148 2.6 65.1 1.0 OD1 B:ASP148 2.8 64.1 1.0 CG B:HIS124 3.2 51.9 1.0 MN B:MN315 3.3 63.4 1.0 CB B:HIS124 3.3 53.3 1.0 CG B:ASP229 3.3 49.3 1.0 CE1 B:HIS124 3.5 52.0 1.0 CG B:ASP144 3.8 55.4 1.0 O B:HIS160 3.8 64.9 1.0 CB B:ASP148 3.8 64.8 1.0 CG1 B:VAL163 4.0 64.3 1.0 CB B:ASP229 4.2 49.5 1.0 OD1 B:ASP229 4.2 52.0 1.0 OD1 B:ASP144 4.2 56.1 1.0 CD2 B:HIS124 4.5 48.8 1.0 NE2 B:HIS124 4.6 49.9 1.0 CG B:GLU272 4.6 48.0 1.0 CA B:HIS124 4.8 54.3 1.0

Manganese binding site 4 out of 6 in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn315 b:63.4 occ:1.00 OD1 B:ASP144 2.4 56.1 1.0 OD2 B:ASP229 2.5 47.6 1.0 OD2 B:ASP231 2.5 57.2 1.0 OD1 B:ASP231 2.7 58.4 1.0 ND1 B:HIS146 2.7 55.6 1.0 OD2 B:ASP144 2.9 55.6 1.0 CG B:ASP229 2.9 49.3 1.0 CG B:ASP144 2.9 55.4 1.0 CG B:ASP231 3.0 52.5 1.0 OD1 B:ASP229 3.1 52.0 1.0 MN B:MN314 3.3 56.3 1.0 CE1 B:HIS146 3.5 54.9 1.0 OD1 B:ASP148 3.6 64.1 1.0 CG B:HIS146 3.9 54.8 1.0 CB B:ASP229 4.1 49.5 1.0 N B:HIS146 4.1 54.2 1.0 CB B:HIS146 4.2 55.5 1.0 N B:ALA145 4.3 51.8 1.0 CB B:ASP144 4.4 53.0 1.0 CB B:ASP231 4.5 48.0 1.0 CG B:ASP148 4.5 65.1 1.0 OD2 B:ASP148 4.5 66.9 1.0 OG1 B:THR243 4.6 50.2 1.0 NE2 B:HIS146 4.7 53.6 1.0 CA B:HIS146 4.7 55.8 1.0 CA B:ASP144 4.8 52.7 1.0 O B:HIS146 4.8 58.2 1.0 CD2 B:HIS146 4.9 54.7 1.0 C B:ALA145 5.0 53.3 1.0 CA B:ALA145 5.0 52.3 1.0 C B:ASP144 5.0 52.2 1.0

Manganese binding site 5 out of 6 in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn314 b:62.6 occ:1.00 OD2 C:ASP231 2.4 53.5 1.0 OD1 C:ASP144 2.5 60.0 1.0 ND1 C:HIS146 2.5 58.3 1.0 OD2 C:ASP229 2.7 57.3 1.0 OD1 C:ASP231 2.8 51.1 1.0 CG C:ASP231 2.9 52.1 1.0 MN C:MN315 3.0 56.5 1.0 CG C:ASP229 3.1 54.6 1.0 CE1 C:HIS146 3.1 58.7 1.0 OD1 C:ASP229 3.1 51.8 1.0 CG C:ASP144 3.3 56.2 1.0 OD2 C:ASP144 3.5 56.8 1.0 CG C:HIS146 3.7 57.7 1.0 CB C:ASP229 4.2 54.1 1.0 N C:HIS146 4.3 55.7 1.0 NE2 C:HIS146 4.3 61.0 1.0 CB C:HIS146 4.3 56.9 1.0 OG1 C:THR243 4.3 55.4 1.0 N C:ALA145 4.4 53.9 1.0 OD1 C:ASP148 4.4 59.7 1.0 CB C:ASP231 4.4 51.4 1.0 OD2 C:ASP148 4.6 61.7 1.0 CB C:ASP144 4.6 55.6 1.0 CD2 C:HIS146 4.6 59.5 1.0 CA C:HIS146 4.9 57.2 1.0 CG C:ASP148 4.9 60.9 1.0 CA C:ASP144 5.0 55.2 1.0

Manganese binding site 6 out of 6 in the The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn315 b:56.5 occ:1.00 OD2 C:ASP148 2.1 61.7 1.0 OD2 C:ASP229 2.4 57.3 1.0 OD2 C:ASP144 2.4 56.8 1.0 ND1 C:HIS124 2.5 61.1 1.0 MN C:MN314 3.0 62.6 1.0 CG C:ASP148 3.0 60.9 1.0 CG C:ASP144 3.1 56.2 1.0 OD1 C:ASP148 3.2 59.7 1.0 CE1 C:HIS124 3.3 64.1 1.0 CG C:ASP229 3.3 54.6 1.0 OD1 C:ASP144 3.5 60.0 1.0 CG C:HIS124 3.6 59.8 1.0 CB C:ASP229 3.7 54.1 1.0 CB C:HIS124 4.0 59.1 1.0 OD1 C:ASP229 4.3 51.8 1.0 CB C:ASP144 4.3 55.6 1.0 CG1 C:VAL163 4.4 65.8 1.0 CB C:ASP148 4.4 62.3 1.0 NE2 C:HIS124 4.5 61.8 1.0 O C:HIS160 4.5 65.0 1.0 CD2 C:HIS124 4.6 59.0 1.0 ND1 C:HIS146 4.8 58.3 1.0 CG C:GLU272 4.9 54.0 1.0 O C:HIS146 5.0 59.2 1.0

Z.Zhang, S.K.Burley, S.Swaminathan. The Crystal Structure of Agmatine Ureohydrolase of Thermoplasma Volcanium To Be Published.