Zinc in PDB 3zvs: Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate

The structure of Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate, PDB code: 3zvs was solved by C.Graef, M.Schacherl, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.542 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.302, 63.490, 64.533, 71.39, 86.68, 82.67
R / Rfree (%)	14.37 / 16.36

The binding sites of Zinc atom in the Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate (pdb code 3zvs). 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 Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate, PDB code: 3zvs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate


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 Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1159 b:10.4 occ:1.00 O7 A:MLI1161 2.0 10.8 1.0 NE2 A:HIS127 2.0 9.5 1.0 NE2 A:HIS121 2.1 10.2 1.0 NE2 A:HIS117 2.1 10.7 1.0 C2 A:MLI1161 2.7 11.6 1.0 O6 A:MLI1161 2.8 12.0 1.0 CD2 A:HIS127 2.9 10.8 1.0 CE1 A:HIS121 3.0 10.2 1.0 CD2 A:HIS117 3.0 10.6 1.0 CE1 A:HIS127 3.0 11.2 1.0 HD2 A:HIS127 3.1 12.9 1.0 CE1 A:HIS117 3.1 8.4 1.0 CD2 A:HIS121 3.1 9.4 1.0 HE1 A:HIS121 3.2 12.3 1.0 HD2 A:HIS117 3.2 12.8 1.0 HE1 A:HIS127 3.3 13.5 1.0 HE1 A:HIS117 3.3 10.1 1.0 HD2 A:HIS121 3.3 11.2 1.0 O A:HOH2221 3.5 38.1 1.0 O A:HOH2171 4.0 11.5 1.0 CG A:HIS127 4.1 9.1 1.0 ND1 A:HIS127 4.1 10.7 1.0 C1 A:MLI1161 4.1 13.7 1.0 ND1 A:HIS121 4.1 10.3 1.0 ND1 A:HIS117 4.2 8.9 1.0 HD1 A:PHE136 4.2 14.8 1.0 CG A:HIS117 4.2 9.7 1.0 CG A:HIS121 4.2 8.8 1.0 O A:HOH2211 4.3 27.2 1.0 HA A:PHE136 4.4 14.0 1.0 H12 A:MLI1161 4.4 16.5 1.0 H11 A:MLI1161 4.4 16.5 1.0 HE2 A:MET134 4.5 13.6 1.0 HE1 A:MET134 4.5 13.6 1.0 OE2 A:GLU118 4.7 12.4 1.0 O A:HOH2238 4.8 12.1 1.0 HD1 A:HIS127 4.9 12.9 1.0 O A:HOH2210 4.9 13.9 1.0 HD1 A:HIS121 4.9 12.3 1.0 HD1 A:HIS117 5.0 10.7 1.0 HB2 A:PHE136 5.0 13.5 1.0 CE A:MET134 5.0 11.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate


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 Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1160 b:11.6 occ:1.00 SG A:CYS154 2.3 12.5 1.0 SG A:CYS151 2.3 10.9 1.0 SG A:CYS128 2.3 11.4 1.0 SG A:CYS132 2.4 10.9 1.0 HB2 A:CYS132 3.0 12.7 1.0 HB2 A:CYS154 3.0 16.4 1.0 HB2 A:CYS128 3.1 11.9 1.0 CB A:CYS132 3.2 10.6 1.0 CB A:CYS128 3.2 9.9 1.0 H A:CYS151 3.3 12.7 1.0 CB A:CYS154 3.3 13.7 1.0 HB3 A:CYS128 3.3 11.9 1.0 HB3 A:CYS132 3.4 12.7 1.0 HB3 A:CYS151 3.4 13.8 1.0 H A:CYS154 3.4 15.6 1.0 CB A:CYS151 3.5 11.5 1.0 HB2 A:ASN130 3.5 13.3 1.0 HD21 A:ASN130 3.5 12.0 1.0 HB2 A:MET134 3.6 12.2 1.0 HB3 A:CYS154 4.0 16.4 1.0 N A:CYS151 4.0 10.6 1.0 N A:CYS154 4.0 13.0 1.0 ND2 A:ASN130 4.2 10.0 1.0 HB2 A:GLU153 4.2 16.2 1.0 O A:HOH2223 4.2 16.5 1.0 HB2 A:CYS151 4.2 13.8 1.0 CA A:CYS151 4.3 11.0 1.0 CA A:CYS154 4.3 12.3 1.0 O A:HOH2261 4.4 18.9 1.0 CB A:ASN130 4.5 11.1 1.0 H A:MET134 4.5 11.9 1.0 CB A:MET134 4.5 10.2 1.0 H A:ASN130 4.5 12.6 1.0 CA A:CYS132 4.6 11.2 1.0 HA A:CYS154 4.6 14.8 1.0 CA A:CYS128 4.6 10.4 1.0 HD22 A:ASN130 4.7 12.0 1.0 HA A:PHE150 4.7 15.3 1.0 HG2 A:MET134 4.7 12.2 1.0 HA A:CYS132 4.8 13.4 1.0 CG A:ASN130 4.8 10.7 1.0 HD1 A:PHE150 4.8 16.1 1.0 C A:CYS151 4.8 13.4 1.0 O A:CYS151 4.8 12.3 1.0 HA A:CYS128 4.9 12.5 1.0 O A:HOH2217 4.9 17.8 1.0 HG3 A:MET134 4.9 12.2 1.0 HB3 A:ASN130 4.9 13.3 1.0 HB3 A:MET134 4.9 12.2 1.0 HB3 A:PHE150 5.0 17.7 1.0 CG A:MET134 5.0 10.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate


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 Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1161 b:10.1 occ:1.00 O7 B:MLI1163 1.9 10.8 1.0 NE2 B:HIS117 2.0 10.2 1.0 NE2 B:HIS127 2.0 8.5 1.0 NE2 B:HIS121 2.1 10.3 1.0 C2 B:MLI1163 2.6 13.7 1.0 O6 B:MLI1163 2.7 11.0 1.0 CD2 B:HIS127 3.0 10.8 1.0 CD2 B:HIS117 3.0 9.5 1.0 CE1 B:HIS117 3.0 9.3 1.0 CE1 B:HIS127 3.0 10.9 1.0 CE1 B:HIS121 3.0 11.3 1.0 CD2 B:HIS121 3.1 9.6 1.0 HD2 B:HIS127 3.1 12.9 1.0 HD2 B:HIS117 3.2 11.4 1.0 HE1 B:HIS121 3.2 13.6 1.0 HE1 B:HIS117 3.2 11.2 1.0 HE1 B:HIS127 3.2 13.1 1.0 HD2 B:HIS121 3.3 11.5 1.0 O B:HOH2166 4.0 11.9 1.0 C1 B:MLI1163 4.1 13.7 1.0 ND1 B:HIS127 4.1 10.9 1.0 ND1 B:HIS117 4.1 8.1 1.0 CG B:HIS127 4.1 10.8 1.0 CG B:HIS117 4.1 8.3 1.0 ND1 B:HIS121 4.2 9.8 1.0 HD1 B:PHE136 4.2 14.2 1.0 CG B:HIS121 4.2 8.4 1.0 H12 B:MLI1163 4.3 16.4 1.0 H11 B:MLI1163 4.3 16.4 1.0 HA B:PHE136 4.4 13.5 1.0 O B:HOH2168 4.4 27.1 1.0 HE2 B:MET134 4.5 12.2 1.0 HE1 B:MET134 4.5 12.2 1.0 OE2 B:GLU118 4.7 13.6 1.0 O B:HOH2230 4.8 11.3 1.0 HB2 B:PHE136 4.8 11.7 1.0 O B:HOH2206 4.9 13.8 1.0 HD1 B:HIS117 4.9 9.7 1.0 HD1 B:HIS127 4.9 13.1 1.0 HD1 B:HIS121 4.9 11.7 1.0 CE B:MET134 5.0 10.2 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate


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 Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1162 b:11.9 occ:1.00 SG B:CYS151 2.3 10.8 1.0 SG B:CYS154 2.3 15.3 1.0 SG B:CYS128 2.4 12.3 1.0 SG B:CYS132 2.4 10.7 1.0 HB2 B:CYS132 3.0 14.4 1.0 HB2 B:CYS154 3.0 14.3 1.0 HB2 B:CYS128 3.1 11.0 1.0 CB B:CYS132 3.2 12.0 1.0 HB3 B:CYS151 3.2 12.4 1.0 CB B:CYS128 3.2 9.2 1.0 H B:CYS151 3.2 13.2 1.0 CB B:CYS154 3.3 11.9 1.0 HB3 B:CYS132 3.3 14.4 1.0 CB B:CYS151 3.4 10.3 1.0 HB3 B:CYS128 3.4 11.0 1.0 H B:CYS154 3.4 15.9 1.0 HD21 B:ASN130 3.6 17.7 1.0 HB2 B:MET134 3.6 11.3 1.0 HB2 B:ASN130 3.6 14.8 1.0 N B:CYS151 3.9 11.0 1.0 HB3 B:CYS154 4.0 14.3 1.0 N B:CYS154 4.1 13.2 1.0 HB2 B:CYS151 4.1 12.4 1.0 CA B:CYS151 4.2 10.3 1.0 ND2 B:ASN130 4.3 14.7 1.0 CA B:CYS154 4.3 13.2 1.0 HB2 B:GLU153 4.3 17.2 1.0 O B:HOH2258 4.4 29.9 1.0 H B:MET134 4.4 10.6 1.0 CB B:ASN130 4.5 12.3 1.0 CB B:MET134 4.5 9.4 1.0 H B:ASN130 4.6 16.5 1.0 O B:HOH2208 4.6 18.8 1.0 CA B:CYS128 4.6 10.7 1.0 CA B:CYS132 4.6 11.1 1.0 HA B:CYS154 4.7 15.8 1.0 HG2 B:MET134 4.7 10.6 1.0 HA B:PHE150 4.7 13.6 1.0 C B:CYS151 4.8 13.2 1.0 HD22 B:ASN130 4.8 17.7 1.0 HD1 B:PHE150 4.8 15.6 1.0 O B:CYS151 4.8 13.1 1.0 HA B:CYS128 4.8 12.8 1.0 HA B:CYS132 4.8 13.3 1.0 CG B:ASN130 4.8 14.7 1.0 HG3 B:MET134 4.9 10.6 1.0 HB3 B:MET134 4.9 11.3 1.0 CG B:MET134 5.0 8.9 1.0 H B:GLU153 5.0 14.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate


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 Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1159 b:12.8 occ:1.00 O7 C:MLI1161 1.9 13.6 1.0 NE2 C:HIS127 2.0 10.7 1.0 NE2 C:HIS121 2.1 14.3 1.0 NE2 C:HIS117 2.1 11.8 1.0 C2 C:MLI1161 2.6 12.6 1.0 O6 C:MLI1161 2.7 11.3 1.0 CD2 C:HIS127 3.0 12.0 1.0 CE1 C:HIS127 3.0 14.1 1.0 CE1 C:HIS117 3.0 11.1 1.0 CD2 C:HIS121 3.0 10.5 1.0 CD2 C:HIS117 3.0 11.6 1.0 CE1 C:HIS121 3.1 13.6 1.0 HD2 C:HIS127 3.1 14.4 1.0 HD2 C:HIS121 3.2 12.6 1.0 HE1 C:HIS117 3.2 13.3 1.0 HE1 C:HIS127 3.2 16.9 1.0 HD2 C:HIS117 3.2 13.9 1.0 HE1 C:HIS121 3.3 16.3 1.0 O C:HOH2191 3.4 33.8 1.0 O C:HOH2145 4.0 16.1 1.0 C1 C:MLI1161 4.1 19.0 1.0 ND1 C:HIS127 4.1 17.7 1.0 CG C:HIS127 4.1 13.7 1.0 ND1 C:HIS117 4.1 9.8 1.0 ND1 C:HIS121 4.2 14.1 1.0 CG C:HIS117 4.2 10.4 1.0 CG C:HIS121 4.2 11.0 1.0 HD1 C:PHE136 4.3 17.5 1.0 H11 C:MLI1161 4.3 22.8 1.0 H12 C:MLI1161 4.4 22.8 1.0 HA C:PHE136 4.4 10.9 1.0 HE2 C:MET134 4.4 14.9 1.0 HE1 C:MET134 4.5 14.9 1.0 OE2 C:GLU118 4.7 14.1 1.0 O C:HOH2210 4.8 13.9 1.0 HD1 C:HIS127 4.9 21.2 1.0 HD1 C:HIS117 4.9 11.7 1.0 O C:HOH2248 4.9 39.6 1.0 O C:HOH2147 4.9 25.2 1.0 CE C:MET134 5.0 12.4 1.0 HD1 C:HIS121 5.0 17.0 1.0 O C:HOH2181 5.0 15.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate


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 Archaemetzincin (Amza) From Archaeoglobus Fulgidus at 1.4 A Resolution Complexed with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1160 b:11.7 occ:1.00 SG C:CYS154 2.3 13.3 1.0 SG C:CYS132 2.3 10.5 1.0 SG C:CYS151 2.4 10.3 1.0 SG C:CYS128 2.4 12.3 1.0 HB2 C:CYS132 3.0 13.8 1.0 HB2 C:CYS154 3.0 15.3 1.0 HB2 C:CYS128 3.1 12.7 1.0 CB C:CYS132 3.1 11.5 1.0 CB C:CYS128 3.2 10.6 1.0 HB3 C:CYS128 3.2 12.7 1.0 H C:CYS151 3.3 12.7 1.0 CB C:CYS154 3.3 12.8 1.0 HB3 C:CYS151 3.3 12.9 1.0 HB3 C:CYS132 3.3 13.8 1.0 H C:CYS154 3.4 13.1 1.0 CB C:CYS151 3.5 10.7 1.0 HB2 C:ASN130 3.5 12.3 1.0 HB2 C:MET134 3.6 12.6 1.0 HD21 C:ASN130 3.6 13.5 1.0 HB3 C:CYS154 4.0 15.3 1.0 N C:CYS151 4.0 10.6 1.0 N C:CYS154 4.1 10.9 1.0 HB2 C:CYS151 4.2 12.9 1.0 CA C:CYS154 4.3 10.9 1.0 ND2 C:ASN130 4.3 11.3 1.0 CA C:CYS151 4.3 11.5 1.0 O C:HOH2193 4.3 20.5 1.0 HB2 C:GLU153 4.3 13.7 1.0 O C:HOH2239 4.4 17.7 1.0 H C:MET134 4.5 12.0 1.0 CB C:ASN130 4.5 10.3 1.0 CB C:MET134 4.5 10.5 1.0 H C:ASN130 4.5 14.4 1.0 CA C:CYS132 4.6 9.1 1.0 HA C:CYS154 4.6 13.1 1.0 CA C:CYS128 4.6 11.7 1.0 HG2 C:MET134 4.7 12.4 1.0 HA C:PHE150 4.7 13.4 1.0 HD22 C:ASN130 4.8 13.5 1.0 HA C:CYS132 4.8 10.9 1.0 C C:CYS151 4.8 9.7 1.0 CG C:ASN130 4.8 9.7 1.0 O C:CYS151 4.9 11.7 1.0 HG3 C:MET134 4.9 12.4 1.0 O C:HOH2187 4.9 18.1 1.0 HA C:CYS128 4.9 14.1 1.0 HB3 C:MET134 4.9 12.6 1.0 HB3 C:ASN130 5.0 12.3 1.0 HD1 C:PHE150 5.0 13.5 1.0 CG C:MET134 5.0 10.3 1.0

C.Graef, M.Schacherl, S.Waltersperger, U.Baumann. Crystal Structures of Archaemetzincin Reveal A Moldable Substrate-Binding Site. Plos One V. 7 43863 2012.
ISSN: ISSN 1932-6203
PubMed: 22937112
DOI: 10.1371/JOURNAL.PONE.0043863