Nickel in PDB 3gw7: Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63

The structure of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63, PDB code: 3gw7 was solved by F.Forouhar, M.Abashidze, J.Seetharaman, J.Janjua, R.Xiao, K.Cunningham, L.Ma, L.Zhao, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.30
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	99.408, 99.408, 130.629, 90.00, 90.00, 120.00
R / Rfree (%)	26 / 29.4

The binding sites of Nickel atom in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 (pdb code 3gw7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63, PDB code: 3gw7:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:87.6 occ:1.00 NE2 A:HIS29 2.5 0.7 1.0 OD1 A:ASP127 2.9 88.4 1.0 NE2 A:HIS58 3.1 0.5 1.0 OD2 A:ASP127 3.2 89.6 1.0 CD2 A:HIS29 3.3 0.2 1.0 OD2 A:ASP59 3.4 0.6 1.0 CG A:ASP127 3.4 90.1 1.0 CE1 A:HIS29 3.4 0.4 1.0 CD2 A:HIS58 3.5 0.0 1.0 OD1 A:ASP59 3.7 0.6 1.0 CG A:ASP59 4.0 0.4 1.0 CE1 A:HIS58 4.4 0.1 1.0 CG A:HIS29 4.4 0.1 1.0 ND1 A:HIS29 4.4 0.5 1.0 CG A:HIS58 4.9 0.8 1.0 CB A:ASP127 4.9 88.8 1.0

Nickel binding site 2 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:9.2 occ:0.33 NE2 A:HIS196 2.5 80.7 1.0 CD2 A:HIS196 3.4 80.1 1.0 OE2 B:GLU217 3.5 0.7 1.0 CE1 A:HIS196 3.5 80.9 1.0 NH1 A:ARG189 3.5 0.7 1.0 CD B:GLU217 4.4 0.7 1.0 OE1 B:GLU217 4.5 0.7 1.0 CG A:HIS196 4.6 78.6 1.0 ND1 A:HIS196 4.6 79.9 1.0 CZ A:ARG189 4.7 0.5 1.0 O A:GLN192 4.9 93.3 1.0

Nickel binding site 3 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:75.5 occ:0.33 NE2 A:HIS235 2.1 80.1 1.0 NE2 A:HIS237 2.3 71.1 1.0 CE1 A:HIS235 2.9 82.8 1.0 CD2 A:HIS235 3.2 82.0 1.0 CD2 A:HIS237 3.2 71.6 1.0 CE1 A:HIS237 3.3 72.0 1.0 ND1 A:HIS235 4.1 81.4 1.0 CG A:HIS235 4.2 81.2 1.0 ND1 A:HIS237 4.4 69.7 1.0 CG A:HIS237 4.4 69.2 1.0 O A:HIS235 4.8 79.8 1.0

Nickel binding site 4 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni306 b:60.5 occ:0.33 NI B:NI307 3.1 62.3 0.3

Nickel binding site 5 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:93.1 occ:1.00 NE2 B:HIS29 2.6 0.2 1.0 OD1 B:ASP127 2.8 89.6 1.0 NE2 B:HIS58 3.0 0.9 1.0 OD2 B:ASP127 3.1 90.7 1.0 CG B:ASP127 3.3 90.8 1.0 CD2 B:HIS58 3.4 0.1 1.0 OD2 B:ASP59 3.4 0.4 1.0 CD2 B:HIS29 3.4 0.5 1.0 CE1 B:HIS29 3.5 0.1 1.0 OD1 B:ASP59 3.7 0.1 1.0 CG B:ASP59 3.9 0.6 1.0 CE1 B:HIS58 4.3 0.1 1.0 CG B:HIS29 4.5 0.2 1.0 ND1 B:HIS29 4.5 0.0 1.0 CG B:HIS58 4.7 0.6 1.0 CB B:ASP127 4.8 89.2 1.0 CD2 B:HIS107 5.0 0.9 1.0

Nickel binding site 6 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni304 b:7.8 occ:0.33 NE2 B:HIS196 2.4 80.0 1.0 CD2 B:HIS196 3.3 79.8 1.0 CE1 B:HIS196 3.4 80.4 1.0 OE2 A:GLU217 3.5 0.6 1.0 NH1 B:ARG189 3.6 0.8 1.0 CD A:GLU217 4.4 0.0 1.0 OE1 A:GLU217 4.5 0.5 1.0 ND1 B:HIS196 4.5 79.6 1.0 CG B:HIS196 4.5 78.5 1.0 CZ B:ARG189 4.8 0.1 1.0 O B:GLN192 4.8 93.3 1.0

Nickel binding site 7 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni305 b:62.1 occ:0.33 NE2 B:HIS235 2.1 77.4 1.0 NE2 B:HIS237 2.2 67.3 1.0 CE1 B:HIS235 3.0 80.3 1.0 CD2 B:HIS237 3.2 67.3 1.0 CD2 B:HIS235 3.2 79.5 1.0 CE1 B:HIS237 3.3 67.0 1.0 ND1 B:HIS235 4.2 78.5 1.0 CG B:HIS235 4.3 79.2 1.0 CG B:HIS237 4.3 66.6 1.0 ND1 B:HIS237 4.3 66.5 1.0 O B:HIS235 5.0 78.8 1.0

Nickel binding site 8 out of 8 in the Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni307 b:62.3 occ:0.33 NI A:NI306 3.1 60.5 0.3

F.Forouhar, M.Abashidze, J.Seetharaman, J.Janjua, R.Xiao, K.Cunningham, L.Ma, L.Zhao, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong. Crystal Structure of A Metal-Dependent Phosphohydrolase with Conserved Hd Domain (Yedj) From Escherichia Coli in Complex with Nickel Ions. Northeast Structural Genomics Consortium Target ER63 To Be Published.