Nickel in PDB 9gof: Mnca Bound to Nickel

The structure of Mnca Bound to Nickel, PDB code: 9gof was solved by A.Glasfeld, N.J.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.63 / 1.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	235.185, 235.185, 132.008, 90, 90, 120
R / Rfree (%)	16.4 / 17.7

The binding sites of Nickel atom in the Mnca Bound to Nickel (pdb code 9gof). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Mnca Bound to Nickel, PDB code: 9gof:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Mnca Bound to Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Mnca Bound to Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:18.6 occ:1.00 O A:HOH1110 2.1 18.7 1.0 OE1 A:GLU108 2.1 18.4 1.0 NE2 A:HIS147 2.1 18.6 1.0 NE2 A:HIS103 2.1 18.5 1.0 NE2 A:HIS101 2.2 19.0 1.0 O A:HOH1182 2.2 20.0 1.0 CE1 A:HIS101 3.1 18.9 1.0 CE1 A:HIS103 3.1 17.8 1.0 CD2 A:HIS147 3.1 17.9 1.0 CE1 A:HIS147 3.1 18.8 1.0 CD A:GLU108 3.1 18.7 1.0 CD2 A:HIS103 3.1 17.4 1.0 CD2 A:HIS101 3.2 19.3 1.0 OE2 A:GLU108 3.4 19.4 1.0 O A:HOH1216 4.1 20.1 1.0 ND1 A:HIS101 4.2 19.6 1.0 ND1 A:HIS103 4.2 17.9 1.0 ND1 A:HIS147 4.2 18.2 1.0 CG A:HIS147 4.3 18.1 1.0 CG A:HIS103 4.3 18.0 1.0 CG A:HIS101 4.3 18.7 1.0 CG A:GLU108 4.4 18.4 1.0 CE2 A:PHE163 4.5 19.7 1.0 OE2 A:GLU170 4.7 22.4 1.0 CB A:GLU108 4.8 18.0 1.0 CZ A:PHE163 4.8 20.2 1.0 CD2 A:PHE141 4.9 19.2 1.0

Nickel binding site 2 out of 6 in the Mnca Bound to Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Mnca Bound to Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1002 b:20.1 occ:1.00 OE1 A:GLU290 2.1 19.9 1.0 NE2 A:HIS285 2.1 18.6 1.0 NE2 A:HIS283 2.1 19.0 1.0 NE2 A:HIS329 2.1 18.8 1.0 N A:GLY1003 2.2 17.9 1.0 OXT A:GLY1003 2.2 21.9 1.0 C A:GLY1003 2.8 25.3 1.0 CA A:GLY1003 2.9 26.1 1.0 CE1 A:HIS285 3.0 19.4 1.0 CD A:GLU290 3.0 22.9 1.0 CE1 A:HIS283 3.1 20.2 1.0 CD2 A:HIS285 3.1 19.4 1.0 CD2 A:HIS329 3.1 19.7 1.0 CE1 A:HIS329 3.1 20.5 1.0 CD2 A:HIS283 3.2 18.9 1.0 OE2 A:GLU290 3.3 22.7 1.0 O A:GLY1003 3.9 29.6 1.0 ND1 A:HIS285 4.1 19.6 1.0 ND1 A:HIS283 4.2 19.9 1.0 CG A:HIS285 4.2 18.2 1.0 ND1 A:HIS329 4.2 18.5 1.0 CG A:HIS329 4.3 18.9 1.0 CG A:HIS283 4.3 18.8 1.0 CE2 A:PHE345 4.4 19.9 1.0 CG A:GLU290 4.4 21.0 1.0 CZ A:PHE345 4.5 20.6 1.0 CB A:GLU290 4.8 19.0 1.0

Nickel binding site 3 out of 6 in the Mnca Bound to Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Mnca Bound to Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1001 b:19.6 occ:1.00 O B:HOH1202 2.0 19.1 1.0 NE2 B:HIS147 2.1 18.1 1.0 OE1 B:GLU108 2.1 18.3 1.0 NE2 B:HIS103 2.1 18.1 1.0 NE2 B:HIS101 2.2 18.2 1.0 O B:HOH1119 2.2 17.6 1.0 CE1 B:HIS147 3.0 18.7 1.0 CE1 B:HIS103 3.0 19.2 1.0 CE1 B:HIS101 3.1 19.1 1.0 CD2 B:HIS147 3.1 18.8 1.0 CD B:GLU108 3.1 19.7 1.0 CD2 B:HIS103 3.2 18.4 1.0 CD2 B:HIS101 3.2 18.3 1.0 OE2 B:GLU108 3.5 20.6 1.0 ND1 B:HIS147 4.2 18.9 1.0 ND1 B:HIS103 4.2 19.1 1.0 O B:HOH1187 4.2 22.6 1.0 ND1 B:HIS101 4.2 18.8 1.0 CG B:HIS147 4.2 17.9 1.0 CG B:HIS103 4.3 18.1 1.0 CG B:HIS101 4.3 18.6 1.0 CE2 B:PHE163 4.4 19.3 1.0 CG B:GLU108 4.4 18.4 1.0 OE2 B:GLU170 4.8 23.6 1.0 CB B:GLU108 4.8 18.3 1.0 CZ B:PHE163 4.8 18.9 1.0 CD2 B:PHE141 4.9 18.1 1.0

Nickel binding site 4 out of 6 in the Mnca Bound to Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Mnca Bound to Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1002 b:19.6 occ:1.00 NE2 B:HIS285 2.0 17.7 1.0 OE1 B:GLU290 2.1 18.7 1.0 OXT B:GLY1003 2.1 20.3 1.0 NE2 B:HIS283 2.1 19.0 1.0 N B:GLY1003 2.2 17.1 1.0 NE2 B:HIS329 2.2 19.5 1.0 C B:GLY1003 2.8 24.9 1.0 CA B:GLY1003 3.0 26.3 1.0 CE1 B:HIS285 3.0 19.9 1.0 CD B:GLU290 3.0 19.9 1.0 CD2 B:HIS285 3.1 18.6 1.0 CE1 B:HIS283 3.1 21.2 1.0 CE1 B:HIS329 3.1 19.4 1.0 CD2 B:HIS283 3.1 19.4 1.0 CD2 B:HIS329 3.2 19.7 1.0 OE2 B:GLU290 3.4 22.2 1.0 O B:GLY1003 3.9 29.5 1.0 ND1 B:HIS285 4.1 19.3 1.0 CG B:HIS285 4.2 17.6 1.0 ND1 B:HIS283 4.2 18.6 1.0 ND1 B:HIS329 4.2 18.6 1.0 CG B:HIS283 4.3 18.3 1.0 CG B:HIS329 4.3 19.4 1.0 CE1 B:PHE345 4.3 21.1 1.0 CG B:GLU290 4.4 18.5 1.0 CZ B:PHE345 4.4 21.0 1.0 CB B:GLU290 4.8 18.5 1.0

Nickel binding site 5 out of 6 in the Mnca Bound to Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Mnca Bound to Nickel within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1001 b:19.1 occ:1.00 OE1 C:GLU108 2.1 18.5 1.0 NE2 C:HIS147 2.1 19.5 1.0 NE2 C:HIS103 2.1 16.2 1.0 O C:HOH1107 2.2 18.8 1.0 NE2 C:HIS101 2.2 18.5 1.0 O C:HOH1155 2.2 20.7 1.0 CE1 C:HIS101 3.1 18.8 1.0 CE1 C:HIS147 3.1 18.4 1.0 CE1 C:HIS103 3.1 18.6 1.0 CD C:GLU108 3.1 19.6 1.0 CD2 C:HIS147 3.1 19.2 1.0 CD2 C:HIS103 3.2 18.5 1.0 CD2 C:HIS101 3.2 17.9 1.0 OE2 C:GLU108 3.4 21.2 1.0 O C:HOH1244 4.1 23.3 1.0 ND1 C:HIS101 4.2 19.4 1.0 ND1 C:HIS147 4.2 17.9 1.0 ND1 C:HIS103 4.2 17.4 1.0 CG C:HIS147 4.2 18.6 1.0 CG C:HIS101 4.3 17.9 1.0 CG C:HIS103 4.3 19.0 1.0 CG C:GLU108 4.4 19.4 1.0 CE2 C:PHE163 4.5 20.3 1.0 OE2 C:GLU170 4.7 23.9 1.0 CB C:GLU108 4.8 19.3 1.0 CZ C:PHE163 4.8 20.3 1.0 CD2 C:PHE141 4.9 18.9 1.0

Nickel binding site 6 out of 6 in the Mnca Bound to Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Mnca Bound to Nickel within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1002 b:20.1 occ:1.00 NE2 C:HIS285 2.0 18.5 1.0 OE1 C:GLU290 2.1 19.4 1.0 N C:GLY1003 2.1 17.1 1.0 NE2 C:HIS283 2.1 19.2 1.0 OXT C:GLY1003 2.1 21.2 1.0 NE2 C:HIS329 2.2 19.5 1.0 C C:GLY1003 2.8 25.1 1.0 CA C:GLY1003 2.9 25.9 1.0 CE1 C:HIS285 3.0 20.0 1.0 CE1 C:HIS283 3.1 20.6 1.0 CD C:GLU290 3.1 21.4 1.0 CD2 C:HIS285 3.1 17.6 1.0 CE1 C:HIS329 3.1 19.6 1.0 CD2 C:HIS283 3.2 19.7 1.0 CD2 C:HIS329 3.2 19.2 1.0 OE2 C:GLU290 3.4 21.9 1.0 O C:GLY1003 3.9 31.1 1.0 ND1 C:HIS285 4.1 20.1 1.0 CG C:HIS285 4.2 17.7 1.0 ND1 C:HIS283 4.2 19.5 1.0 ND1 C:HIS329 4.3 17.8 1.0 CG C:HIS283 4.3 18.5 1.0 CG C:HIS329 4.3 18.4 1.0 CE2 C:PHE345 4.3 19.5 1.0 CZ C:PHE345 4.4 19.4 1.0 CG C:GLU290 4.4 19.0 1.0 CB C:GLU290 4.8 17.6 1.0 OH C:TYR350 5.0 30.7 1.0

S.E.Clough, T.R.Young, E.Tarrant, A.J.P.Scott, P.T.Chivers, A.Glasfeld, N.J.Robinson. A Metal-Trap Tests and Refines Blueprints to Engineer Cellular Protein Metalation with Different Elements To Be Published.