Nickel in PDB 7sog: Thermostable Actophorin

The structure of Thermostable Actophorin, PDB code: 7sog was solved by R.L.Lieberman, S.Quirk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.58 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.72, 41.29, 55.5, 90, 95.84, 90
R / Rfree (%)	19.1 / 22.5

The binding sites of Nickel atom in the Thermostable Actophorin (pdb code 7sog). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Thermostable Actophorin, PDB code: 7sog:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Thermostable Actophorin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Thermostable Actophorin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:34.6 occ:0.90 HZ3 A:LYS13 1.5 47.8 1.0 HZ1 A:LYS13 1.7 47.8 1.0 O A:HOH306 1.9 40.6 1.0 NZ A:LYS13 1.9 39.7 1.0 OE1 A:GLU16 2.0 35.0 1.0 NE2 A:HIS23 2.1 30.6 1.0 HZ1 A:LYS22 2.2 55.5 1.0 HZ2 A:LYS22 2.5 55.5 1.0 HZ2 A:LYS13 2.5 47.8 1.0 NZ A:LYS22 2.7 46.1 1.0 HZ3 A:LYS22 2.9 55.5 1.0 CD A:GLU16 3.0 39.1 1.0 CE1 A:HIS23 3.1 31.9 1.0 CE A:LYS13 3.1 40.1 1.0 HE2 A:LYS13 3.1 48.3 1.0 CD2 A:HIS23 3.1 31.6 1.0 HE1 A:HIS23 3.2 38.4 1.0 HD2 A:HIS23 3.3 38.1 1.0 OE2 A:GLU16 3.4 43.9 1.0 HD3 A:LYS13 3.7 41.7 1.0 HE3 A:LYS13 3.8 48.3 1.0 CD A:LYS13 3.9 34.6 1.0 HD2 A:LYS13 4.0 41.7 1.0 CE A:LYS22 4.1 73.1 1.0 HE3 A:LYS22 4.2 87.8 1.0 ND1 A:HIS23 4.2 30.0 1.0 HB3 A:GLU16 4.2 38.2 1.0 CG A:HIS23 4.3 25.9 1.0 CG A:GLU16 4.4 36.3 1.0 HB3 A:LYS22 4.4 41.2 1.0 O A:HOH327 4.6 37.9 1.0 HB2 A:GLU16 4.6 38.2 1.0 HE2 A:LYS22 4.6 87.8 1.0 HG11 A:VAL42 4.6 30.4 0.2 CB A:GLU16 4.7 31.7 1.0 HD3 A:LYS22 4.7 56.9 1.0 HG21 A:VAL42 4.8 35.5 0.8 HG2 A:GLU16 4.8 43.7 1.0 HB2 A:LYS22 4.9 41.2 1.0 HD1 A:HIS23 5.0 36.1 1.0 HG3 A:GLU16 5.0 43.7 1.0

Nickel binding site 2 out of 4 in the Thermostable Actophorin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Thermostable Actophorin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:35.5 occ:0.91 O A:GLY1 2.0 30.8 1.0 O A:HOH375 2.1 35.7 1.0 N A:GLY1 2.1 29.6 1.0 O B:HOH317 2.3 34.9 1.0 C A:GLY1 2.7 28.7 1.0 CA A:GLY1 2.9 32.1 1.0 HG1 B:THR119 3.7 31.9 1.0 O B:HOH313 3.8 34.8 1.0 OD2 B:ASP88 3.9 33.1 1.0 OG1 B:THR119 4.0 26.4 1.0 N A:PRO2 4.0 27.3 1.0 OD1 B:ASP88 4.3 26.0 1.0 OD2 B:ASP120 4.4 33.0 1.0 HA A:PRO2 4.5 31.9 1.0 CG B:ASP88 4.5 24.6 1.0 CA A:PRO2 4.7 26.5 1.0 HB B:THR119 4.9 30.4 1.0 C A:PRO2 4.9 28.5 1.0

Nickel binding site 3 out of 4 in the Thermostable Actophorin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Thermostable Actophorin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:34.8 occ:0.90 O B:HOH309 1.9 33.4 1.0 OE1 B:GLU16 2.0 37.8 1.0 O B:HOH311 2.1 35.5 1.0 NE2 B:HIS23 2.1 34.4 1.0 NZ B:LYS13 2.1 39.5 1.0 HZ2 B:LYS22 2.6 61.9 1.0 HE2 B:LYS22 2.7 62.1 1.0 HE3 B:LYS22 2.9 62.1 1.0 CD B:GLU16 3.0 36.8 1.0 CE B:LYS13 3.0 35.4 1.0 CD2 B:HIS23 3.0 32.3 1.0 CE B:LYS22 3.1 51.6 1.0 CE1 B:HIS23 3.1 30.2 1.0 HD2 B:HIS23 3.2 38.9 1.0 NZ B:LYS22 3.2 51.4 1.0 OE2 B:GLU16 3.3 42.1 1.0 HE1 B:HIS23 3.3 36.4 1.0 HZ3 B:LYS22 3.7 61.9 1.0 HZ1 B:LYS22 3.9 61.9 1.0 CD B:LYS13 3.9 33.2 1.0 ND1 B:HIS23 4.2 31.0 1.0 CG B:HIS23 4.2 27.4 1.0 HB3 B:GLU16 4.3 37.6 1.0 CG B:GLU16 4.3 32.6 1.0 HG11 B:VAL42 4.5 35.6 1.0 HB2 B:GLU16 4.5 37.6 1.0 HB3 B:LYS22 4.5 47.3 1.0 CD B:LYS22 4.6 61.1 1.0 CB B:GLU16 4.6 31.2 1.0 HG2 B:GLU16 4.8 39.3 1.0 HD3 B:LYS22 4.9 73.5 1.0 HG3 B:GLU16 4.9 39.3 1.0 HD1 B:HIS23 5.0 37.4 1.0

Nickel binding site 4 out of 4 in the Thermostable Actophorin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Thermostable Actophorin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:34.9 occ:0.66 O B:HOH306 2.1 37.8 1.0 OD1 B:ASP103 2.1 39.9 1.0 O B:HOH304 2.4 40.1 1.0 HE2 B:LYS102 2.4 48.0 1.0 HZ3 B:LYS102 2.7 51.5 1.0 CE B:LYS102 3.0 39.9 1.0 CG B:ASP103 3.1 42.7 1.0 HE3 B:LYS102 3.1 48.0 1.0 NZ B:LYS102 3.3 42.8 1.0 OD2 B:ASP103 3.4 40.0 1.0 HZ2 B:LYS102 3.6 51.5 1.0 HZ1 B:LYS102 4.0 51.5 1.0 HB3 B:LYS102 4.0 37.1 1.0 OE1 B:GLU115 4.2 45.6 1.0 O B:HOH319 4.2 26.0 1.0 HG2 B:LYS102 4.3 41.7 1.0 HA B:ASP103 4.4 43.7 1.0 CD B:LYS102 4.4 34.0 1.0 CB B:ASP103 4.4 41.5 1.0 H B:ASP103 4.5 38.5 1.0 OE2 B:GLU115 4.5 44.7 1.0 HE2 B:LYS106 4.6 74.7 1.0 N B:ASP103 4.7 31.9 1.0 HZ1 B:LYS106 4.7 71.7 1.0 CG B:LYS102 4.7 34.6 1.0 CA B:ASP103 4.7 36.3 1.0 CD B:GLU115 4.8 44.9 1.0 CB B:LYS102 4.8 30.8 1.0 HB2 B:ASP103 4.8 50.0 1.0 HD3 B:LYS102 4.9 40.9 1.0 HD2 B:LYS102 5.0 40.9 1.0

S.Quirk, R.L.Lieberman. Structure and Activity of A Thermally Stable Mutant of Acanthamoeba Actophorin. Acta Crystallogr.,Sect.F V. 78 150 2022.
ISSN: ESSN 2053-230X
PubMed: 35400667
DOI: 10.1107/S2053230X22002448