Nickel in PDB 5ht9: Crystal Structure of M-Crystallin in the Presence of Nickel

The structure of Crystal Structure of M-Crystallin in the Presence of Nickel, PDB code: 5ht9 was solved by A.Jamkhindikar, S.S.Srivastava, R.Sankaranarayanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.77 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.151, 52.934, 85.933, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 21.4

The structure of Crystal Structure of M-Crystallin in the Presence of Nickel also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of M-Crystallin in the Presence of Nickel (pdb code 5ht9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of M-Crystallin in the Presence of Nickel, PDB code: 5ht9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of M-Crystallin in the Presence of Nickel


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 M-Crystallin in the Presence of Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:24.8 occ:1.00 O8 A:BTB104 1.9 24.3 1.0 O3 A:BTB104 2.0 25.9 1.0 N A:BTB104 2.0 25.4 1.0 O6 A:BTB104 2.1 25.1 1.0 NE2 A:HIS10 2.1 20.2 1.0 O4 A:BTB104 2.2 25.5 1.0 C2 A:BTB104 2.7 27.8 1.0 C3 A:BTB104 2.8 27.3 1.0 C8 A:BTB104 2.8 23.6 1.0 C7 A:BTB104 2.9 24.5 1.0 C5 A:BTB104 2.9 29.2 1.0 C6 A:BTB104 3.0 31.0 1.0 C4 A:BTB104 3.0 29.9 1.0 CE1 A:HIS10 3.1 24.7 1.0 CD2 A:HIS10 3.1 21.9 1.0 OE2 A:GLU9 3.9 25.2 1.0 OE1 A:GLU9 4.0 22.5 1.0 CD A:GLU9 4.0 24.6 1.0 C1 A:BTB104 4.2 32.6 1.0 ND1 A:HIS10 4.2 23.7 1.0 CG A:HIS10 4.2 20.1 1.0 O A:HOH246 4.3 30.3 1.0 CA A:GLY15 4.8 17.6 1.0 O1 A:BTB104 4.8 32.1 1.0 CG A:GLU9 5.0 19.1 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of M-Crystallin in the Presence of Nickel


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 M-Crystallin in the Presence of Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:27.3 occ:1.00 O8 B:BTB104 1.9 22.8 1.0 N B:BTB104 2.0 24.6 1.0 O6 B:BTB104 2.1 29.6 1.0 NE2 B:HIS10 2.1 18.1 1.0 O3 B:BTB104 2.2 27.0 1.0 O4 B:BTB104 2.2 23.0 1.0 C2 B:BTB104 2.7 25.9 1.0 C7 B:BTB104 2.8 23.3 1.0 C8 B:BTB104 2.8 24.5 1.0 C5 B:BTB104 2.9 26.1 1.0 C6 B:BTB104 2.9 29.2 1.0 C3 B:BTB104 2.9 29.4 1.0 C4 B:BTB104 3.0 28.2 1.0 CE1 B:HIS10 3.1 22.8 1.0 CD2 B:HIS10 3.1 20.4 1.0 OE2 B:GLU9 3.8 20.6 1.0 OE1 B:GLU9 3.9 24.5 1.0 CD B:GLU9 4.0 22.9 1.0 O B:HOH238 4.2 29.5 1.0 C1 B:BTB104 4.2 30.8 1.0 ND1 B:HIS10 4.2 22.8 1.0 CG B:HIS10 4.3 21.9 1.0 O1 B:BTB104 4.8 34.6 1.0 CA B:GLY15 4.9 16.6 1.0

A.Jamkhindikar, S.S.Srivastava, Y.Sharma, R.Sankaranarayanan. Inconspicuous Nickel-Binding Methanoarchaeal Betagamma-Crystallins To Be Published.