Magnesium 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:

Nickel

(Ni)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of M-Crystallin in the Presence of Nickel, PDB code: 5ht9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of M-Crystallin in the Presence of Nickel


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg102 b:21.0 occ:1.00 O A:GLU49 2.0 18.3 1.0 O A:HOH244 2.0 20.4 1.0 OG A:SER79 2.1 20.3 1.0 OD1 A:ASP33 2.1 23.5 1.0 O A:SER77 2.1 21.6 1.0 O A:HOH249 2.2 22.8 1.0 C A:SER77 3.2 24.1 1.0 C A:GLU49 3.2 18.5 1.0 CG A:ASP33 3.2 34.1 1.0 CB A:SER79 3.3 20.0 1.0 OD2 A:ASP33 3.7 36.9 1.0 CA A:SER77 3.8 23.1 1.0 CA A:GLU49 4.0 17.7 1.0 N A:SER79 4.0 16.9 1.0 OD1 A:ASN32 4.1 31.6 1.0 CA A:SER79 4.2 20.7 1.0 N A:TYR50 4.2 17.7 1.0 C A:ILE78 4.2 20.8 1.0 N A:ILE78 4.3 22.4 1.0 O A:HOH265 4.3 19.1 1.0 CA A:TYR50 4.3 19.7 1.0 CD1 A:TYR50 4.4 22.1 1.0 CB A:ASP33 4.5 29.7 1.0 O A:HOH226 4.5 24.1 1.0 CB A:GLU49 4.5 19.0 1.0 O A:ILE78 4.5 20.3 1.0 CB A:SER77 4.6 25.4 1.0 CA A:ILE78 4.6 19.1 1.0 CA A:ASP33 4.6 28.5 1.0 N A:ASP33 4.8 25.9 1.0 N A:SER77 4.9 22.9 1.0 CE1 A:TYR50 5.0 21.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of M-Crystallin in the Presence of Nickel


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg103 b:27.5 occ:1.00 O A:GLU9 2.3 21.7 1.0 OD1 A:ASN76 2.3 28.5 1.0 OG A:SER36 2.4 22.2 1.0 O A:LYS34 2.4 26.4 1.0 C A:LYS34 3.2 24.1 1.0 CG A:ASN76 3.4 28.9 1.0 C A:GLU9 3.4 18.0 1.0 O A:HOH255 3.5 27.4 1.0 CB A:SER36 3.5 21.0 1.0 CA A:LYS34 3.7 27.7 1.0 ND2 A:ASN76 3.9 34.8 1.0 N A:SER36 4.2 16.3 1.0 CA A:GLU9 4.2 18.8 1.0 CB A:LYS34 4.2 28.8 1.0 N A:ILE35 4.3 20.9 1.0 C A:ILE35 4.3 19.3 1.0 CG A:GLU9 4.3 19.1 1.0 CA A:SER36 4.4 19.2 1.0 N A:HIS10 4.4 17.8 1.0 OD1 A:ASP75 4.5 30.2 1.0 ND1 A:HIS10 4.5 23.7 1.0 CA A:HIS10 4.6 19.3 1.0 O A:ILE35 4.6 18.8 1.0 CA A:ILE35 4.7 17.8 1.0 CB A:ASN76 4.7 27.1 1.0 O A:HOH262 4.8 22.1 1.0 CB A:GLU9 4.9 21.0 1.0 CA A:ASN76 5.0 26.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of M-Crystallin in the Presence of Nickel


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of M-Crystallin in the Presence of Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:33.8 occ:1.00 OG B:SER79 2.0 32.2 1.0 O B:GLU49 2.1 30.0 1.0 O B:SER77 2.1 29.8 1.0 OD1 B:ASP33 2.1 31.9 1.0 O B:HOH228 2.3 32.3 1.0 O B:HOH248 2.4 31.3 1.0 CB B:SER79 3.0 28.3 1.0 C B:SER77 3.1 31.8 1.0 CG B:ASP33 3.2 33.3 1.0 C B:GLU49 3.2 26.7 1.0 OD2 B:ASP33 3.6 33.7 1.0 N B:SER79 3.7 24.8 1.0 CA B:SER77 3.8 29.2 1.0 CA B:SER79 3.9 24.7 1.0 C B:ILE78 3.9 27.0 1.0 CA B:GLU49 4.1 27.1 1.0 OG B:SER77 4.2 36.5 1.0 N B:ILE78 4.2 28.6 1.0 OD1 B:ASN32 4.2 33.6 1.0 N B:TYR50 4.2 25.8 1.0 O B:ILE78 4.3 30.2 1.0 CA B:TYR50 4.4 26.4 1.0 CA B:ILE78 4.4 27.3 1.0 O B:HOH263 4.5 28.5 1.0 CB B:ASP33 4.5 32.9 1.0 CA B:ASP33 4.6 33.3 1.0 CB B:SER77 4.6 33.2 1.0 N B:ASP33 4.7 29.9 1.0 CB B:GLU49 4.7 28.3 1.0 O B:TYR48 4.9 21.9 1.0 CD1 B:TYR50 4.9 31.8 1.0 N B:SER77 4.9 28.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of M-Crystallin in the Presence of Nickel


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of M-Crystallin in the Presence of Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:29.1 occ:1.00 O B:GLU9 2.0 23.2 1.0 OD1 B:ASN76 2.2 29.5 1.0 OG B:SER36 2.2 26.1 1.0 O B:HOH220 2.3 35.6 1.0 O B:LYS34 2.4 27.0 1.0 O B:HOH277 2.6 30.7 1.0 C B:GLU9 3.2 19.4 1.0 CG B:ASN76 3.2 32.7 1.0 C B:LYS34 3.3 27.1 1.0 CB B:SER36 3.4 21.8 1.0 ND2 B:ASN76 3.7 36.7 1.0 CA B:LYS34 3.9 26.1 1.0 ND1 B:HIS10 4.0 22.8 1.0 N B:SER36 4.0 19.8 1.0 CA B:GLU9 4.1 19.0 1.0 N B:HIS10 4.1 19.0 1.0 C B:ILE35 4.2 18.1 1.0 CG B:GLU9 4.2 21.3 1.0 CA B:HIS10 4.3 20.7 1.0 CA B:SER36 4.3 21.6 1.0 N B:ILE35 4.3 23.3 1.0 CB B:LYS34 4.4 27.1 1.0 O B:HOH229 4.5 30.0 1.0 CB B:ASN76 4.5 29.9 1.0 CA B:ILE35 4.6 19.6 1.0 O B:ILE35 4.6 21.0 1.0 CE1 B:HIS10 4.7 22.8 1.0 OD1 B:ASP75 4.7 33.2 1.0 CB B:GLU9 4.8 18.9 1.0 O B:HOH280 4.8 21.1 1.0 CA B:ASN76 4.8 29.1 1.0 CG B:HIS10 5.0 21.9 1.0 O B:TYR8 5.0 18.4 1.0 OD2 B:ASP75 5.0 35.0 1.0 N B:ASN76 5.0 29.9 1.0

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