Magnesium in PDB 6l8s: High Resolution Crystal Structure of Crustacean Hemocyanin.

The structure of High Resolution Crystal Structure of Crustacean Hemocyanin., PDB code: 6l8s was solved by T.Masuda, B.Mikami, S.Baba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.70 / 1.58
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.454, 207.596, 187.364, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.6

The structure of High Resolution Crystal Structure of Crustacean Hemocyanin. also contains other interesting chemical elements:

Copper	(Cu)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the High Resolution Crystal Structure of Crustacean Hemocyanin. (pdb code 6l8s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the High Resolution Crystal Structure of Crustacean Hemocyanin., PDB code: 6l8s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg707 b:65.4 occ:1.00 NE2 A:HIS70 3.3 30.3 1.0 O A:HOH1113 3.7 52.0 1.0 CE1 A:HIS70 4.1 29.6 1.0 CD2 A:HIS70 4.4 28.8 1.0 NE1 A:TRP71 4.9 29.7 1.0

Magnesium binding site 2 out of 5 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg707 b:34.5 occ:1.00 OD1 B:ASP24 2.1 32.3 1.0 O B:HOH1046 2.3 43.9 1.0 O B:HOH1192 2.4 28.9 1.0 OE1 B:GLN68 2.4 25.7 1.0 O B:HOH1230 2.4 23.3 1.0 O B:HOH938 2.6 44.6 1.0 CD B:GLN68 3.3 24.8 1.0 CG B:ASP24 3.4 30.9 1.0 NE2 B:GLN68 3.5 23.8 1.0 N B:ASP24 3.9 22.3 1.0 CA B:ASP24 4.0 23.6 1.0 OD2 B:ASP24 4.2 34.6 1.0 CB B:ASP24 4.3 25.9 1.0 O B:HOH1063 4.3 26.8 1.0 C B:GLU23 4.5 21.8 1.0 O B:GLU108 4.6 25.6 1.0 O B:HOH970 4.6 25.2 1.0 CG B:GLN68 4.7 23.3 1.0 OE2 B:GLU108 4.9 34.8 1.0 O B:HOH1172 4.9 31.3 1.0 O B:GLU23 4.9 22.7 1.0

Magnesium binding site 3 out of 5 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg708 b:55.8 occ:1.00 O B:HOH1228 2.0 35.6 1.0 OG1 B:THR292 3.5 19.6 1.0 O B:HOH1179 3.6 56.6 1.0 SD B:MET289 3.8 21.8 1.0 O B:ASP288 4.0 21.4 1.0 CB B:ASP288 4.0 24.5 1.0 C B:ASP288 4.3 21.4 1.0 CG2 B:THR346 4.3 18.4 1.0 CB B:ALA284 4.4 22.2 1.0 CB B:THR292 4.5 16.8 1.0 OG1 B:THR346 4.5 20.0 1.0 N B:MET289 4.6 18.9 1.0 CB B:THR346 4.6 16.9 1.0 CA B:MET289 4.8 18.1 1.0 CE B:MET289 4.8 21.6 1.0 CA B:ASP288 4.8 22.1 1.0 CG2 B:THR292 5.0 19.6 1.0

Magnesium binding site 4 out of 5 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg706 b:42.7 occ:1.00 O C:VAL635 2.7 27.6 1.0 ND1 C:HIS403 2.7 31.2 1.0 O C:HOH1241 3.2 45.2 1.0 CA C:GLY638 3.3 30.4 1.0 C C:GLY638 3.3 29.1 1.0 CB C:HIS403 3.5 28.9 1.0 CG C:HIS403 3.5 29.7 1.0 C C:VAL635 3.5 26.6 1.0 O C:GLY638 3.6 30.9 1.0 N C:GLY638 3.7 29.8 1.0 CA C:VAL635 3.7 25.9 1.0 CE1 C:HIS403 3.8 30.8 1.0 N C:VAL639 3.8 27.0 1.0 O C:ARG634 3.9 28.3 1.0 CG2 C:VAL639 4.0 29.2 1.0 CA C:HIS403 4.1 26.6 1.0 CG1 C:VAL635 4.5 27.2 1.0 CA C:VAL639 4.6 28.1 1.0 C C:ARG634 4.7 27.3 1.0 N C:VAL635 4.7 26.1 1.0 CB C:VAL635 4.7 26.2 1.0 CD2 C:HIS403 4.7 32.0 1.0 N C:PHE636 4.8 27.0 1.0 NE2 C:HIS403 4.8 33.5 1.0 N C:HIS403 4.8 27.7 1.0 CB C:VAL639 4.9 27.7 1.0

Magnesium binding site 5 out of 5 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg707 b:51.9 occ:1.00 O C:THR529 2.5 22.5 1.0 O C:GLY604 2.6 26.6 1.0 O C:SER526 2.7 24.0 1.0 O C:HOH805 2.8 41.8 1.0 OE1 C:GLU559 3.0 36.5 0.6 C C:GLY604 3.5 26.0 1.0 C C:THR529 3.7 20.4 1.0 CA C:GLY604 3.7 28.0 1.0 C C:SER526 3.9 23.2 1.0 CD C:GLU559 3.9 37.4 0.6 OE2 C:GLU559 4.1 40.4 0.6 CA C:VAL530 4.4 21.2 1.0 O C:ASP525 4.4 26.3 1.0 OG1 C:THR529 4.4 23.8 1.0 C C:ASP525 4.5 25.8 1.0 N C:VAL530 4.5 21.1 1.0 O C:LYS524 4.5 32.3 1.0 CG1 C:VAL530 4.6 23.9 1.0 N C:SER526 4.6 24.2 1.0 N C:THR529 4.7 21.3 1.0 CA C:SER527 4.7 21.1 1.0 N C:THR605 4.7 23.8 1.0 CA C:THR529 4.7 20.8 1.0 OE1 C:GLU559 4.7 34.9 0.4 N C:SER527 4.7 22.2 1.0 CA C:SER526 4.9 23.8 1.0 OD1 C:ASP566 4.9 31.9 0.3 CG C:GLU559 5.0 32.4 0.4

T.Masuda, S.Baba, K.Matsuo, S.Ito, B.Mikami. The High-Resolution Crystal Structure of Lobster Hemocyanin Shows Its Enzymatic Capability As A Phenoloxidase. Arch.Biochem.Biophys. 08370 2020.
ISSN: ESSN 1096-0384
PubMed: 32380017
DOI: 10.1016/J.ABB.2020.108370