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

Protein crystallography data

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

Other elements in 6l8s:

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

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

Magnesium Binding Sites:

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 6l8s

Go back to Magnesium Binding Sites List in 6l8s
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 6l8s

Go back to Magnesium Binding Sites List in 6l8s
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 6l8s

Go back to Magnesium Binding Sites List in 6l8s
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 6l8s

Go back to Magnesium Binding Sites List in 6l8s
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 6l8s

Go back to Magnesium Binding Sites List in 6l8s
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

Reference:

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
Page generated: Mon Dec 14 23:12:35 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy