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Copper 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:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 1 atom

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 6l8s

Go back to Copper Binding Sites List in 6l8s
Copper binding site 1 out of 6 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:21.7
occ:1.00
O A:O704 1.9 50.0 1.0
NE2 A:HIS194 2.0 19.5 1.0
NE2 A:HIS198 2.0 18.1 1.0
O A:O705 2.1 25.1 1.0
NE2 A:HIS224 2.1 18.6 1.0
CE1 A:HIS194 2.9 20.0 1.0
CD2 A:HIS194 3.0 20.5 1.0
CE1 A:HIS198 3.0 18.3 1.0
CD2 A:HIS198 3.0 17.6 1.0
CE1 A:HIS224 3.0 20.2 1.0
CD2 A:HIS224 3.1 19.3 1.0
CU A:CU702 3.4 25.8 1.0
CE1 A:PHE371 3.9 20.5 1.0
ND1 A:HIS194 4.0 20.7 1.0
CD1 A:PHE371 4.0 20.0 1.0
CG A:HIS194 4.1 19.0 1.0
ND1 A:HIS198 4.1 16.8 1.0
CG A:HIS198 4.2 15.3 1.0
ND1 A:HIS224 4.2 19.8 1.0
CG A:HIS224 4.2 18.0 1.0
NE2 A:HIS384 4.6 20.8 1.0
NE2 A:HIS344 4.6 19.1 1.0
CZ A:PHE380 4.6 19.9 1.0
CE2 A:PHE380 4.6 19.2 1.0
CE1 A:HIS344 4.8 21.6 1.0
CZ A:PHE371 4.8 19.8 1.0
NE2 A:HIS348 5.0 20.8 1.0

Copper binding site 2 out of 6 in 6l8s

Go back to Copper Binding Sites List in 6l8s
Copper binding site 2 out of 6 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:25.8
occ:1.00
O A:O705 1.9 25.1 1.0
NE2 A:HIS344 1.9 19.1 1.0
NE2 A:HIS384 2.1 20.8 1.0
O A:O704 2.2 50.0 1.0
NE2 A:HIS348 2.4 20.8 1.0
CE1 A:HIS384 2.7 23.2 1.0
CE1 A:HIS344 2.8 21.6 1.0
CD2 A:HIS344 3.0 19.5 1.0
CE1 A:HIS348 3.2 19.8 1.0
CD2 A:HIS384 3.3 20.2 1.0
CU A:CU701 3.4 21.7 1.0
CD2 A:HIS348 3.4 19.6 1.0
NE2 A:HIS224 3.8 18.6 1.0
ND1 A:HIS344 3.9 20.9 1.0
CD2 A:HIS224 3.9 19.3 1.0
ND1 A:HIS384 3.9 22.0 1.0
CG A:HIS344 4.1 19.3 1.0
CE2 A:PHE380 4.1 19.2 1.0
CG A:HIS384 4.3 19.8 1.0
ND1 A:HIS348 4.4 19.3 1.0
CG A:HIS348 4.5 18.0 1.0
CZ A:PHE380 4.5 19.9 1.0
CE1 A:HIS224 4.6 20.2 1.0
NE2 A:HIS194 4.7 19.5 1.0
CG A:HIS224 4.8 18.0 1.0
NE2 A:HIS198 4.8 18.1 1.0
CE1 A:PHE371 4.8 20.5 1.0
CE1 A:HIS194 4.9 20.0 1.0

Copper binding site 3 out of 6 in 6l8s

Go back to Copper Binding Sites List in 6l8s
Copper binding site 3 out of 6 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:20.2
occ:1.00
NE2 B:HIS194 2.0 16.9 1.0
NE2 B:HIS198 2.0 16.6 1.0
O B:O704 2.0 42.1 1.0
NE2 B:HIS224 2.1 18.9 1.0
O B:O705 2.2 24.5 1.0
CE1 B:HIS194 3.0 20.4 1.0
CD2 B:HIS194 3.0 17.6 1.0
CD2 B:HIS198 3.0 16.8 1.0
CE1 B:HIS198 3.0 18.3 1.0
CE1 B:HIS224 3.1 19.1 1.0
CD2 B:HIS224 3.1 17.1 1.0
CU B:CU702 3.3 23.9 1.0
CE1 B:PHE371 3.7 20.9 1.0
CD1 B:PHE371 3.9 20.9 1.0
ND1 B:HIS194 4.1 20.1 1.0
CG B:HIS194 4.1 17.4 1.0
ND1 B:HIS198 4.1 16.4 1.0
CG B:HIS198 4.1 15.6 1.0
ND1 B:HIS224 4.2 18.1 1.0
CG B:HIS224 4.2 17.2 1.0
NE2 B:HIS344 4.6 17.7 1.0
NE2 B:HIS384 4.6 20.2 1.0
CZ B:PHE380 4.6 18.9 1.0
CZ B:PHE371 4.7 21.1 1.0
CE2 B:PHE380 4.7 18.7 1.0
CE1 B:HIS344 4.8 19.5 1.0
NE2 B:HIS348 5.0 19.8 1.0
CG B:PHE371 5.0 20.0 1.0

Copper binding site 4 out of 6 in 6l8s

Go back to Copper Binding Sites List in 6l8s
Copper binding site 4 out of 6 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:23.9
occ:1.00
O B:O705 1.9 24.5 1.0
NE2 B:HIS344 1.9 17.7 1.0
O B:O704 2.0 42.1 1.0
NE2 B:HIS384 2.1 20.2 1.0
NE2 B:HIS348 2.4 19.8 1.0
CE1 B:HIS344 2.8 19.5 1.0
CE1 B:HIS384 2.8 22.0 1.0
CD2 B:HIS344 3.0 17.3 1.0
CE1 B:HIS348 3.2 17.1 1.0
CD2 B:HIS384 3.3 21.1 1.0
CU B:CU701 3.3 20.2 1.0
CD2 B:HIS348 3.4 18.1 1.0
NE2 B:HIS224 3.7 18.9 1.0
CD2 B:HIS224 3.8 17.1 1.0
ND1 B:HIS344 3.9 18.6 1.0
ND1 B:HIS384 4.0 20.8 1.0
CG B:HIS344 4.1 17.9 1.0
CE2 B:PHE380 4.2 18.7 1.0
CG B:HIS384 4.2 19.0 1.0
ND1 B:HIS348 4.4 16.6 1.0
CG B:HIS348 4.5 16.6 1.0
CZ B:PHE380 4.5 18.9 1.0
CE1 B:HIS224 4.5 19.1 1.0
NE2 B:HIS194 4.7 16.9 1.0
CE1 B:PHE371 4.7 20.9 1.0
CG B:HIS224 4.7 17.2 1.0
NE2 B:HIS198 4.8 16.6 1.0
CE1 B:HIS194 4.9 20.4 1.0

Copper binding site 5 out of 6 in 6l8s

Go back to Copper Binding Sites List in 6l8s
Copper binding site 5 out of 6 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu701

b:20.8
occ:1.00
NE2 C:HIS194 2.0 18.1 1.0
O C:O704 2.0 43.8 1.0
NE2 C:HIS198 2.0 17.1 1.0
O C:O703 2.1 24.7 1.0
NE2 C:HIS224 2.1 18.5 1.0
CE1 C:HIS194 2.9 19.7 1.0
CE1 C:HIS198 3.0 18.2 1.0
CD2 C:HIS198 3.0 17.0 1.0
CD2 C:HIS194 3.0 16.3 1.0
CE1 C:HIS224 3.1 20.0 1.0
CD2 C:HIS224 3.1 18.9 1.0
CU C:CU702 3.3 21.9 1.0
CE1 C:PHE371 3.7 20.1 1.0
CD1 C:PHE371 3.9 18.0 1.0
ND1 C:HIS194 4.0 18.8 1.0
ND1 C:HIS198 4.1 17.0 1.0
CG C:HIS194 4.1 17.2 1.0
CG C:HIS198 4.2 17.3 1.0
ND1 C:HIS224 4.2 19.3 1.0
CG C:HIS224 4.3 18.3 1.0
NE2 C:HIS344 4.6 18.0 1.0
NE2 C:HIS384 4.7 23.8 1.0
CZ C:PHE371 4.7 20.5 1.0
CZ C:PHE380 4.7 20.2 1.0
CE2 C:PHE380 4.8 19.1 1.0
CE1 C:HIS344 4.8 19.1 1.0
NE2 C:HIS348 4.9 18.6 1.0

Copper binding site 6 out of 6 in 6l8s

Go back to Copper Binding Sites List in 6l8s
Copper binding site 6 out of 6 in the High Resolution Crystal Structure of Crustacean Hemocyanin.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of High Resolution Crystal Structure of Crustacean Hemocyanin. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu702

b:21.9
occ:1.00
O C:O703 1.9 24.7 1.0
NE2 C:HIS344 1.9 18.0 1.0
NE2 C:HIS384 2.1 23.8 1.0
O C:O704 2.1 43.8 1.0
NE2 C:HIS348 2.3 18.6 1.0
CE1 C:HIS384 2.8 23.7 1.0
CE1 C:HIS344 2.8 19.1 1.0
CD2 C:HIS344 3.0 18.5 1.0
CD2 C:HIS384 3.2 22.5 1.0
CE1 C:HIS348 3.2 17.9 1.0
CU C:CU701 3.3 20.8 1.0
CD2 C:HIS348 3.4 18.5 1.0
NE2 C:HIS224 3.7 18.5 1.0
CD2 C:HIS224 3.8 18.9 1.0
ND1 C:HIS344 4.0 19.0 1.0
ND1 C:HIS384 4.0 21.8 1.0
CG C:HIS344 4.1 18.2 1.0
CE2 C:PHE380 4.2 19.1 1.0
CG C:HIS384 4.2 19.8 1.0
ND1 C:HIS348 4.4 19.2 1.0
CG C:HIS348 4.5 17.9 1.0
CZ C:PHE380 4.5 20.2 1.0
CE1 C:HIS224 4.6 20.0 1.0
NE2 C:HIS194 4.7 18.1 1.0
CG C:HIS224 4.8 18.3 1.0
CE1 C:PHE371 4.8 20.1 1.0
NE2 C:HIS198 4.8 17.1 1.0
CE1 C:HIS194 4.9 19.7 1.0

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: Sun Dec 13 11:24:04 2020

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