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Copper in PDB 6kzy: Cu(II) Loaded Tegillarca Granosa Ferritin

Enzymatic activity of Cu(II) Loaded Tegillarca Granosa Ferritin

All present enzymatic activity of Cu(II) Loaded Tegillarca Granosa Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Cu(II) Loaded Tegillarca Granosa Ferritin, PDB code: 6kzy was solved by Q.Q.Jiang, X.R.Su, T.H.Ming, H.S.Huan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.72 / 2.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 217.054, 217.054, 132.874, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 19.5

Other elements in 6kzy:

The structure of Cu(II) Loaded Tegillarca Granosa Ferritin also contains other interesting chemical elements:

Sodium (Na) 37 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cu(II) Loaded Tegillarca Granosa Ferritin (pdb code 6kzy). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Cu(II) Loaded Tegillarca Granosa Ferritin, PDB code: 6kzy:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6kzy

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Copper binding site 1 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:70.4
occ:1.00
 OE2 A:GLU25 2.4 47.7 1.0
OE2 A:GLU60 2.5 41.0 1.0
ND1 A:HIS63 2.6 49.2 1.0
O A:HOH341 2.8 48.2 1.0
OE1 A:GLU60 3.1 51.1 1.0
CD A:GLU60 3.1 41.0 1.0
CD A:GLU25 3.3 39.4 1.0
OE1 A:GLN139 3.4 46.1 1.0
CG A:HIS63 3.5 45.4 1.0
OE1 A:GLU25 3.5 37.2 1.0
CE1 A:HIS63 3.6 49.0 1.0
CB A:HIS63 3.7 28.4 1.0
CG1 A:VAL108 4.3 28.5 1.0
CG A:GLU60 4.5 30.3 1.0
CD A:GLN139 4.5 27.9 1.0
CG A:GLU25 4.6 33.3 1.0
CA A:GLU60 4.6 31.5 1.0
CD2 A:HIS63 4.7 41.3 1.0
NE2 A:HIS63 4.7 58.1 1.0
CB A:GLU60 4.9 27.5 1.0
CB A:GLU25 5.0 26.9 1.0

Copper binding site 2 out of 8 in 6kzy

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Copper binding site 2 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:48.4
occ:1.00
 OD1 B:ASP129 2.7 29.2 1.0
OD1 D:ASP129 2.7 29.4 1.0
OD1 A:ASP129 2.7 29.2 1.0
OE1 D:GLU132 2.7 29.8 1.0
O B:HOH308 2.8 52.5 1.0
OE1 A:GLU132 2.8 30.1 1.0
OE2 B:GLU132 2.8 28.1 1.0
O A:HOH337 3.0 53.5 1.0
O D:HOH354 3.1 54.1 1.0
CG B:ASP129 3.8 38.3 1.0
CG D:ASP129 3.8 35.5 1.0
CG A:ASP129 3.8 37.1 1.0
CD D:GLU132 3.9 39.2 1.0
CD A:GLU132 4.0 38.9 1.0
CD B:GLU132 4.0 39.0 1.0
CB B:ASP129 4.3 30.1 1.0
CB D:ASP129 4.3 29.9 1.0
CB A:ASP129 4.3 28.0 1.0
CU B:CU201 4.5 93.9 1.0
OE2 A:GLU132 4.5 34.9 1.0
OE2 D:GLU132 4.5 33.6 1.0
CA B:ASP129 4.5 28.1 1.0
OE1 B:GLU132 4.6 32.9 1.0
CA D:ASP129 4.6 27.7 1.0
CA A:ASP129 4.6 28.2 1.0
O3 A:TRS211 4.6 47.1 1.0
O1 A:TRS211 4.6 46.0 1.0
N A:TRS211 4.7 41.0 1.0
OD2 B:ASP129 4.8 34.7 1.0
OD2 D:ASP129 4.8 35.5 1.0
OD2 A:ASP129 4.9 33.4 1.0
CB D:GLU132 5.0 27.5 1.0

Copper binding site 3 out of 8 in 6kzy

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Copper binding site 3 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:93.9
occ:1.00
 O A:HOH337 2.5 53.5 1.0
O B:HOH308 2.5 52.5 1.0
O D:HOH321 2.6 51.9 1.0
O A:HOH312 2.6 52.0 1.0
O D:HOH354 2.7 54.1 1.0
O B:HOH305 2.9 54.3 1.0
OE1 B:GLU132 3.8 32.9 1.0
OE2 A:GLU132 4.0 34.9 1.0
OE2 D:GLU132 4.0 33.6 1.0
OE2 B:GLU132 4.4 28.1 1.0
CU A:CU202 4.5 48.4 1.0
CD B:GLU132 4.5 39.0 1.0
OE1 D:GLU132 4.5 29.8 1.0
OE1 A:GLU132 4.6 30.1 1.0
CD D:GLU132 4.7 39.2 1.0
CD A:GLU132 4.7 38.9 1.0
O A:HOH375 4.9 41.2 1.0
SD B:MET128 5.0 33.1 1.0
O D:HOH366 5.0 46.2 1.0

Copper binding site 4 out of 8 in 6kzy

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Copper binding site 4 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:69.9
occ:1.00
 OE2 B:GLU25 2.3 47.2 1.0
ND1 B:HIS63 2.4 51.8 1.0
OE2 B:GLU60 2.5 41.5 1.0
O B:HOH348 2.6 49.1 1.0
OE1 B:GLU60 3.1 53.0 1.0
CD B:GLU60 3.1 41.0 1.0
O B:HOH332 3.2 50.9 1.0
CD B:GLU25 3.2 36.0 1.0
CG B:HIS63 3.4 48.8 1.0
CE1 B:HIS63 3.4 58.1 1.0
OE1 B:GLU25 3.5 38.8 1.0
OE1 B:GLN139 3.5 47.8 1.0
CB B:HIS63 3.6 28.9 1.0
O B:HOH342 3.9 50.2 1.0
CG1 B:VAL108 4.4 29.8 1.0
NE2 B:HIS63 4.5 63.5 1.0
CG B:GLU60 4.5 32.2 1.0
CA B:GLU60 4.5 29.2 1.0
CD2 B:HIS63 4.5 44.8 1.0
CG B:GLU25 4.6 32.9 1.0
CD B:GLN139 4.7 30.7 1.0
CB B:GLU60 4.8 28.0 1.0
O B:HOH325 4.9 49.3 1.0
CB B:GLU25 4.9 26.2 1.0

Copper binding site 5 out of 8 in 6kzy

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Copper binding site 5 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:69.4
occ:1.00
 OE2 C:GLU25 2.3 48.9 1.0
OE2 C:GLU60 2.5 41.2 1.0
ND1 C:HIS63 2.6 48.6 1.0
O C:HOH342 2.7 49.9 1.0
OE1 C:GLU60 3.1 55.3 1.0
CD C:GLU60 3.1 40.7 1.0
CD C:GLU25 3.2 36.0 1.0
OE1 C:GLU25 3.5 44.0 1.0
CG C:HIS63 3.5 46.7 1.0
OE1 C:GLN139 3.5 44.7 1.0
CE1 C:HIS63 3.6 50.6 1.0
CB C:HIS63 3.6 28.8 1.0
CG1 C:VAL108 4.3 29.7 1.0
CG C:GLU60 4.5 29.8 1.0
CG C:GLU25 4.6 35.2 1.0
CA C:GLU60 4.6 30.1 1.0
CD C:GLN139 4.6 29.6 1.0
CD2 C:HIS63 4.7 38.6 1.0
NE2 C:HIS63 4.7 58.2 1.0
CB C:GLU25 4.9 26.7 1.0
CB C:GLU60 4.9 27.9 1.0

Copper binding site 6 out of 8 in 6kzy

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Copper binding site 6 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu202

b:52.5
occ:0.33
 OD1 C:ASP129 2.7 28.3 1.0
OE1 C:GLU132 2.8 34.6 1.0
CG C:ASP129 3.8 33.5 1.0
CU C:CU203 3.8 0.3 0.3
CD C:GLU132 4.0 42.1 1.0
CB C:ASP129 4.3 32.4 1.0
O C:HOH324 4.3 0.7 1.0
CA C:ASP129 4.6 29.1 1.0
OE2 C:GLU132 4.6 39.5 1.0
OD2 C:ASP129 4.8 34.0 1.0

Copper binding site 7 out of 8 in 6kzy

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Copper binding site 7 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu203

b:0.3
occ:0.33
 O C:HOH381 2.4 59.6 1.0
O C:HOH308 3.5 62.0 1.0
OE2 C:GLU132 3.7 39.5 1.0
O C:HOH324 3.8 0.7 1.0
CU C:CU202 3.8 52.5 0.3
OE1 C:GLU132 4.0 34.6 1.0
CD C:GLU132 4.3 42.1 1.0

Copper binding site 8 out of 8 in 6kzy

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Copper binding site 8 out of 8 in the Cu(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:72.2
occ:1.00
 OE2 D:GLU25 2.4 48.5 1.0
OE2 D:GLU60 2.6 42.9 1.0
CD2 D:HIS63 2.7 48.8 1.0
O D:HOH323 2.8 50.5 1.0
OE1 D:GLU60 3.1 57.0 1.0
CD D:GLU60 3.2 43.2 1.0
CD D:GLU25 3.3 37.3 1.0
NE2 D:GLN139 3.3 45.1 1.0
CG D:HIS63 3.4 48.3 1.0
OE1 D:GLU25 3.5 40.1 1.0
CB D:HIS63 3.6 29.1 1.0
NE2 D:HIS63 3.8 56.5 1.0
CG1 D:VAL108 4.3 28.7 1.0
CG D:GLU60 4.6 30.8 1.0
CG D:GLU25 4.6 33.5 1.0
CD D:GLN139 4.6 31.9 1.0
ND1 D:HIS63 4.6 46.3 1.0
CA D:GLU60 4.6 30.6 1.0
NA D:NA211 4.7 59.8 1.0
CE1 D:HIS63 4.8 59.5 1.0
CB D:GLU60 4.9 28.0 1.0
CB D:GLU25 4.9 28.4 1.0

Reference:

Q.Q.Jiang, X.R.Su, T.H.Ming, H.S.Huan. Crystal Structure Analysis Unravels How CU2+ in CU2+-Ferritin Nanocage Perturb the Functions of Tegillarca Granosa Ferritin To Be Published.
Page generated: Wed Jul 31 06:30:00 2024

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