Copper in PDB 6l58: Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)

Enzymatic activity of Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)

All present enzymatic activity of Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II):
1.16.3.1;

Protein crystallography data

The structure of Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II), PDB code: 6l58 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) 36.40 / 3.90
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 217.288, 217.288, 134.083, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 26.4

Copper Binding Sites:

The binding sites of Copper atom in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II) (pdb code 6l58). 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 M-Ferritin Soaked with Fe(II), PDB code: 6l58:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6l58

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Copper binding site 1 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:0.7
occ:1.00
 OE2 A:GLU25 2.8 85.3 1.0
ND1 A:HIS63 2.9 99.0 1.0
NE2 A:GLN139 2.9 89.8 1.0
OE1 A:GLU60 2.9 0.0 1.0
OE2 A:GLU60 3.0 94.3 1.0
CD A:GLU60 3.3 0.4 1.0
CG A:HIS63 3.5 92.2 1.0
CE1 A:HIS63 3.6 99.0 1.0
CD A:GLU25 3.7 82.8 1.0
CB A:HIS63 3.7 84.0 1.0
OE1 A:GLU25 3.8 80.2 1.0
CD A:GLN139 4.2 79.8 1.0
CD1 A:TYR135 4.3 72.8 1.0
CG1 A:VAL108 4.4 72.3 1.0
CD2 A:HIS63 4.4 88.8 1.0
NE2 A:HIS63 4.5 93.3 1.0
CE1 A:TYR135 4.6 75.7 1.0
OE1 A:GLU105 4.6 97.9 1.0
CG A:GLU60 4.7 88.8 1.0
CG A:GLN139 4.8 78.4 1.0

Copper binding site 2 out of 8 in 6l58

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Copper binding site 2 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:0.2
occ:1.00
 OE1 A:GLU132 3.4 75.6 1.0
OE1 C:GLU132 3.6 78.4 1.0
CE C:MET128 3.6 86.5 1.0
CU B:CU201 3.9 100.0 1.0
OE2 A:GLU132 4.1 77.2 1.0
OE2 B:GLU132 4.1 88.8 1.0
CD A:GLU132 4.2 78.1 1.0
OE1 B:GLU132 4.2 75.2 1.0
OE2 C:GLU132 4.3 82.4 1.0
OD1 C:ASP129 4.3 95.5 1.0
CD C:GLU132 4.3 79.4 1.0
CD B:GLU132 4.6 79.0 1.0
CE A:MET128 4.7 75.4 1.0
CE B:MET128 4.7 78.1 1.0

Copper binding site 3 out of 8 in 6l58

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Copper binding site 3 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:100.0
occ:1.00
 OE1 C:GLU132 2.4 78.4 1.0
OD1 B:ASP129 2.5 88.2 1.0
OD1 C:ASP129 2.6 95.5 1.0
OE2 B:GLU132 2.9 88.8 1.0
OE1 A:GLU132 3.0 75.6 1.0
OD1 A:ASP129 3.1 94.5 1.0
CD B:GLU132 3.1 79.0 1.0
CG C:ASP129 3.3 90.2 1.0
OE1 B:GLU132 3.4 75.2 1.0
OD2 C:ASP129 3.5 85.7 1.0
CD C:GLU132 3.6 79.4 1.0
CG B:ASP129 3.7 84.8 1.0
CU A:CU202 3.9 0.2 1.0
CG B:GLU132 4.0 80.9 1.0
CG A:ASP129 4.1 93.6 1.0
CD A:GLU132 4.1 78.1 1.0
CB A:ASP129 4.3 77.7 1.0
CG C:GLU132 4.3 76.1 1.0
OE2 C:GLU132 4.5 82.4 1.0
CA A:ASP129 4.5 76.6 1.0
OD2 B:ASP129 4.5 95.7 1.0
CB B:ASP129 4.5 72.7 1.0
CB C:ASP129 4.6 80.4 1.0
CA B:ASP129 4.6 77.1 1.0
CA C:ASP129 4.8 81.5 1.0
OE2 A:GLU132 4.8 77.2 1.0
CG A:GLU132 4.9 82.7 1.0

Copper binding site 4 out of 8 in 6l58

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Copper binding site 4 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:0.8
occ:1.00
 OE2 B:GLU60 2.1 0.8 1.0
CD B:GLU60 2.9 0.2 1.0
OE1 B:GLU60 3.0 0.6 1.0
OE2 B:GLU25 3.0 93.4 1.0
CD2 B:HIS63 3.1 78.9 1.0
NE2 B:GLN139 3.3 83.4 1.0
OE1 B:GLU25 3.3 88.3 1.0
CD B:GLU25 3.5 93.2 1.0
OE1 B:GLN139 4.0 94.6 1.0
CG B:HIS63 4.0 76.9 1.0
NE2 B:HIS63 4.0 89.9 1.0
CD B:GLN139 4.1 82.1 1.0
OE1 B:GLU105 4.2 95.1 1.0
CG1 B:VAL108 4.3 79.4 1.0
CB B:HIS63 4.3 74.1 1.0
CG B:GLU60 4.4 91.1 1.0
CB B:GLU60 4.9 78.8 1.0
CD1 B:TYR135 5.0 79.3 1.0

Copper binding site 5 out of 8 in 6l58

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Copper binding site 5 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:0.4
occ:1.00
 OE1 C:GLU60 2.4 0.1 1.0
OE2 C:GLU60 2.7 93.6 1.0
CD C:GLU60 2.8 1.0 1.0
OE2 C:GLU25 2.9 88.5 1.0
ND1 C:HIS63 3.1 77.8 1.0
NE2 C:GLN139 3.4 83.6 1.0
OE1 C:GLU25 3.5 78.3 1.0
CD C:GLU25 3.6 84.8 1.0
CE1 C:HIS63 3.8 85.1 1.0
CG C:HIS63 3.8 80.8 1.0
CB C:HIS63 4.1 79.3 1.0
OE1 C:GLU105 4.2 90.6 1.0
CG C:GLU60 4.3 88.7 1.0
CD C:GLN139 4.5 74.7 1.0
CA C:GLU60 4.6 77.2 1.0
NE2 C:HIS63 4.7 85.7 1.0
OE2 C:GLU105 4.7 0.1 1.0
CD2 C:HIS63 4.7 84.9 1.0
CB C:GLU60 4.7 78.9 1.0
CG1 C:VAL108 4.9 71.5 1.0
CD C:GLU105 4.9 97.1 1.0

Copper binding site 6 out of 8 in 6l58

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Copper binding site 6 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:0.3
occ:1.00
 OE2 D:GLU60 2.1 0.8 1.0
OE2 D:GLU25 2.7 83.8 1.0
CD D:GLU60 2.8 99.2 1.0
CD2 D:HIS63 2.8 90.1 1.0
OE1 D:GLU60 2.8 92.5 1.0
NE2 D:GLN139 2.9 0.3 1.0
OE1 D:GLU25 3.1 93.1 1.0
CD D:GLU25 3.3 86.3 1.0
NE2 D:HIS63 3.6 99.1 1.0
CG D:HIS63 3.7 85.2 1.0
OE1 D:GLU105 4.0 91.2 1.0
CG1 D:VAL108 4.0 69.5 1.0
CD D:GLN139 4.1 89.3 1.0
CG D:GLU60 4.3 91.0 1.0
CB D:HIS63 4.3 88.1 1.0
CE1 D:HIS63 4.6 94.8 1.0
ND1 D:HIS63 4.7 79.5 1.0
CB D:GLU60 4.8 80.3 1.0
CG D:GLU25 4.8 75.7 1.0
OE1 D:GLN139 4.9 87.4 1.0
CD D:GLU105 4.9 95.5 1.0
CA D:GLU60 4.9 76.0 1.0
OE2 D:GLU105 5.0 87.6 1.0

Copper binding site 7 out of 8 in 6l58

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Copper binding site 7 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu202

b:89.4
occ:0.34
 CU D:CU203 3.6 94.7 0.3
OE2 D:GLU132 3.9 80.0 1.0
OE1 D:GLU132 4.3 74.7 1.0
CD D:GLU132 4.5 79.5 1.0
SD D:MET128 4.5 100.0 1.0

Copper binding site 8 out of 8 in 6l58

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Copper binding site 8 out of 8 in the Cu(II) Loaded Tegillarca Granosa M-Ferritin Soaked with Fe(II)


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 M-Ferritin Soaked with Fe(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu203

b:94.7
occ:0.33
 OE2 D:GLU132 2.3 80.0 1.0
OD1 D:ASP129 2.7 93.6 1.0
CD D:GLU132 3.5 79.5 1.0
CU D:CU202 3.6 89.4 0.3
CG D:ASP129 3.7 92.5 1.0
CG D:GLU132 4.3 86.8 1.0
OE1 D:GLU132 4.3 74.7 1.0
OD2 D:ASP129 4.5 94.8 1.0
CB D:ASP129 4.6 83.4 1.0
O D:HOH301 4.6 0.9 0.3
CA D:ASP129 4.7 82.8 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 06:38:04 2024

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