Copper in PDB 9jqc: Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)

Enzymatic activity of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)

All present enzymatic activity of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II):
1.16.3.1;

Other elements in 9jqc:

The structure of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) also contains other interesting chemical elements:

Bromine (Br) 48 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Copper atom in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) (pdb code 9jqc). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II), PDB code: 9jqc:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in 9jqc

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Copper binding site 1 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:42.0
occ:1.00
 ND1 A:HIS65 2.1 12.1 1.0
OE1 A:GLU27 2.1 15.1 1.0
O A:HOH330 2.2 16.2 1.0
O A:HOH303 2.5 20.4 1.0
OE1 A:GLU62 2.5 17.1 1.0
OE2 A:GLU62 2.9 23.1 1.0
CD A:GLU62 3.0 8.6 1.0
CD A:GLU27 3.1 10.1 1.0
CE1 A:HIS65 3.1 14.2 1.0
CG A:HIS65 3.1 11.8 1.0
OE2 A:GLU27 3.3 16.9 1.0
CB A:HIS65 3.4 5.8 1.0
O A:HOH392 3.5 22.3 1.0
OE1 A:GLN141 3.9 17.9 1.0
NE2 A:HIS65 4.2 13.7 1.0
CD2 A:HIS65 4.2 11.4 1.0
CG A:GLU62 4.4 10.3 1.0
CA A:GLU62 4.4 8.0 1.0
O A:HOH321 4.4 18.4 1.0
CG1 A:VAL110 4.4 9.5 1.0
CG A:GLU27 4.4 5.1 1.0
CB A:GLU62 4.7 10.0 1.0
CD A:GLN141 4.8 10.1 1.0
CB A:GLU27 4.8 9.8 1.0
O A:GLU62 4.9 5.0 1.0
CA A:HIS65 4.9 5.5 1.0
CD2 A:TYR137 5.0 7.9 1.0
O A:HOH327 5.0 18.9 1.0

Copper binding site 2 out of 24 in 9jqc

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Copper binding site 2 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:42.0
occ:1.00
 ND1 B:HIS65 2.1 12.1 1.0
OE1 B:GLU27 2.1 15.1 1.0
O B:HOH330 2.2 16.2 1.0
O B:HOH303 2.5 20.4 1.0
OE1 B:GLU62 2.5 17.1 1.0
OE2 B:GLU62 2.9 23.1 1.0
CD B:GLU62 3.0 8.6 1.0
CD B:GLU27 3.1 10.1 1.0
CE1 B:HIS65 3.1 14.2 1.0
CG B:HIS65 3.1 11.8 1.0
OE2 B:GLU27 3.3 16.9 1.0
CB B:HIS65 3.4 5.8 1.0
O B:HOH392 3.5 22.3 1.0
OE1 B:GLN141 3.9 17.9 1.0
NE2 B:HIS65 4.2 13.7 1.0
CD2 B:HIS65 4.2 11.4 1.0
CG B:GLU62 4.4 10.3 1.0
CA B:GLU62 4.4 8.0 1.0
O B:HOH321 4.4 18.4 1.0
CG1 B:VAL110 4.4 9.5 1.0
CG B:GLU27 4.4 5.1 1.0
CB B:GLU62 4.7 10.0 1.0
CD B:GLN141 4.8 10.1 1.0
CB B:GLU27 4.8 9.8 1.0
O B:GLU62 4.9 5.0 1.0
CA B:HIS65 4.9 5.5 1.0
CD2 B:TYR137 5.0 7.9 1.0
O B:HOH327 5.0 18.9 1.0

Copper binding site 3 out of 24 in 9jqc

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Copper binding site 3 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:42.0
occ:1.00
 ND1 C:HIS65 2.1 12.1 1.0
OE1 C:GLU27 2.1 15.1 1.0
O C:HOH330 2.2 16.2 1.0
O C:HOH303 2.5 20.4 1.0
OE1 C:GLU62 2.5 17.1 1.0
OE2 C:GLU62 2.9 23.1 1.0
CD C:GLU62 3.0 8.6 1.0
CD C:GLU27 3.1 10.1 1.0
CE1 C:HIS65 3.1 14.2 1.0
CG C:HIS65 3.1 11.8 1.0
OE2 C:GLU27 3.3 16.9 1.0
CB C:HIS65 3.4 5.8 1.0
O C:HOH392 3.5 22.3 1.0
OE1 C:GLN141 3.9 17.9 1.0
NE2 C:HIS65 4.2 13.7 1.0
CD2 C:HIS65 4.2 11.4 1.0
CG C:GLU62 4.4 10.3 1.0
CA C:GLU62 4.4 8.0 1.0
O C:HOH321 4.4 18.4 1.0
CG1 C:VAL110 4.4 9.5 1.0
CG C:GLU27 4.4 5.1 1.0
CB C:GLU62 4.7 10.0 1.0
CD C:GLN141 4.8 10.1 1.0
CB C:GLU27 4.8 9.8 1.0
O C:GLU62 4.9 5.0 1.0
CA C:HIS65 4.9 5.5 1.0
CD2 C:TYR137 5.0 7.9 1.0
O C:HOH327 5.0 18.9 1.0

Copper binding site 4 out of 24 in 9jqc

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Copper binding site 4 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:42.0
occ:1.00
 ND1 D:HIS65 2.1 12.1 1.0
OE1 D:GLU27 2.1 15.1 1.0
O D:HOH330 2.2 16.2 1.0
O D:HOH303 2.5 20.4 1.0
OE1 D:GLU62 2.5 17.1 1.0
OE2 D:GLU62 2.9 23.1 1.0
CD D:GLU62 3.0 8.6 1.0
CD D:GLU27 3.1 10.1 1.0
CE1 D:HIS65 3.1 14.2 1.0
CG D:HIS65 3.1 11.8 1.0
OE2 D:GLU27 3.3 16.9 1.0
CB D:HIS65 3.4 5.8 1.0
O D:HOH392 3.5 22.3 1.0
OE1 D:GLN141 3.9 17.9 1.0
NE2 D:HIS65 4.2 13.7 1.0
CD2 D:HIS65 4.2 11.4 1.0
CG D:GLU62 4.4 10.3 1.0
CA D:GLU62 4.4 8.0 1.0
O D:HOH321 4.4 18.4 1.0
CG1 D:VAL110 4.4 9.5 1.0
CG D:GLU27 4.4 5.1 1.0
CB D:GLU62 4.7 10.0 1.0
CD D:GLN141 4.8 10.1 1.0
CB D:GLU27 4.8 9.8 1.0
O D:GLU62 4.9 5.0 1.0
CA D:HIS65 4.9 5.5 1.0
CD2 D:TYR137 5.0 7.9 1.0
O D:HOH327 5.0 18.9 1.0

Copper binding site 5 out of 24 in 9jqc

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Copper binding site 5 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu201

b:42.0
occ:1.00
 ND1 E:HIS65 2.1 12.1 1.0
OE1 E:GLU27 2.1 15.1 1.0
O E:HOH330 2.2 16.2 1.0
O E:HOH303 2.5 20.4 1.0
OE1 E:GLU62 2.5 17.1 1.0
OE2 E:GLU62 2.9 23.1 1.0
CD E:GLU62 3.0 8.6 1.0
CD E:GLU27 3.1 10.1 1.0
CE1 E:HIS65 3.1 14.2 1.0
CG E:HIS65 3.1 11.8 1.0
OE2 E:GLU27 3.3 16.9 1.0
CB E:HIS65 3.4 5.8 1.0
O E:HOH392 3.5 22.3 1.0
OE1 E:GLN141 3.9 17.9 1.0
NE2 E:HIS65 4.2 13.7 1.0
CD2 E:HIS65 4.2 11.4 1.0
CG E:GLU62 4.4 10.3 1.0
CA E:GLU62 4.4 8.0 1.0
O E:HOH321 4.4 18.4 1.0
CG1 E:VAL110 4.4 9.5 1.0
CG E:GLU27 4.4 5.1 1.0
CB E:GLU62 4.7 10.0 1.0
CD E:GLN141 4.8 10.1 1.0
CB E:GLU27 4.8 9.8 1.0
O E:GLU62 4.9 5.0 1.0
CA E:HIS65 4.9 5.5 1.0
CD2 E:TYR137 5.0 7.9 1.0
O E:HOH327 5.0 18.9 1.0

Copper binding site 6 out of 24 in 9jqc

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Copper binding site 6 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu201

b:42.0
occ:1.00
 ND1 F:HIS65 2.1 12.1 1.0
OE1 F:GLU27 2.1 15.1 1.0
O F:HOH330 2.2 16.2 1.0
O F:HOH303 2.5 20.4 1.0
OE1 F:GLU62 2.5 17.1 1.0
OE2 F:GLU62 2.9 23.1 1.0
CD F:GLU62 3.0 8.6 1.0
CD F:GLU27 3.1 10.1 1.0
CE1 F:HIS65 3.1 14.2 1.0
CG F:HIS65 3.1 11.8 1.0
OE2 F:GLU27 3.3 16.9 1.0
CB F:HIS65 3.4 5.8 1.0
O F:HOH392 3.5 22.3 1.0
OE1 F:GLN141 3.9 17.9 1.0
NE2 F:HIS65 4.2 13.7 1.0
CD2 F:HIS65 4.2 11.4 1.0
CG F:GLU62 4.4 10.3 1.0
CA F:GLU62 4.4 8.0 1.0
O F:HOH321 4.4 18.4 1.0
CG1 F:VAL110 4.4 9.5 1.0
CG F:GLU27 4.4 5.1 1.0
CB F:GLU62 4.7 10.0 1.0
CD F:GLN141 4.8 10.1 1.0
CB F:GLU27 4.8 9.8 1.0
O F:GLU62 4.9 5.0 1.0
CA F:HIS65 4.9 5.5 1.0
CD2 F:TYR137 5.0 7.9 1.0
O F:HOH327 5.0 18.9 1.0

Copper binding site 7 out of 24 in 9jqc

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Copper binding site 7 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu201

b:42.0
occ:1.00
 ND1 G:HIS65 2.1 12.1 1.0
OE1 G:GLU27 2.1 15.1 1.0
O G:HOH330 2.2 16.2 1.0
O G:HOH303 2.5 20.4 1.0
OE1 G:GLU62 2.5 17.1 1.0
OE2 G:GLU62 2.9 23.1 1.0
CD G:GLU62 3.0 8.6 1.0
CD G:GLU27 3.1 10.1 1.0
CE1 G:HIS65 3.1 14.2 1.0
CG G:HIS65 3.1 11.8 1.0
OE2 G:GLU27 3.3 16.9 1.0
CB G:HIS65 3.4 5.8 1.0
O G:HOH392 3.5 22.3 1.0
OE1 G:GLN141 3.9 17.9 1.0
NE2 G:HIS65 4.2 13.7 1.0
CD2 G:HIS65 4.2 11.4 1.0
CG G:GLU62 4.4 10.3 1.0
CA G:GLU62 4.4 8.0 1.0
O G:HOH321 4.4 18.4 1.0
CG1 G:VAL110 4.4 9.5 1.0
CG G:GLU27 4.4 5.1 1.0
CB G:GLU62 4.7 10.0 1.0
CD G:GLN141 4.8 10.1 1.0
CB G:GLU27 4.8 9.8 1.0
O G:GLU62 4.9 5.0 1.0
CA G:HIS65 4.9 5.5 1.0
CD2 G:TYR137 5.0 7.9 1.0
O G:HOH327 5.0 18.9 1.0

Copper binding site 8 out of 24 in 9jqc

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Copper binding site 8 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu201

b:42.0
occ:1.00
 ND1 H:HIS65 2.1 12.1 1.0
OE1 H:GLU27 2.1 15.1 1.0
O H:HOH330 2.2 16.2 1.0
O H:HOH303 2.5 20.4 1.0
OE1 H:GLU62 2.5 17.1 1.0
OE2 H:GLU62 2.9 23.1 1.0
CD H:GLU62 3.0 8.6 1.0
CD H:GLU27 3.1 10.1 1.0
CE1 H:HIS65 3.1 14.2 1.0
CG H:HIS65 3.1 11.8 1.0
OE2 H:GLU27 3.3 16.9 1.0
CB H:HIS65 3.4 5.8 1.0
O H:HOH392 3.5 22.3 1.0
OE1 H:GLN141 3.9 17.9 1.0
NE2 H:HIS65 4.2 13.7 1.0
CD2 H:HIS65 4.2 11.4 1.0
CG H:GLU62 4.4 10.3 1.0
CA H:GLU62 4.4 8.0 1.0
O H:HOH321 4.4 18.4 1.0
CG1 H:VAL110 4.4 9.5 1.0
CG H:GLU27 4.4 5.1 1.0
CB H:GLU62 4.7 10.0 1.0
CD H:GLN141 4.8 10.1 1.0
CB H:GLU27 4.8 9.8 1.0
O H:GLU62 4.9 5.0 1.0
CA H:HIS65 4.9 5.5 1.0
CD2 H:TYR137 5.0 7.9 1.0
O H:HOH327 5.0 18.9 1.0

Copper binding site 9 out of 24 in 9jqc

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Copper binding site 9 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu201

b:42.0
occ:1.00
 ND1 I:HIS65 2.1 12.1 1.0
OE1 I:GLU27 2.1 15.1 1.0
O I:HOH330 2.2 16.2 1.0
O I:HOH303 2.5 20.4 1.0
OE1 I:GLU62 2.5 17.1 1.0
OE2 I:GLU62 2.9 23.1 1.0
CD I:GLU62 3.0 8.6 1.0
CD I:GLU27 3.1 10.1 1.0
CE1 I:HIS65 3.1 14.2 1.0
CG I:HIS65 3.1 11.8 1.0
OE2 I:GLU27 3.3 16.9 1.0
CB I:HIS65 3.4 5.8 1.0
O I:HOH392 3.5 22.3 1.0
OE1 I:GLN141 3.9 17.9 1.0
NE2 I:HIS65 4.2 13.7 1.0
CD2 I:HIS65 4.2 11.4 1.0
CG I:GLU62 4.4 10.3 1.0
CA I:GLU62 4.4 8.0 1.0
O I:HOH321 4.4 18.4 1.0
CG1 I:VAL110 4.4 9.5 1.0
CG I:GLU27 4.4 5.1 1.0
CB I:GLU62 4.7 10.0 1.0
CD I:GLN141 4.8 10.1 1.0
CB I:GLU27 4.8 9.8 1.0
O I:GLU62 4.9 5.0 1.0
CA I:HIS65 4.9 5.5 1.0
CD2 I:TYR137 5.0 7.9 1.0
O I:HOH327 5.0 18.9 1.0

Copper binding site 10 out of 24 in 9jqc

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Copper binding site 10 out of 24 in the Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Cryo-Em Structure of Ferritin Variant R63BRTHA/E67BRTHA with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu201

b:42.0
occ:1.00
 ND1 J:HIS65 2.1 12.1 1.0
OE1 J:GLU27 2.1 15.1 1.0
O J:HOH330 2.2 16.2 1.0
O J:HOH303 2.5 20.4 1.0
OE1 J:GLU62 2.5 17.1 1.0
OE2 J:GLU62 2.9 23.1 1.0
CD J:GLU62 3.0 8.6 1.0
CD J:GLU27 3.1 10.1 1.0
CE1 J:HIS65 3.1 14.2 1.0
CG J:HIS65 3.1 11.8 1.0
OE2 J:GLU27 3.3 16.9 1.0
CB J:HIS65 3.4 5.8 1.0
O J:HOH392 3.5 22.3 1.0
OE1 J:GLN141 3.9 17.9 1.0
NE2 J:HIS65 4.2 13.7 1.0
CD2 J:HIS65 4.2 11.4 1.0
CG J:GLU62 4.4 10.3 1.0
CA J:GLU62 4.4 8.0 1.0
O J:HOH321 4.4 18.4 1.0
CG1 J:VAL110 4.4 9.5 1.0
CG J:GLU27 4.4 5.1 1.0
CB J:GLU62 4.7 10.0 1.0
CD J:GLN141 4.8 10.1 1.0
CB J:GLU27 4.8 9.8 1.0
O J:GLU62 4.9 5.0 1.0
CA J:HIS65 4.9 5.5 1.0
CD2 J:TYR137 5.0 7.9 1.0
O J:HOH327 5.0 18.9 1.0

Reference:

J.C.Tsou, C.J.Tsou, C.H.Wang, A.A.Ko, Y.H.Wang, H.H.Liang, J.C.Sun, K.F.Huang, T.P.Ko, S.Y.Lin, Y.S.Wang. Site-Specific Histidine Aza-Michael Addition in Proteins Enabled By A Ferritin-Based Metalloenzyme. J.Am.Chem.Soc. 2024.
ISSN: ESSN 1520-5126
PubMed: 39499210
DOI: 10.1021/JACS.4C14446
Page generated: Tue Dec 10 19:38:00 2024

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