Copper in PDB 9jqe: Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH with Cu(II)

Enzymatic activity of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH with Cu(II)

All present enzymatic activity of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH with Cu(II):
1.16.3.1;

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Copper atom in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH with Cu(II) (pdb code 9jqe). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 48 binding sites of Copper where determined in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH with Cu(II), PDB code: 9jqe:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 48 in 9jqe

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Copper binding site 1 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:33.2
occ:1.00
 OE1 A:GLU27 2.2 18.1 1.0
ND1 A:HIS65 2.2 14.6 1.0
O A:HOH343 2.5 17.0 1.0
OE1 A:GLU62 2.6 13.9 1.0
OE2 A:GLU62 3.0 23.8 1.0
CD A:GLU27 3.0 10.1 1.0
CD A:GLU62 3.1 7.8 1.0
CE1 A:HIS65 3.2 11.9 1.0
OE2 A:GLU27 3.2 20.1 1.0
CU A:CU202 3.2 56.8 1.0
CG A:HIS65 3.3 12.5 1.0
CB A:HIS65 3.6 8.8 1.0
OE1 A:GLN141 3.7 20.9 1.0
O A:HOH375 4.0 21.1 1.0
NE2 A:HIS65 4.3 13.3 1.0
CG1 A:VAL110 4.3 8.0 1.0
CD2 A:HIS65 4.4 9.7 1.0
CA A:GLU62 4.4 10.7 1.0
CG A:GLU27 4.5 6.2 1.0
CG A:GLU62 4.5 8.8 1.0
CD A:GLN141 4.7 6.6 1.0
CB A:GLU62 4.8 7.9 1.0
O A:HOH405 4.9 21.1 1.0
CB A:GLU27 4.9 5.7 1.0
O A:HOH370 5.0 13.8 1.0
CD2 A:TYR137 5.0 8.4 1.0

Copper binding site 2 out of 48 in 9jqe

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Copper binding site 2 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:56.8
occ:1.00
 OE2 A:GLU62 2.1 23.8 1.0
OE1 A:GLU107 2.3 16.0 1.0
OE2 A:GLU107 2.4 23.3 1.0
O A:HOH370 2.6 13.8 1.0
CD A:GLU107 2.7 10.3 1.0
CD A:GLU62 2.8 7.8 1.0
OE1 A:GLU62 3.0 13.9 1.0
CU A:CU201 3.2 33.2 1.0
OE1 A:GLN141 3.2 20.9 1.0
O A:HOH405 3.6 21.1 1.0
NE2 A:GLN141 4.0 8.1 1.0
CD A:GLN141 4.0 6.6 1.0
CG A:GLU62 4.1 8.8 1.0
CG A:GLU107 4.2 2.3 1.0
ND1 A:HIS65 4.4 14.6 1.0
CE1 A:HIS65 4.4 11.9 1.0
O A:HOH343 4.5 17.0 1.0
CE2 A:TYR34 4.6 6.0 1.0
O A:HOH319 4.8 19.5 1.0
OH A:TYR34 4.8 17.5 1.0
CG1 A:VAL110 4.9 8.0 1.0
OE1 A:GLU27 4.9 18.1 1.0

Copper binding site 3 out of 48 in 9jqe

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Copper binding site 3 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:33.2
occ:1.00
 OE1 B:GLU27 2.2 18.1 1.0
ND1 B:HIS65 2.2 14.6 1.0
O B:HOH343 2.5 17.0 1.0
OE1 B:GLU62 2.6 13.9 1.0
OE2 B:GLU62 3.0 23.8 1.0
CD B:GLU27 3.0 10.1 1.0
CD B:GLU62 3.1 7.8 1.0
CE1 B:HIS65 3.2 11.9 1.0
OE2 B:GLU27 3.2 20.1 1.0
CU B:CU202 3.2 56.8 1.0
CG B:HIS65 3.3 12.5 1.0
CB B:HIS65 3.6 8.8 1.0
OE1 B:GLN141 3.7 20.9 1.0
O B:HOH375 4.0 21.1 1.0
NE2 B:HIS65 4.3 13.3 1.0
CG1 B:VAL110 4.3 8.0 1.0
CD2 B:HIS65 4.4 9.7 1.0
CA B:GLU62 4.4 10.7 1.0
CG B:GLU27 4.5 6.2 1.0
CG B:GLU62 4.5 8.8 1.0
CD B:GLN141 4.7 6.6 1.0
CB B:GLU62 4.8 7.9 1.0
O B:HOH405 4.9 21.1 1.0
CB B:GLU27 4.9 5.7 1.0
O B:HOH370 5.0 13.8 1.0
CD2 B:TYR137 5.0 8.4 1.0

Copper binding site 4 out of 48 in 9jqe

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Copper binding site 4 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:56.8
occ:1.00
 OE2 B:GLU62 2.1 23.8 1.0
OE1 B:GLU107 2.3 16.0 1.0
OE2 B:GLU107 2.4 23.3 1.0
O B:HOH370 2.6 13.8 1.0
CD B:GLU107 2.7 10.3 1.0
CD B:GLU62 2.8 7.8 1.0
OE1 B:GLU62 3.0 13.9 1.0
OE1 B:GLN141 3.2 20.9 1.0
CU B:CU201 3.2 33.2 1.0
O B:HOH405 3.6 21.1 1.0
NE2 B:GLN141 4.0 8.1 1.0
CD B:GLN141 4.0 6.6 1.0
CG B:GLU62 4.1 8.8 1.0
CG B:GLU107 4.2 2.3 1.0
ND1 B:HIS65 4.4 14.6 1.0
CE1 B:HIS65 4.4 11.9 1.0
O B:HOH343 4.5 17.0 1.0
CE2 B:TYR34 4.6 6.0 1.0
O B:HOH319 4.8 19.5 1.0
OH B:TYR34 4.8 17.5 1.0
CG1 B:VAL110 4.9 8.0 1.0
OE1 B:GLU27 4.9 18.1 1.0

Copper binding site 5 out of 48 in 9jqe

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Copper binding site 5 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:33.2
occ:1.00
 OE1 C:GLU27 2.2 18.1 1.0
ND1 C:HIS65 2.2 14.6 1.0
O C:HOH343 2.5 17.0 1.0
OE1 C:GLU62 2.6 13.9 1.0
OE2 C:GLU62 3.0 23.8 1.0
CD C:GLU27 3.0 10.1 1.0
CD C:GLU62 3.1 7.8 1.0
CE1 C:HIS65 3.2 11.9 1.0
OE2 C:GLU27 3.2 20.1 1.0
CU C:CU202 3.2 56.8 1.0
CG C:HIS65 3.3 12.5 1.0
CB C:HIS65 3.6 8.8 1.0
OE1 C:GLN141 3.7 20.9 1.0
O C:HOH375 4.0 21.1 1.0
NE2 C:HIS65 4.3 13.3 1.0
CG1 C:VAL110 4.3 8.0 1.0
CD2 C:HIS65 4.4 9.7 1.0
CA C:GLU62 4.4 10.7 1.0
CG C:GLU27 4.5 6.2 1.0
CG C:GLU62 4.5 8.8 1.0
CD C:GLN141 4.7 6.6 1.0
CB C:GLU62 4.8 7.9 1.0
O C:HOH405 4.9 21.1 1.0
CB C:GLU27 4.9 5.7 1.0
O C:HOH370 5.0 13.8 1.0
CD2 C:TYR137 5.0 8.4 1.0

Copper binding site 6 out of 48 in 9jqe

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Copper binding site 6 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu202

b:56.8
occ:1.00
 OE2 C:GLU62 2.1 23.8 1.0
OE1 C:GLU107 2.3 16.0 1.0
OE2 C:GLU107 2.4 23.3 1.0
O C:HOH370 2.6 13.8 1.0
CD C:GLU107 2.7 10.3 1.0
CD C:GLU62 2.8 7.8 1.0
OE1 C:GLU62 3.0 13.9 1.0
OE1 C:GLN141 3.2 20.9 1.0
CU C:CU201 3.2 33.2 1.0
O C:HOH405 3.6 21.1 1.0
NE2 C:GLN141 4.0 8.1 1.0
CD C:GLN141 4.0 6.6 1.0
CG C:GLU62 4.1 8.8 1.0
CG C:GLU107 4.2 2.3 1.0
ND1 C:HIS65 4.4 14.6 1.0
CE1 C:HIS65 4.4 11.9 1.0
O C:HOH343 4.5 17.0 1.0
CE2 C:TYR34 4.6 6.0 1.0
O C:HOH319 4.8 19.5 1.0
OH C:TYR34 4.8 17.5 1.0
CG1 C:VAL110 4.9 8.0 1.0
OE1 C:GLU27 4.9 18.1 1.0

Copper binding site 7 out of 48 in 9jqe

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Copper binding site 7 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:33.2
occ:1.00
 OE1 D:GLU27 2.2 18.1 1.0
ND1 D:HIS65 2.2 14.6 1.0
O D:HOH343 2.5 17.0 1.0
OE1 D:GLU62 2.6 13.9 1.0
OE2 D:GLU62 3.0 23.8 1.0
CD D:GLU27 3.0 10.1 1.0
CD D:GLU62 3.1 7.8 1.0
CE1 D:HIS65 3.2 11.9 1.0
OE2 D:GLU27 3.2 20.1 1.0
CU D:CU202 3.2 56.8 1.0
CG D:HIS65 3.3 12.5 1.0
CB D:HIS65 3.6 8.8 1.0
OE1 D:GLN141 3.7 20.9 1.0
O D:HOH375 4.0 21.1 1.0
NE2 D:HIS65 4.3 13.3 1.0
CG1 D:VAL110 4.3 8.0 1.0
CD2 D:HIS65 4.4 9.7 1.0
CA D:GLU62 4.4 10.7 1.0
CG D:GLU27 4.5 6.2 1.0
CG D:GLU62 4.5 8.8 1.0
CD D:GLN141 4.7 6.6 1.0
CB D:GLU62 4.8 7.9 1.0
O D:HOH405 4.9 21.1 1.0
CB D:GLU27 4.9 5.7 1.0
O D:HOH370 5.0 13.8 1.0
CD2 D:TYR137 5.0 8.4 1.0

Copper binding site 8 out of 48 in 9jqe

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Copper binding site 8 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu202

b:56.8
occ:1.00
 OE2 D:GLU62 2.1 23.8 1.0
OE1 D:GLU107 2.3 16.0 1.0
OE2 D:GLU107 2.4 23.3 1.0
O D:HOH370 2.6 13.8 1.0
CD D:GLU107 2.7 10.3 1.0
CD D:GLU62 2.8 7.8 1.0
OE1 D:GLU62 3.0 13.9 1.0
OE1 D:GLN141 3.2 20.9 1.0
CU D:CU201 3.2 33.2 1.0
O D:HOH405 3.6 21.1 1.0
NE2 D:GLN141 4.0 8.1 1.0
CD D:GLN141 4.0 6.6 1.0
CG D:GLU62 4.1 8.8 1.0
CG D:GLU107 4.2 2.3 1.0
ND1 D:HIS65 4.4 14.6 1.0
CE1 D:HIS65 4.4 11.9 1.0
O D:HOH343 4.5 17.0 1.0
CE2 D:TYR34 4.6 6.0 1.0
O D:HOH319 4.8 19.5 1.0
OH D:TYR34 4.8 17.5 1.0
CG1 D:VAL110 4.9 8.0 1.0
OE1 D:GLU27 4.9 18.1 1.0

Copper binding site 9 out of 48 in 9jqe

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Copper binding site 9 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu201

b:33.2
occ:1.00
 OE1 E:GLU27 2.2 18.1 1.0
ND1 E:HIS65 2.2 14.6 1.0
O E:HOH343 2.5 17.0 1.0
OE1 E:GLU62 2.6 13.9 1.0
OE2 E:GLU62 3.0 23.8 1.0
CD E:GLU27 3.0 10.1 1.0
CD E:GLU62 3.1 7.8 1.0
CE1 E:HIS65 3.2 11.9 1.0
OE2 E:GLU27 3.2 20.1 1.0
CU E:CU202 3.2 56.8 1.0
CG E:HIS65 3.3 12.5 1.0
CB E:HIS65 3.6 8.8 1.0
OE1 E:GLN141 3.7 20.9 1.0
O E:HOH375 4.0 21.1 1.0
NE2 E:HIS65 4.3 13.3 1.0
CG1 E:VAL110 4.3 8.0 1.0
CD2 E:HIS65 4.4 9.7 1.0
CA E:GLU62 4.4 10.7 1.0
CG E:GLU27 4.5 6.2 1.0
CG E:GLU62 4.5 8.8 1.0
CD E:GLN141 4.7 6.6 1.0
CB E:GLU62 4.8 7.9 1.0
O E:HOH405 4.9 21.1 1.0
CB E:GLU27 4.9 5.7 1.0
O E:HOH370 5.0 13.8 1.0
CD2 E:TYR137 5.0 8.4 1.0

Copper binding site 10 out of 48 in 9jqe

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Copper binding site 10 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH 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 R63MEH/R67MEH with Cu(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu202

b:56.8
occ:1.00
 OE2 E:GLU62 2.1 23.8 1.0
OE1 E:GLU107 2.3 16.0 1.0
OE2 E:GLU107 2.4 23.3 1.0
O E:HOH370 2.6 13.8 1.0
CD E:GLU107 2.7 10.3 1.0
CD E:GLU62 2.8 7.8 1.0
OE1 E:GLU62 3.0 13.9 1.0
OE1 E:GLN141 3.2 20.9 1.0
CU E:CU201 3.2 33.2 1.0
O E:HOH405 3.6 21.1 1.0
NE2 E:GLN141 4.0 8.1 1.0
CD E:GLN141 4.0 6.6 1.0
CG E:GLU62 4.1 8.8 1.0
CG E:GLU107 4.2 2.3 1.0
ND1 E:HIS65 4.4 14.6 1.0
CE1 E:HIS65 4.4 11.9 1.0
O E:HOH343 4.5 17.0 1.0
CE2 E:TYR34 4.6 6.0 1.0
O E:HOH319 4.8 19.5 1.0
OH E:TYR34 4.8 17.5 1.0
CG1 E:VAL110 4.9 8.0 1.0
OE1 E:GLU27 4.9 18.1 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 19:38:03 2024

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