Iron in PDB 9jqd: Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH

Enzymatic activity of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH

All present enzymatic activity of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH:
1.16.3.1;

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

Iron binding site 1 out of 48 in 9jqd

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Iron binding site 1 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:41.1
occ:1.00
 OE1 A:GLU27 2.2 17.3 1.0
ND1 A:HIS65 2.3 15.1 1.0
O A:HOH359 2.3 11.0 1.0
OE1 A:GLU62 2.4 12.2 1.0
CD A:GLU62 3.0 12.6 1.0
CD A:GLU27 3.0 11.5 1.0
OE2 A:GLU62 3.1 20.2 1.0
OE2 A:GLU27 3.2 17.6 1.0
CE1 A:HIS65 3.2 12.6 1.0
CG A:HIS65 3.3 12.7 1.0
CB A:HIS65 3.6 10.0 1.0
OE1 A:GLN141 3.7 16.5 1.0
O A:HOH370 4.0 18.2 1.0
CG1 A:VAL110 4.3 7.0 1.0
NE2 A:HIS65 4.4 15.6 1.0
CG A:GLU62 4.4 8.1 1.0
CA A:GLU62 4.4 8.8 1.0
CD2 A:HIS65 4.4 10.1 1.0
CG A:GLU27 4.5 6.4 1.0
CD A:GLN141 4.7 7.4 1.0
CB A:GLU62 4.7 9.1 1.0
O A:HOH363 4.8 18.3 1.0
CB A:GLU27 4.9 7.4 1.0
O A:GLU62 5.0 8.3 1.0

Iron binding site 2 out of 48 in 9jqd

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Iron binding site 2 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:50.7
occ:1.00
 NE2 V:MHS63 2.9 16.5 1.0
ND1 A:HIS60 3.0 19.2 0.5
OG A:SER59 3.0 11.3 1.0
CE1 A:HIS60 3.1 15.9 0.5
CE1 V:MHS67 3.4 12.5 1.0
NE2 V:MHS67 3.6 14.7 1.0
CB A:SER59 3.7 6.2 1.0
CD2 V:MHS63 3.7 16.8 1.0
CE1 V:MHS63 3.9 15.5 1.0
CD1 A:LEU35 4.2 7.1 1.0
N A:HIS60 4.2 3.9 0.5
C A:SER59 4.2 3.5 1.0
N A:HIS60 4.2 3.9 0.5
CG A:HIS60 4.3 13.7 0.5
CD1 A:LEU56 4.4 4.6 1.0
OG A:SER31 4.4 15.7 1.0
O A:HOH399 4.4 16.1 1.0
NE2 A:HIS60 4.4 16.5 0.5
O A:SER59 4.5 13.6 1.0
CA A:SER59 4.6 4.8 1.0
CA A:HIS60 4.6 9.8 0.5
CA A:HIS60 4.6 9.8 0.5
ND1 V:MHS67 4.7 14.9 1.0
O A:LEU56 4.8 7.3 1.0
CB A:LEU35 4.9 0.3 1.0
CG V:MHS63 4.9 12.2 1.0
CG A:LEU35 4.9 4.1 1.0
CD2 V:MHS67 4.9 6.6 1.0
CD2 A:LEU35 4.9 4.8 1.0
ND1 V:MHS63 5.0 16.4 1.0

Iron binding site 3 out of 48 in 9jqd

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Iron binding site 3 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:41.1
occ:1.00
 OE1 B:GLU27 2.2 17.3 1.0
ND1 B:HIS65 2.3 15.1 1.0
O B:HOH359 2.3 11.0 1.0
OE1 B:GLU62 2.4 12.2 1.0
CD B:GLU62 3.0 12.6 1.0
CD B:GLU27 3.0 11.5 1.0
OE2 B:GLU62 3.1 20.2 1.0
OE2 B:GLU27 3.2 17.6 1.0
CE1 B:HIS65 3.2 12.6 1.0
CG B:HIS65 3.3 12.7 1.0
CB B:HIS65 3.6 10.0 1.0
OE1 B:GLN141 3.7 16.5 1.0
O B:HOH370 4.0 18.2 1.0
CG1 B:VAL110 4.3 7.0 1.0
NE2 B:HIS65 4.4 15.6 1.0
CG B:GLU62 4.4 8.1 1.0
CA B:GLU62 4.4 8.8 1.0
CD2 B:HIS65 4.4 10.1 1.0
CG B:GLU27 4.5 6.4 1.0
CD B:GLN141 4.7 7.4 1.0
CB B:GLU62 4.7 9.1 1.0
O B:HOH363 4.8 18.3 1.0
CB B:GLU27 4.9 7.4 1.0
O B:GLU62 5.0 8.3 1.0

Iron binding site 4 out of 48 in 9jqd

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Iron binding site 4 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:50.7
occ:1.00
 NE2 X:MHS63 2.9 16.5 1.0
ND1 B:HIS60 3.0 19.2 0.5
OG B:SER59 3.0 11.3 1.0
CE1 B:HIS60 3.1 15.9 0.5
CE1 X:MHS67 3.4 12.5 1.0
NE2 X:MHS67 3.6 14.7 1.0
CB B:SER59 3.7 6.2 1.0
CD2 X:MHS63 3.7 16.8 1.0
CE1 X:MHS63 3.9 15.5 1.0
CD1 B:LEU35 4.2 7.1 1.0
N B:HIS60 4.2 3.9 0.5
C B:SER59 4.2 3.5 1.0
N B:HIS60 4.2 3.9 0.5
CG B:HIS60 4.3 13.7 0.5
CD1 B:LEU56 4.4 4.6 1.0
OG B:SER31 4.4 15.7 1.0
O B:HOH399 4.4 16.1 1.0
NE2 B:HIS60 4.4 16.5 0.5
O B:SER59 4.5 13.6 1.0
CA B:SER59 4.6 4.8 1.0
CA B:HIS60 4.6 9.8 0.5
CA B:HIS60 4.6 9.8 0.5
ND1 X:MHS67 4.7 14.9 1.0
O B:LEU56 4.8 7.3 1.0
CB B:LEU35 4.9 0.3 1.0
CG X:MHS63 4.9 12.2 1.0
CG B:LEU35 4.9 4.1 1.0
CD2 X:MHS67 4.9 6.6 1.0
CD2 B:LEU35 4.9 4.8 1.0
ND1 X:MHS63 5.0 16.4 1.0

Iron binding site 5 out of 48 in 9jqd

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Iron binding site 5 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:41.1
occ:1.00
 OE1 C:GLU27 2.2 17.3 1.0
ND1 C:HIS65 2.3 15.1 1.0
O C:HOH359 2.3 11.0 1.0
OE1 C:GLU62 2.4 12.2 1.0
CD C:GLU62 3.0 12.6 1.0
CD C:GLU27 3.0 11.5 1.0
OE2 C:GLU62 3.1 20.2 1.0
OE2 C:GLU27 3.2 17.6 1.0
CE1 C:HIS65 3.2 12.6 1.0
CG C:HIS65 3.3 12.7 1.0
CB C:HIS65 3.6 10.0 1.0
OE1 C:GLN141 3.7 16.5 1.0
O C:HOH370 4.0 18.2 1.0
CG1 C:VAL110 4.3 7.0 1.0
NE2 C:HIS65 4.4 15.6 1.0
CG C:GLU62 4.4 8.1 1.0
CA C:GLU62 4.4 8.8 1.0
CD2 C:HIS65 4.4 10.1 1.0
CG C:GLU27 4.5 6.4 1.0
CD C:GLN141 4.7 7.4 1.0
CB C:GLU62 4.7 9.1 1.0
O C:HOH363 4.8 18.3 1.0
CB C:GLU27 4.9 7.4 1.0
O C:GLU62 5.0 8.3 1.0

Iron binding site 6 out of 48 in 9jqd

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Iron binding site 6 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:50.7
occ:1.00
 NE2 L:MHS63 2.9 16.5 1.0
ND1 C:HIS60 3.0 19.2 0.5
OG C:SER59 3.0 11.3 1.0
CE1 C:HIS60 3.1 15.9 0.5
CE1 L:MHS67 3.4 12.5 1.0
NE2 L:MHS67 3.6 14.7 1.0
CB C:SER59 3.7 6.2 1.0
CD2 L:MHS63 3.7 16.8 1.0
CE1 L:MHS63 3.9 15.5 1.0
CD1 C:LEU35 4.2 7.1 1.0
N C:HIS60 4.2 3.9 0.5
C C:SER59 4.2 3.5 1.0
N C:HIS60 4.2 3.9 0.5
CG C:HIS60 4.3 13.7 0.5
CD1 C:LEU56 4.4 4.6 1.0
OG C:SER31 4.4 15.7 1.0
O C:HOH399 4.4 16.1 1.0
NE2 C:HIS60 4.4 16.5 0.5
O C:SER59 4.5 13.6 1.0
CA C:SER59 4.6 4.8 1.0
CA C:HIS60 4.6 9.8 0.5
CA C:HIS60 4.6 9.8 0.5
ND1 L:MHS67 4.7 14.9 1.0
O C:LEU56 4.8 7.3 1.0
CB C:LEU35 4.9 0.3 1.0
CG L:MHS63 4.9 12.2 1.0
CG C:LEU35 4.9 4.1 1.0
CD2 L:MHS67 4.9 6.6 1.0
CD2 C:LEU35 4.9 4.8 1.0
ND1 L:MHS63 5.0 16.4 1.0

Iron binding site 7 out of 48 in 9jqd

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Iron binding site 7 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:41.1
occ:1.00
 OE1 D:GLU27 2.2 17.3 1.0
ND1 D:HIS65 2.3 15.1 1.0
O D:HOH359 2.3 11.0 1.0
OE1 D:GLU62 2.4 12.2 1.0
CD D:GLU62 3.0 12.6 1.0
CD D:GLU27 3.0 11.5 1.0
OE2 D:GLU62 3.1 20.2 1.0
OE2 D:GLU27 3.2 17.6 1.0
CE1 D:HIS65 3.2 12.6 1.0
CG D:HIS65 3.3 12.7 1.0
CB D:HIS65 3.6 10.0 1.0
OE1 D:GLN141 3.7 16.5 1.0
O D:HOH370 4.0 18.2 1.0
CG1 D:VAL110 4.3 7.0 1.0
NE2 D:HIS65 4.4 15.6 1.0
CG D:GLU62 4.4 8.1 1.0
CA D:GLU62 4.4 8.8 1.0
CD2 D:HIS65 4.4 10.1 1.0
CG D:GLU27 4.5 6.4 1.0
CD D:GLN141 4.7 7.4 1.0
CB D:GLU62 4.7 9.1 1.0
O D:HOH363 4.8 18.3 1.0
CB D:GLU27 4.9 7.4 1.0
O D:GLU62 5.0 8.3 1.0

Iron binding site 8 out of 48 in 9jqd

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Iron binding site 8 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:50.7
occ:1.00
 NE2 N:MHS63 2.9 16.5 1.0
ND1 D:HIS60 3.0 19.2 0.5
OG D:SER59 3.0 11.3 1.0
CE1 D:HIS60 3.1 15.9 0.5
CE1 N:MHS67 3.4 12.5 1.0
NE2 N:MHS67 3.6 14.7 1.0
CB D:SER59 3.7 6.2 1.0
CD2 N:MHS63 3.7 16.8 1.0
CE1 N:MHS63 3.9 15.5 1.0
CD1 D:LEU35 4.2 7.1 1.0
N D:HIS60 4.2 3.9 0.5
C D:SER59 4.2 3.5 1.0
N D:HIS60 4.2 3.9 0.5
CG D:HIS60 4.3 13.7 0.5
CD1 D:LEU56 4.4 4.6 1.0
OG D:SER31 4.4 15.7 1.0
O D:HOH399 4.4 16.1 1.0
NE2 D:HIS60 4.4 16.5 0.5
O D:SER59 4.5 13.6 1.0
CA D:SER59 4.6 4.8 1.0
CA D:HIS60 4.6 9.8 0.5
CA D:HIS60 4.6 9.8 0.5
ND1 N:MHS67 4.7 14.9 1.0
O D:LEU56 4.8 7.3 1.0
CB D:LEU35 4.9 0.3 1.0
CG N:MHS63 4.9 12.2 1.0
CG D:LEU35 4.9 4.1 1.0
CD2 N:MHS67 4.9 6.6 1.0
CD2 D:LEU35 4.9 4.8 1.0
ND1 N:MHS63 5.0 16.4 1.0

Iron binding site 9 out of 48 in 9jqd

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Iron binding site 9 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:41.1
occ:1.00
 OE1 E:GLU27 2.2 17.3 1.0
ND1 E:HIS65 2.3 15.1 1.0
O E:HOH359 2.3 11.0 1.0
OE1 E:GLU62 2.4 12.2 1.0
CD E:GLU62 3.0 12.6 1.0
CD E:GLU27 3.0 11.5 1.0
OE2 E:GLU62 3.1 20.2 1.0
OE2 E:GLU27 3.2 17.6 1.0
CE1 E:HIS65 3.2 12.6 1.0
CG E:HIS65 3.3 12.7 1.0
CB E:HIS65 3.6 10.0 1.0
OE1 E:GLN141 3.7 16.5 1.0
O E:HOH370 4.0 18.2 1.0
CG1 E:VAL110 4.3 7.0 1.0
NE2 E:HIS65 4.4 15.6 1.0
CG E:GLU62 4.4 8.1 1.0
CA E:GLU62 4.4 8.8 1.0
CD2 E:HIS65 4.4 10.1 1.0
CG E:GLU27 4.5 6.4 1.0
CD E:GLN141 4.7 7.4 1.0
CB E:GLU62 4.7 9.1 1.0
O E:HOH363 4.8 18.3 1.0
CB E:GLU27 4.9 7.4 1.0
O E:GLU62 5.0 8.3 1.0

Iron binding site 10 out of 48 in 9jqd

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Iron binding site 10 out of 48 in the Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Ferritin Variant R63MEH/R67MEH within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe202

b:50.7
occ:1.00
 NE2 P:MHS63 2.9 16.5 1.0
ND1 E:HIS60 3.0 19.2 0.5
OG E:SER59 3.0 11.3 1.0
CE1 E:HIS60 3.1 15.9 0.5
CE1 P:MHS67 3.4 12.5 1.0
NE2 P:MHS67 3.6 14.7 1.0
CB E:SER59 3.7 6.2 1.0
CD2 P:MHS63 3.7 16.8 1.0
CE1 P:MHS63 3.9 15.5 1.0
CD1 E:LEU35 4.2 7.1 1.0
N E:HIS60 4.2 3.9 0.5
C E:SER59 4.2 3.5 1.0
N E:HIS60 4.2 3.9 0.5
CG E:HIS60 4.3 13.7 0.5
CD1 E:LEU56 4.4 4.6 1.0
OG E:SER31 4.4 15.7 1.0
O E:HOH399 4.4 16.1 1.0
NE2 E:HIS60 4.4 16.5 0.5
O E:SER59 4.5 13.6 1.0
CA E:SER59 4.6 4.8 1.0
CA E:HIS60 4.6 9.8 0.5
CA E:HIS60 4.6 9.8 0.5
ND1 P:MHS67 4.7 14.9 1.0
O E:LEU56 4.8 7.3 1.0
CB E:LEU35 4.9 0.3 1.0
CG P:MHS63 4.9 12.2 1.0
CG E:LEU35 4.9 4.1 1.0
CD2 P:MHS67 4.9 6.6 1.0
CD2 E:LEU35 4.9 4.8 1.0
ND1 P:MHS63 5.0 16.4 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 20:12:41 2024

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