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Iron in PDB 6kh0: Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes

Enzymatic activity of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes

All present enzymatic activity of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes:
1.16.3.1;

Protein crystallography data

The structure of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes, PDB code: 6kh0 was solved by C.Gu, T.Zhang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.95 / 2.00
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 125.304, 125.304, 175.655, 90.00, 90.00, 90.00
R / Rfree (%) 10.1 / 14.1

Iron Binding Sites:

The binding sites of Iron atom in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes (pdb code 6kh0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes, PDB code: 6kh0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6kh0

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Iron binding site 1 out of 6 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:31.2
occ:0.67
O A:HOH382 2.0 38.3 1.0
OE1 A:GLU24 2.0 31.0 1.0
OE1 A:GLU60 2.1 29.8 1.0
ND1 A:HIS63 2.5 36.8 1.0
CD A:GLU60 2.9 23.4 1.0
CD A:GLU24 3.0 26.1 1.0
HB2 A:HIS63 3.2 21.6 1.0
OE2 A:GLU60 3.2 34.9 1.0
OE2 A:GLU24 3.3 31.1 1.0
HA A:GLU60 3.3 21.2 1.0
CG A:HIS63 3.4 28.7 1.0
HB3 A:HIS63 3.4 21.6 1.0
CE1 A:HIS63 3.5 46.7 1.0
CB A:HIS63 3.5 18.0 1.0
HG11 A:VAL108 3.6 26.8 1.0
HE1 A:HIS63 3.7 56.0 1.0
O A:HOH309 4.0 26.8 1.0
O A:HOH410 4.0 25.1 1.0
HB3 A:GLU24 4.2 20.3 1.0
OE1 A:GLN139 4.2 23.8 1.0
CA A:GLU60 4.2 17.7 1.0
CG A:GLU60 4.2 22.0 1.0
HD1 A:TYR135 4.3 21.4 1.0
CG A:GLU24 4.3 22.7 1.0
HB3 A:GLU60 4.4 27.3 1.0
O A:HOH384 4.4 38.7 1.0
CG1 A:VAL108 4.5 22.4 1.0
HA A:GLU24 4.5 15.6 1.0
CB A:GLU60 4.5 22.8 1.0
CD2 A:HIS63 4.5 28.3 1.0
HG12 A:VAL108 4.5 26.8 1.0
NE2 A:HIS63 4.6 43.9 1.0
HE1 A:TYR135 4.7 23.5 1.0
CB A:GLU24 4.7 16.9 1.0
HG3 A:GLU24 4.7 27.2 1.0
HG3 A:GLU60 4.8 26.4 1.0
HG2 A:GLU60 4.8 26.4 1.0
HD11 A:LEU112 4.8 22.8 1.0
HE22 A:GLN139 4.8 28.5 1.0
O A:GLU60 4.8 15.9 1.0
HG13 A:VAL108 4.9 26.8 1.0
HG2 A:GLU24 5.0 27.2 1.0

Iron binding site 2 out of 6 in 6kh0

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Iron binding site 2 out of 6 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:31.1
occ:0.59
O B:HOH391 2.0 40.1 1.0
OE1 B:GLU24 2.1 34.0 1.0
OE1 B:GLU60 2.2 31.6 1.0
ND1 B:HIS63 2.2 30.6 1.0
CD B:GLU60 2.9 26.2 1.0
O B:HOH302 3.0 51.5 1.0
CD B:GLU24 3.1 31.2 1.0
OE2 B:GLU60 3.2 32.4 1.0
HB2 B:HIS63 3.2 23.4 1.0
CE1 B:HIS63 3.2 35.0 1.0
CG B:HIS63 3.2 25.2 1.0
HA B:GLU60 3.4 18.1 1.0
HE1 B:HIS63 3.4 42.0 1.0
OE2 B:GLU24 3.4 31.0 1.0
HB3 B:HIS63 3.4 23.4 1.0
CB B:HIS63 3.5 19.5 1.0
HG11 B:VAL108 3.7 26.1 1.0
O B:HOH373 3.8 24.2 1.0
O B:HOH305 3.9 29.6 1.0
OE1 B:GLN139 4.2 22.5 1.0
HB3 B:GLU24 4.2 20.3 1.0
CA B:GLU60 4.3 15.1 1.0
CG B:GLU60 4.3 24.4 1.0
HD1 B:TYR135 4.3 26.1 1.0
NE2 B:HIS63 4.3 43.9 1.0
CD2 B:HIS63 4.4 28.9 1.0
HB3 B:GLU60 4.4 22.9 1.0
CG B:GLU24 4.4 22.6 1.0
CB B:GLU60 4.5 19.1 1.0
HA B:GLU24 4.5 17.8 1.0
CG1 B:VAL108 4.6 21.8 1.0
HE1 B:TYR135 4.6 24.8 1.0
O B:HOH389 4.6 34.0 1.0
HG12 B:VAL108 4.6 26.1 1.0
HG3 B:GLU24 4.7 27.1 1.0
CB B:GLU24 4.8 16.9 1.0
HG3 B:GLU60 4.8 29.3 1.0
HE22 B:GLN139 4.8 27.3 1.0
O B:GLU60 4.8 17.9 1.0
HD11 B:LEU112 4.8 23.6 1.0
HG2 B:GLU60 4.9 29.3 1.0
HG13 B:VAL108 4.9 26.1 1.0

Iron binding site 3 out of 6 in 6kh0

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Iron binding site 3 out of 6 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:32.2
occ:0.72
OE1 C:GLU24 2.0 33.2 1.0
OE1 C:GLU60 2.0 31.3 1.0
O C:HOH456 2.1 33.4 1.0
ND1 C:HIS63 2.5 31.2 1.0
CD C:GLU60 2.8 25.7 1.0
OE2 C:GLU60 3.0 36.9 1.0
CD C:GLU24 3.1 26.9 1.0
HB2 C:HIS63 3.2 25.7 1.0
HB3 C:HIS63 3.4 25.7 1.0
CG C:HIS63 3.4 25.6 1.0
HA C:GLU60 3.4 22.3 1.0
CE1 C:HIS63 3.5 39.1 1.0
OE2 C:GLU24 3.5 32.5 1.0
CB C:HIS63 3.5 21.4 1.0
O C:HOH319 3.6 34.2 1.0
HG11 C:VAL108 3.6 25.2 1.0
HE1 C:HIS63 3.7 47.0 1.0
O C:HOH390 4.0 24.7 1.0
HB3 C:GLU24 4.1 25.4 1.0
OE1 C:GLN139 4.2 24.1 1.0
CG C:GLU60 4.2 22.7 1.0
CA C:GLU60 4.3 18.6 1.0
HB3 C:GLU60 4.3 22.6 1.0
O C:HOH404 4.3 33.6 1.0
CG C:GLU24 4.4 25.2 1.0
HD1 C:TYR135 4.4 22.2 1.0
HA C:GLU24 4.4 19.0 1.0
CG1 C:VAL108 4.5 21.0 1.0
CB C:GLU60 4.5 18.8 1.0
CD2 C:HIS63 4.5 29.7 1.0
NE2 C:HIS63 4.6 40.9 1.0
HG12 C:VAL108 4.6 25.2 1.0
HE22 C:GLN139 4.6 25.9 1.0
HG3 C:GLU60 4.7 27.2 1.0
CB C:GLU24 4.7 21.1 1.0
HE1 C:TYR135 4.7 24.8 1.0
HG2 C:GLU60 4.7 27.2 1.0
HG3 C:GLU24 4.7 30.2 1.0
HG13 C:VAL108 4.8 25.2 1.0
HD11 C:LEU112 4.9 23.3 1.0
O C:GLU60 4.9 15.8 1.0
HB3 C:ALA27 5.0 21.6 1.0

Iron binding site 4 out of 6 in 6kh0

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Iron binding site 4 out of 6 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:38.2
occ:0.73
O D:HOH403 1.9 33.6 1.0
OE1 D:GLU24 2.2 38.1 1.0
OE1 D:GLU60 2.3 30.4 1.0
ND1 D:HIS63 2.4 34.9 1.0
CD D:GLU60 2.9 29.3 1.0
OE2 D:GLU60 2.9 43.2 1.0
CD D:GLU24 3.2 33.3 1.0
CE1 D:HIS63 3.3 41.4 1.0
CG D:HIS63 3.3 28.9 1.0
HB2 D:HIS63 3.4 21.6 1.0
HA D:GLU60 3.4 23.1 1.0
HE1 D:HIS63 3.5 49.6 1.0
HB3 D:HIS63 3.5 21.6 1.0
OE2 D:GLU24 3.6 35.2 1.0
CB D:HIS63 3.6 18.0 1.0
O D:HOH333 3.6 28.6 1.0
HG11 D:VAL108 3.7 22.1 1.0
O D:HOH339 3.8 27.1 1.0
OE1 D:GLN139 3.9 22.3 1.0
O D:HOH408 4.0 31.9 1.0
HD1 D:TYR135 4.3 18.4 1.0
HB3 D:GLU24 4.3 20.4 1.0
CG D:GLU60 4.3 20.3 1.0
CA D:GLU60 4.3 19.2 1.0
NE2 D:HIS63 4.4 46.5 1.0
CD2 D:HIS63 4.4 27.6 1.0
HE22 D:GLN139 4.5 25.1 1.0
CG1 D:VAL108 4.5 18.4 1.0
CG D:GLU24 4.5 25.5 1.0
HB3 D:GLU60 4.5 26.2 1.0
HG12 D:VAL108 4.6 22.1 1.0
CB D:GLU60 4.6 21.8 1.0
HA D:GLU24 4.7 20.3 1.0
HG2 D:GLU60 4.8 24.4 1.0
HD11 D:LEU112 4.8 23.9 1.0
HE1 D:TYR135 4.8 18.7 1.0
HG3 D:GLU60 4.8 24.4 1.0
CD D:GLN139 4.8 15.5 1.0
HG3 D:GLU24 4.9 30.6 1.0
CB D:GLU24 4.9 17.0 1.0
HG13 D:VAL108 5.0 22.1 1.0

Iron binding site 5 out of 6 in 6kh0

Go back to Iron Binding Sites List in 6kh0
Iron binding site 5 out of 6 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:34.8
occ:0.68
HD2 E:HIS63 1.8 39.2 1.0
O E:HOH363 1.8 41.3 1.0
OE1 E:GLU24 2.1 34.2 1.0
OE1 E:GLU60 2.2 28.2 1.0
CD2 E:HIS63 2.6 32.7 1.0
CD E:GLU60 2.9 26.4 1.0
CD E:GLU24 3.0 28.8 1.0
OE2 E:GLU60 3.0 38.7 1.0
HB2 E:HIS63 3.2 26.0 1.0
CG E:HIS63 3.3 23.1 1.0
HA E:GLU60 3.3 19.9 1.0
OE2 E:GLU24 3.3 32.0 1.0
HB3 E:HIS63 3.3 26.0 1.0
CB E:HIS63 3.5 21.6 1.0
HG11 E:VAL108 3.7 25.6 1.0
NE2 E:HIS63 3.8 49.8 1.0
O E:HOH354 4.0 26.2 1.0
HE2 E:HIS63 4.1 59.7 1.0
O E:HOH421 4.1 30.3 1.0
O E:HOH333 4.1 30.2 1.0
HB3 E:GLU24 4.2 25.0 1.0
OE1 E:GLN139 4.2 24.0 1.0
CA E:GLU60 4.2 16.6 1.0
CG E:GLU60 4.3 22.3 1.0
HD1 E:TYR135 4.3 21.5 1.0
CG E:GLU24 4.3 18.4 1.0
HB3 E:GLU60 4.4 25.6 1.0
HA E:GLU24 4.5 17.8 1.0
CB E:GLU60 4.5 21.3 1.0
CG1 E:VAL108 4.6 21.3 1.0
ND1 E:HIS63 4.6 34.3 1.0
HE1 E:TYR135 4.6 25.2 1.0
HG12 E:VAL108 4.6 25.6 1.0
HG3 E:GLU24 4.7 22.1 1.0
CB E:GLU24 4.7 20.8 1.0
O E:GLU60 4.7 16.6 1.0
HE22 E:GLN139 4.8 27.5 1.0
HD11 E:LEU112 4.8 26.2 1.0
CE1 E:HIS63 4.8 40.9 1.0
HG3 E:GLU60 4.8 26.8 1.0
HG2 E:GLU60 4.8 26.8 1.0
HG13 E:VAL108 5.0 25.6 1.0

Iron binding site 6 out of 6 in 6kh0

Go back to Iron Binding Sites List in 6kh0
Iron binding site 6 out of 6 in the Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Design and Crystal Structure of Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:26.3
occ:0.48
HD2 F:HIS63 1.9 44.2 1.0
OE1 F:GLU24 1.9 36.7 1.0
O F:HOH319 1.9 37.1 1.0
OE1 F:GLU60 2.0 33.1 1.0
CD2 F:HIS63 2.7 36.9 1.0
CD F:GLU24 2.9 24.9 1.0
CD F:GLU60 2.9 34.2 1.0
OE2 F:GLU60 3.2 42.9 1.0
OE2 F:GLU24 3.3 28.7 1.0
HB2 F:HIS63 3.3 24.8 1.0
HA F:GLU60 3.4 24.2 1.0
CG F:HIS63 3.5 30.2 1.0
HG11 F:VAL108 3.5 24.1 1.0
HB3 F:HIS63 3.5 24.8 1.0
CB F:HIS63 3.6 20.6 1.0
O F:HOH434 3.7 34.5 1.0
O F:HOH380 3.8 26.5 1.0
NE2 F:HIS63 3.8 46.7 1.0
HE2 F:HIS63 4.1 56.0 1.0
OE1 F:GLN139 4.1 20.9 1.0
CG F:GLU24 4.2 22.8 1.0
O F:HOH416 4.2 31.6 1.0
CG F:GLU60 4.3 21.9 1.0
CA F:GLU60 4.3 20.2 1.0
HA F:GLU24 4.3 23.7 1.0
HD1 F:TYR135 4.3 20.8 1.0
HB3 F:GLU60 4.3 24.5 1.0
CG1 F:VAL108 4.3 20.1 1.0
HG12 F:VAL108 4.4 24.1 1.0
HB3 F:GLU24 4.4 23.8 1.0
CB F:GLU60 4.5 20.4 1.0
HG3 F:GLU24 4.5 27.4 1.0
HE22 F:GLN139 4.6 26.4 1.0
HD11 F:LEU112 4.7 26.8 1.0
ND1 F:HIS63 4.7 35.5 1.0
HG3 F:GLU60 4.7 26.2 1.0
HE1 F:TYR135 4.7 22.9 1.0
CB F:GLU24 4.8 19.8 1.0
HG13 F:VAL108 4.8 24.1 1.0
HG2 F:GLU60 4.9 26.2 1.0
CE1 F:HIS63 4.9 42.2 1.0
HG2 F:GLU24 4.9 27.4 1.0
O F:GLU60 4.9 16.6 1.0
HG21 F:VAL108 5.0 23.9 1.0
CD F:GLN139 5.0 15.8 1.0

Reference:

C.Gu, H.Chen, Y.Wang, T.Zhang, H.Wang, G.Zhao. Structural Insight Into Binary Protein Mofs with Ferritin Nanocages As Linkers and Nickel Clusters As Nodes. Chemistry 2019.
ISSN: ISSN 0947-6539
PubMed: 31820500
DOI: 10.1002/CHEM.201905315
Page generated: Wed Aug 7 00:16:29 2024

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