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Iron in PDB 6wyh: Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution

Enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution

All present enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution, PDB code: 6wyh was solved by J.B.Bailey, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.27 / 2.22
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 128.880, 128.880, 291.810, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 24.5

Other elements in 6wyh:

The structure of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution (pdb code 6wyh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution, PDB code: 6wyh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 6wyh

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Iron binding site 1 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:37.1
occ:0.50
OE1 A:GLU27 2.2 47.7 1.0
OE2 A:GLU62 2.2 38.6 1.0
FE A:FE202 2.6 89.7 0.2
CD2 A:HIS65 2.9 46.0 1.0
CD A:GLU62 2.9 36.9 1.0
OE1 A:GLU62 3.1 41.8 1.0
CD A:GLU27 3.1 41.9 1.0
OE2 A:GLU27 3.4 41.9 1.0
CG A:HIS65 3.7 41.4 1.0
NE2 A:HIS65 3.9 47.4 1.0
CB A:HIS65 3.9 29.8 1.0
OE1 A:GLN141 4.1 44.2 1.0
FE A:FE204 4.2 0.6 0.8
CG A:GLU62 4.3 30.8 1.0
CG A:GLU27 4.5 36.7 1.0
CG1 A:VAL110 4.6 28.2 1.0
CA A:GLU62 4.7 26.2 1.0
CB A:GLU62 4.7 25.3 1.0
ND1 A:HIS65 4.8 46.0 1.0
CB A:GLU27 4.8 29.4 1.0
CD2 A:TYR137 4.9 44.4 1.0
CE1 A:HIS65 4.9 49.7 1.0
CE2 A:TYR137 4.9 41.1 1.0

Iron binding site 2 out of 10 in 6wyh

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Iron binding site 2 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:89.7
occ:0.25
FE A:FE204 2.2 0.6 0.8
OE1 A:GLU62 2.5 41.8 1.0
FE A:FE201 2.6 37.1 0.5
OE1 A:GLN141 2.6 44.2 1.0
OE2 A:GLU107 2.8 47.9 1.0
CD A:GLU62 3.3 36.9 1.0
CD A:GLN141 3.4 42.5 1.0
OE2 A:GLU62 3.4 38.6 1.0
NE2 A:GLN141 3.5 50.7 1.0
OE1 A:GLU107 3.5 46.6 1.0
CD A:GLU107 3.6 43.7 1.0
CD2 A:HIS65 4.3 46.0 1.0
OE1 A:GLU27 4.5 47.7 1.0
NE2 A:HIS65 4.6 47.4 1.0
CG1 A:VAL110 4.7 28.2 1.0
CG A:GLU62 4.8 30.8 1.0
CG A:GLN141 4.8 36.8 1.0
O A:HOH460 4.8 44.5 1.0

Iron binding site 3 out of 10 in 6wyh

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Iron binding site 3 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:26.0
occ:0.50
NE2 A:HIS173 3.0 38.6 1.0
NE2 D:HIS173 3.1 38.5 1.0
NE2 C:HIS173 3.1 39.7 1.0
NE2 B:HIS173 3.2 36.3 1.0
CD2 A:LEU169 3.8 25.4 1.0
CD2 D:LEU169 3.8 19.7 1.0
CD2 D:HIS173 3.9 36.9 1.0
CE1 A:HIS173 3.9 40.1 1.0
CE1 C:HIS173 4.0 42.0 1.0
CD2 A:HIS173 4.0 37.8 1.0
CE1 B:HIS173 4.0 39.0 1.0
CD2 B:LEU169 4.1 19.5 1.0
CE1 D:HIS173 4.1 39.6 1.0
CD2 B:HIS173 4.1 34.9 1.0
CD2 C:HIS173 4.1 38.8 1.0
CD2 C:LEU169 4.1 21.6 1.0
CD1 C:LEU169 4.6 22.8 1.0
CD1 B:LEU169 4.8 20.6 1.0
CD1 A:LEU169 4.8 22.8 1.0
CD1 D:LEU169 4.8 17.8 1.0
CG D:LEU169 4.9 23.9 1.0
CG A:LEU169 4.9 26.4 1.0
CG C:LEU169 5.0 23.0 1.0

Iron binding site 4 out of 10 in 6wyh

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Iron binding site 4 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:0.6
occ:0.75
FE A:FE202 2.2 89.7 0.2
OE1 A:GLU62 2.5 41.8 1.0
O A:HOH460 2.9 44.5 1.0
OE2 A:GLU107 3.3 47.9 1.0
OE1 A:GLU107 3.4 46.6 1.0
CD A:GLU107 3.6 43.7 1.0
CD A:GLU62 3.8 36.9 1.0
CB A:ALA144 4.0 24.2 1.0
OE1 A:GLN141 4.0 44.2 1.0
FE A:FE201 4.2 37.1 0.5
NE2 A:HIS65 4.5 47.4 1.0
OE2 A:GLU62 4.5 38.6 1.0
OE1 A:GLN58 4.6 44.5 1.0
CD2 A:HIS65 4.7 46.0 1.0
CG A:GLU62 4.8 30.8 1.0
CD A:GLN141 4.8 42.5 1.0
O A:HOH437 4.9 46.9 1.0
CG A:GLU107 4.9 35.2 1.0
NE2 A:GLN141 5.0 50.7 1.0

Iron binding site 5 out of 10 in 6wyh

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Iron binding site 5 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:40.8
occ:0.50
OE1 B:GLU27 2.3 46.3 1.0
OE2 B:GLU62 2.3 44.8 1.0
O B:HOH371 2.6 35.5 1.0
FE B:FE202 2.9 46.8 0.2
CD B:GLU62 3.0 41.1 1.0
OE1 B:GLU62 3.0 47.2 1.0
O B:HOH387 3.0 49.0 1.0
ND1 B:HIS65 3.2 51.4 1.0
CD B:GLU27 3.2 42.9 1.0
OE2 B:GLU27 3.4 47.5 1.0
OE1 B:GLN141 3.5 47.7 1.0
CE1 B:HIS65 4.1 55.2 1.0
CG B:HIS65 4.1 45.8 1.0
CB B:HIS65 4.2 31.2 1.0
CG1 B:VAL110 4.4 27.2 1.0
CG B:GLU62 4.5 30.3 1.0
CD B:GLN141 4.6 38.1 1.0
CG B:GLU27 4.6 33.0 1.0
O B:HOH324 4.8 56.4 1.0
CA B:GLU62 4.8 22.7 1.0
OE2 B:GLU107 4.9 42.0 1.0
CB B:GLU62 4.9 23.6 1.0

Iron binding site 6 out of 10 in 6wyh

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Iron binding site 6 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:46.8
occ:0.25
O B:HOH387 2.1 49.0 1.0
O B:HOH371 2.3 35.5 1.0
O B:HOH324 2.3 56.4 1.0
OE1 B:GLN141 2.4 47.7 1.0
OE2 B:GLU107 2.5 42.0 1.0
OE1 B:GLU62 2.5 47.2 1.0
OE1 B:GLU107 2.9 37.2 1.0
FE B:FE201 2.9 40.8 0.5
CD B:GLU107 3.0 38.1 1.0
CD B:GLN141 3.4 38.1 1.0
CD B:GLU62 3.5 41.1 1.0
OE2 B:GLU62 3.8 44.8 1.0
NE2 B:GLN141 3.8 39.3 1.0
O B:HOH391 4.1 56.0 1.0
CG B:GLU107 4.5 31.8 1.0
ND1 B:HIS65 4.7 51.4 1.0
CB B:ALA144 4.7 22.0 1.0
CG B:GLN141 4.8 32.8 1.0
CE1 B:HIS65 4.8 55.2 1.0
CG B:GLU62 4.9 30.3 1.0

Iron binding site 7 out of 10 in 6wyh

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Iron binding site 7 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:40.6
occ:0.50
OE1 C:GLU27 2.2 46.4 1.0
OE2 C:GLU62 2.3 45.1 1.0
O C:HOH307 2.5 55.5 1.0
OE1 C:GLU62 2.6 48.1 1.0
CD C:GLU62 2.7 42.0 1.0
ND1 C:HIS65 2.8 48.6 1.0
CD C:GLU27 3.3 42.1 1.0
OE2 C:GLU27 3.6 39.8 1.0
CE1 C:HIS65 3.7 51.2 1.0
CG C:HIS65 3.8 45.3 1.0
FE C:FE202 3.9 58.4 0.2
CB C:HIS65 3.9 32.2 1.0
OE1 C:GLN141 4.1 43.3 1.0
CG C:GLU62 4.1 32.7 1.0
CA C:GLU62 4.5 31.8 1.0
CB C:GLU62 4.6 31.0 1.0
CG C:GLU27 4.6 37.3 1.0
CG1 C:VAL110 4.6 26.8 1.0
CB C:GLU27 4.8 31.1 1.0
NE2 C:HIS65 4.8 51.6 1.0
CD2 C:HIS65 4.9 49.5 1.0
CD C:GLN141 4.9 36.8 1.0

Iron binding site 8 out of 10 in 6wyh

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Iron binding site 8 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:58.4
occ:0.25
O C:HOH307 2.1 55.5 1.0
O C:HOH347 2.1 62.9 1.0
OE1 C:GLU62 2.5 48.1 1.0
OE1 C:GLU107 3.1 45.9 1.0
OE2 C:GLU107 3.2 49.0 1.0
OE1 C:GLN141 3.4 43.3 1.0
CD C:GLU107 3.5 44.5 1.0
O C:HOH437 3.6 52.5 1.0
CD C:GLU62 3.6 42.0 1.0
FE C:FE201 3.9 40.6 0.5
CB C:ALA144 4.3 23.7 1.0
OE2 C:GLU62 4.4 45.1 1.0
CD C:GLN141 4.6 36.8 1.0
CE1 C:HIS65 4.6 51.2 1.0
CG C:GLU62 4.6 32.7 1.0
ND1 C:HIS65 4.7 48.6 1.0
OE1 C:GLN58 4.8 41.9 1.0
CG C:GLU107 4.9 36.0 1.0

Iron binding site 9 out of 10 in 6wyh

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Iron binding site 9 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:39.5
occ:0.50
OE1 D:GLU27 2.1 51.3 1.0
OE2 D:GLU62 2.2 50.4 1.0
ND1 D:HIS65 2.5 30.7 0.5
ND1 D:HIS65 2.9 32.5 0.5
CD D:GLU27 3.0 45.6 1.0
CD D:GLU62 3.1 47.6 1.0
FE D:FE202 3.1 52.2 0.2
OE2 D:GLU27 3.2 50.3 1.0
OE1 D:GLU62 3.4 50.6 1.0
CE1 D:HIS65 3.4 32.5 0.5
CG D:HIS65 3.5 30.0 0.5
OE1 D:GLN141 3.7 88.3 1.0
CG D:HIS65 3.7 30.5 0.5
CB D:HIS65 3.8 26.1 0.5
CB D:HIS65 3.8 26.2 0.5
CE1 D:HIS65 3.8 35.2 0.5
CG D:GLU27 4.4 33.7 1.0
CG D:GLU62 4.4 39.5 1.0
NE2 D:HIS65 4.5 33.1 0.5
CD2 D:HIS65 4.6 31.4 0.5
CA D:GLU62 4.6 28.6 1.0
CD D:GLN141 4.6 67.4 1.0
CG1 D:VAL110 4.7 33.1 1.0
CB D:GLU62 4.7 30.6 1.0
CB D:GLU27 4.9 26.4 1.0
CD2 D:HIS65 4.9 32.5 0.5
CD2 D:TYR137 5.0 42.6 1.0
NE2 D:HIS65 5.0 35.0 0.5

Iron binding site 10 out of 10 in 6wyh

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Iron binding site 10 out of 10 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent Soaked in An Acrylate Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:52.2
occ:0.25
OE1 D:GLN141 2.1 88.3 1.0
OE2 D:GLU107 2.4 46.2 1.0
OE1 D:GLU62 2.7 50.6 1.0
CD D:GLU107 3.1 43.0 1.0
OE1 D:GLU107 3.1 46.0 1.0
FE D:FE201 3.1 39.5 0.5
CD D:GLN141 3.2 67.4 1.0
OE2 D:GLU62 3.3 50.4 1.0
CD D:GLU62 3.3 47.6 1.0
NE2 D:GLN141 3.5 59.0 1.0
O D:HOH302 3.9 51.9 1.0
CE1 D:HIS65 4.4 32.5 0.5
ND1 D:HIS65 4.5 30.7 0.5
CG D:GLN141 4.5 55.0 1.0
CG D:GLU107 4.6 35.0 1.0
CG D:GLU62 4.8 39.5 1.0
O D:HOH360 4.8 59.4 1.0
CB D:ALA144 4.9 33.9 1.0
OE1 D:GLU27 4.9 51.3 1.0
ND1 D:HIS65 5.0 32.5 0.5

Reference:

K.Han, J.B.Bailey, L.Zhang, F.A.Tezcan. Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks. J.Am.Chem.Soc. V. 142 19402 2020.
ISSN: ESSN 1520-5126
PubMed: 33124805
DOI: 10.1021/JACS.0C10065
Page generated: Wed Aug 7 14:30:52 2024

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