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Iron in PDB 6wyg: Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent

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

All present enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent:
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, PDB code: 6wyg 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) 50.07 / 2.27
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 126.810, 126.810, 281.285, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 26

Other elements in 6wyg:

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

Calcium (Ca) 8 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 (pdb code 6wyg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 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, PDB code: 6wyg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 6wyg

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Iron binding site 1 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:56.9
occ:0.40
 OE1 A:GLU62 2.5 77.7 1.0
OE1 A:GLU27 2.5 67.3 1.0
FE A:FE202 2.8 46.6 0.2
OE2 A:GLU62 3.0 77.5 1.0
CD A:GLU62 3.1 61.8 1.0
OE2 A:GLU27 3.1 60.3 1.0
CD A:GLU27 3.1 59.4 1.0
ND1 A:HIS65 3.2 71.7 1.0
NE2 A:GLN141 3.3 71.8 1.0
CE1 A:HIS65 4.0 71.5 1.0
OE1 A:GLN141 4.0 75.5 1.0
CD A:GLN141 4.1 63.8 1.0
CG A:HIS65 4.2 61.6 1.0
CG1 A:VAL110 4.3 61.0 1.0
OE2 A:GLU107 4.3 63.3 1.0
CB A:HIS65 4.4 54.2 1.0
CG A:GLU62 4.6 49.9 1.0
CG A:GLU27 4.6 46.2 1.0
CD2 A:TYR137 4.7 52.9 1.0
CE2 A:TYR137 5.0 50.3 1.0
OE1 A:GLU107 5.0 75.9 1.0

Iron binding site 2 out of 9 in 6wyg

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Iron binding site 2 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:46.6
occ:0.25
 OE1 A:GLU107 2.5 75.9 1.0
OE2 A:GLU62 2.5 77.5 1.0
OE1 A:GLU62 2.8 77.7 1.0
FE A:FE201 2.8 56.9 0.4
CD A:GLU62 2.9 61.8 1.0
OE2 A:GLU107 3.0 63.3 1.0
CD A:GLU107 3.1 60.8 1.0
OE1 A:GLN141 3.4 75.5 1.0
NE2 A:GLN141 3.9 71.8 1.0
CD A:GLN141 4.0 63.8 1.0
CG A:GLU62 4.2 49.9 1.0
ND1 A:HIS65 4.4 71.7 1.0
CG A:GLU107 4.6 49.5 1.0
CB A:ALA144 4.6 39.0 1.0
CE1 A:HIS65 4.8 71.5 1.0
OE1 A:GLU27 4.8 67.3 1.0

Iron binding site 3 out of 9 in 6wyg

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Iron binding site 3 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:71.3
occ:1.00
 NE2 D:HIS173 2.9 50.6 1.0
NE2 A:HIS173 3.1 52.1 1.0
NE2 C:HIS173 3.1 48.2 1.0
NE2 B:HIS173 3.1 46.2 1.0
CE1 D:HIS173 3.8 56.9 1.0
CE1 C:HIS173 3.8 54.9 1.0
CE1 B:HIS173 3.8 42.7 1.0
CE1 A:HIS173 3.8 47.1 1.0
CD2 A:LEU169 3.9 40.3 1.0
CD2 D:LEU169 3.9 40.7 1.0
CD2 D:HIS173 4.0 47.2 1.0
CD2 B:LEU169 4.1 44.6 1.0
CD2 C:LEU169 4.1 44.5 1.0
CD2 A:HIS173 4.1 47.7 1.0
CD2 C:HIS173 4.2 47.5 1.0
CD2 B:HIS173 4.2 46.8 1.0
CD1 A:LEU169 4.8 41.5 1.0
CD1 C:LEU169 4.9 46.8 1.0
CG A:LEU169 4.9 45.8 1.0
ND1 D:HIS173 4.9 55.8 1.0
ND1 C:HIS173 5.0 50.5 1.0

Iron binding site 4 out of 9 in 6wyg

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Iron binding site 4 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:67.6
occ:0.40
 OE1 B:GLU62 2.3 65.5 1.0
OE2 B:GLU62 2.4 66.3 1.0
CD B:GLU62 2.7 56.0 1.0
OE1 B:GLU27 2.7 60.8 1.0
ND1 B:HIS65 2.8 74.6 1.0
NE2 B:GLN141 3.0 62.3 1.0
FE B:FE202 3.1 42.1 0.2
CE1 B:HIS65 3.5 76.2 1.0
CD B:GLU27 3.7 59.2 1.0
CG B:HIS65 3.8 67.9 1.0
OE2 B:GLU27 3.9 51.8 1.0
CG B:GLU62 4.1 46.3 1.0
CB B:HIS65 4.2 52.0 1.0
CD B:GLN141 4.3 63.6 1.0
OE2 B:GLU107 4.4 64.6 1.0
CG1 B:VAL110 4.5 47.2 1.0
O B:HOH306 4.6 53.3 1.0
NE2 B:HIS65 4.7 80.7 1.0
CA B:GLU62 4.7 48.1 1.0
CB B:GLU62 4.8 39.2 1.0
CD2 B:HIS65 4.8 77.9 1.0
OE1 B:GLU107 4.9 65.4 1.0

Iron binding site 5 out of 9 in 6wyg

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Iron binding site 5 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:42.1
occ:0.25
 OE1 B:GLU62 2.3 65.5 1.0
O B:HOH306 2.5 53.3 1.0
OE2 B:GLU107 2.6 64.6 1.0
OE1 B:GLU107 2.6 65.4 1.0
CD B:GLU107 2.9 58.1 1.0
NE2 B:GLN141 3.0 62.3 1.0
FE B:FE201 3.1 67.6 0.4
CD B:GLU62 3.5 56.0 1.0
CB B:ALA144 4.0 43.1 1.0
CD B:GLN141 4.0 63.6 1.0
OE2 B:GLU61 4.1 86.5 1.0
OE2 B:GLU62 4.1 66.3 1.0
CG B:GLU107 4.3 54.8 1.0
OE1 B:GLN141 4.4 71.7 1.0
CG B:GLU62 4.5 46.3 1.0
CE1 B:HIS65 4.7 76.2 1.0
OE1 B:GLN58 4.7 77.3 1.0
ND1 B:HIS65 4.7 74.6 1.0
OH B:TYR34 5.0 61.8 1.0

Iron binding site 6 out of 9 in 6wyg

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Iron binding site 6 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:83.0
occ:0.40
 OE1 C:GLU27 2.4 66.2 1.0
FE C:FE202 2.7 40.6 0.2
OE2 C:GLU62 2.7 64.4 1.0
OE1 C:GLU62 2.9 75.4 1.0
OE1 C:GLN141 3.1 69.9 1.0
CD C:GLU62 3.2 62.7 1.0
CD C:GLU27 3.3 66.0 1.0
OE2 C:GLU27 3.4 69.0 1.0
ND1 C:HIS65 3.8 73.2 1.0
CB C:HIS65 4.1 51.7 1.0
CG1 C:VAL110 4.2 54.2 1.0
CG C:HIS65 4.2 67.1 1.0
CD C:GLN141 4.2 65.0 1.0
O C:HOH310 4.3 62.9 1.0
CD2 C:TYR137 4.5 64.3 1.0
CE2 C:TYR137 4.6 65.6 1.0
CG C:GLU62 4.6 55.6 1.0
OE2 C:GLU107 4.6 66.7 1.0
CG C:GLU27 4.7 54.5 1.0
CE1 C:HIS65 4.7 77.8 1.0
CG C:GLN141 4.9 65.3 1.0
CA C:GLU62 5.0 51.0 1.0

Iron binding site 7 out of 9 in 6wyg

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Iron binding site 7 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:40.6
occ:0.25
 OE1 C:GLU62 2.1 75.4 1.0
OE1 C:GLN141 2.3 69.9 1.0
O C:HOH310 2.4 62.9 1.0
OE2 C:GLU107 2.4 66.7 1.0
FE C:FE201 2.7 83.0 0.4
OE1 C:GLU107 2.7 67.9 1.0
CD C:GLU107 2.9 59.4 1.0
CD C:GLU62 3.0 62.7 1.0
OE2 C:GLU62 3.3 64.4 1.0
CD C:GLN141 3.4 65.0 1.0
NE2 C:GLN141 4.1 56.9 1.0
CG C:GLU62 4.3 55.6 1.0
CG C:GLU107 4.4 52.0 1.0
CG C:GLN141 4.6 65.3 1.0
OE1 C:GLU27 4.7 66.2 1.0
CG1 C:VAL110 4.8 54.2 1.0
CB C:ALA144 5.0 43.0 1.0

Iron binding site 8 out of 9 in 6wyg

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Iron binding site 8 out of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:71.1
occ:0.40
 OE1 D:GLN141 2.3 84.7 1.0
FE D:FE202 2.4 58.0 0.2
OE2 D:GLU62 2.4 64.7 1.0
OE1 D:GLU62 2.7 71.9 1.0
OE1 D:GLU27 2.8 73.5 1.0
CD D:GLU62 2.9 64.7 1.0
ND1 D:HIS65 3.2 74.7 1.0
CD D:GLN141 3.3 82.1 1.0
OE2 D:GLU27 3.4 71.3 1.0
CD D:GLU27 3.5 71.5 1.0
CE1 D:HIS65 3.7 76.9 1.0
NE2 D:GLN141 3.8 77.1 1.0
OE2 D:GLU107 4.0 77.3 1.0
O D:HOH312 4.2 63.1 1.0
OE1 D:GLU107 4.3 71.8 1.0
CG D:HIS65 4.4 72.5 1.0
CG D:GLU62 4.4 63.6 1.0
CG1 D:VAL110 4.4 57.1 1.0
CD D:GLU107 4.6 71.3 1.0
CG D:GLN141 4.6 78.8 1.0
CB D:HIS65 4.8 67.6 1.0
NE2 D:HIS65 5.0 79.4 1.0

Iron binding site 9 out of 9 in 6wyg

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:58.0
occ:0.25
 O D:HOH312 2.2 63.1 1.0
OE2 D:GLU107 2.4 77.3 1.0
FE D:FE201 2.4 71.1 0.4
OE1 D:GLU62 2.4 71.9 1.0
OE1 D:GLN141 2.5 84.7 1.0
OE1 D:GLU107 2.7 71.8 1.0
CD D:GLU107 2.8 71.3 1.0
CD D:GLN141 3.2 82.1 1.0
CD D:GLU62 3.3 64.7 1.0
NE2 D:GLN141 3.3 77.1 1.0
OE2 D:GLU62 3.5 64.7 1.0
CG D:GLU107 4.2 69.8 1.0
CB D:ALA144 4.5 51.4 1.0
CE1 D:HIS65 4.6 76.9 1.0
CG D:GLN141 4.6 78.8 1.0
CG D:GLU62 4.6 63.6 1.0
ND1 D:HIS65 4.7 74.7 1.0

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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