Iron in PDB 7ek4: Prawn Ferritin to Coordinate with Heavy Metal Ions

Enzymatic activity of Prawn Ferritin to Coordinate with Heavy Metal Ions

All present enzymatic activity of Prawn Ferritin to Coordinate with Heavy Metal Ions:
1.16.3.1;

Protein crystallography data

The structure of Prawn Ferritin to Coordinate with Heavy Metal Ions, PDB code: 7ek4 was solved by Y.Wang, J.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.30
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 125.372, 125.372, 176.189, 90, 90, 90
R / Rfree (%) 19.5 / 23.7

Other elements in 7ek4:

The structure of Prawn Ferritin to Coordinate with Heavy Metal Ions also contains other interesting chemical elements:

Mercury (Hg) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Prawn Ferritin to Coordinate with Heavy Metal Ions (pdb code 7ek4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Prawn Ferritin to Coordinate with Heavy Metal Ions, PDB code: 7ek4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7ek4

Go back to Iron Binding Sites List in 7ek4
Iron binding site 1 out of 6 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:42.9
occ:1.00
 O A:HOH309 2.0 38.3 1.0
OE1 A:GLU60 2.2 30.7 1.0
OE1 A:GLU24 2.3 41.3 1.0
ND1 A:HIS63 2.5 42.8 1.0
CD A:GLU60 3.0 38.7 1.0
CD A:GLU24 3.1 34.9 1.0
OE2 A:GLU60 3.2 43.2 1.0
CG A:HIS63 3.3 37.3 1.0
OE2 A:GLU24 3.4 33.0 1.0
CE1 A:HIS63 3.5 44.6 1.0
CB A:HIS63 3.5 28.8 1.0
OE1 A:GLN140 4.1 34.1 1.0
OE1 A:GLU139 4.3 54.7 1.0
O A:HOH301 4.3 53.7 1.0
CG A:GLU60 4.4 27.7 1.0
CA A:GLU60 4.4 33.1 1.0
CD2 A:HIS63 4.4 42.8 1.0
CG A:GLU24 4.5 23.9 1.0
CG1 A:VAL109 4.5 32.8 1.0
NE2 A:HIS63 4.5 52.6 1.0
CB A:GLU60 4.7 29.8 1.0
CB A:GLU24 4.8 26.1 1.0
CD1 A:TYR136 4.9 33.0 1.0
O A:GLU60 5.0 27.5 1.0
CA A:HIS63 5.0 28.1 1.0

Iron binding site 2 out of 6 in 7ek4

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Iron binding site 2 out of 6 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:42.9
occ:1.00
 ND1 B:HIS63 2.2 35.4 1.0
OE1 B:GLU60 2.3 28.6 1.0
OE1 B:GLU24 2.3 39.8 1.0
CD B:GLU60 3.1 34.2 1.0
CE1 B:HIS63 3.1 41.9 1.0
CG B:HIS63 3.1 37.5 1.0
OE2 B:GLU60 3.2 44.2 1.0
CD B:GLU24 3.2 30.6 1.0
CB B:HIS63 3.4 25.2 1.0
OE2 B:GLU24 3.5 35.8 1.0
O B:HOH302 3.9 40.6 1.0
OE1 B:GLN140 4.0 33.5 1.0
NE2 B:HIS63 4.2 52.3 1.0
CD2 B:HIS63 4.2 42.6 1.0
OE1 B:GLU139 4.4 53.5 1.0
CG B:GLU60 4.4 29.3 1.0
CA B:GLU60 4.4 28.4 1.0
CG1 B:VAL109 4.6 21.9 1.0
CG B:GLU24 4.6 24.7 1.0
CB B:GLU60 4.7 27.5 1.0
CD1 B:TYR136 4.9 32.3 1.0
O B:GLU60 5.0 33.5 1.0
CA B:HIS63 5.0 26.4 1.0
CB B:GLU24 5.0 26.7 1.0
OE2 B:GLU139 5.0 57.2 1.0

Iron binding site 3 out of 6 in 7ek4

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Iron binding site 3 out of 6 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:42.0
occ:1.00
 OE1 C:GLU60 2.0 33.0 1.0
ND1 C:HIS63 2.2 37.6 1.0
OE1 C:GLU24 2.3 33.4 1.0
CD C:GLU60 2.7 29.9 1.0
OE2 C:GLU60 2.9 36.8 1.0
CG C:HIS63 3.2 39.1 1.0
CE1 C:HIS63 3.2 43.5 1.0
CD C:GLU24 3.3 35.5 1.0
CB C:HIS63 3.5 31.9 1.0
OE2 C:GLU24 3.6 35.7 1.0
O C:HOH347 3.6 40.9 1.0
CG C:GLU60 4.1 29.4 1.0
OE1 C:GLN140 4.2 29.5 1.0
NE2 C:HIS63 4.2 51.1 1.0
CA C:GLU60 4.3 29.9 1.0
CD2 C:HIS63 4.3 43.4 1.0
CB C:GLU60 4.5 27.6 1.0
CG C:GLU24 4.6 26.4 1.0
CG1 C:VAL109 4.7 24.3 1.0
O C:GLU60 4.8 27.9 1.0
CB C:GLU24 4.9 23.9 1.0
O C:GLU59 4.9 34.9 1.0
CA C:HIS63 5.0 35.1 1.0

Iron binding site 4 out of 6 in 7ek4

Go back to Iron Binding Sites List in 7ek4
Iron binding site 4 out of 6 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:46.3
occ:1.00
 OE1 D:GLU24 2.3 31.3 1.0
OE1 D:GLU60 2.4 31.2 1.0
ND1 D:HIS63 2.4 41.7 1.0
CD D:GLU60 3.1 28.7 1.0
CD D:GLU24 3.2 35.7 1.0
OE2 D:GLU60 3.2 38.9 1.0
CE1 D:HIS63 3.3 44.9 1.0
CG D:HIS63 3.3 35.7 1.0
OE2 D:GLU24 3.4 31.1 1.0
CB D:HIS63 3.6 31.2 1.0
O D:HOH303 3.9 43.2 1.0
O D:HOH301 3.9 45.8 1.0
O D:HOH307 4.0 39.0 1.0
OE1 D:GLN140 4.1 32.7 1.0
OE2 D:GLU139 4.1 51.3 1.0
NE2 D:HIS63 4.3 48.6 1.0
CD2 D:HIS63 4.4 35.4 1.0
CG D:GLU60 4.5 28.5 1.0
CA D:GLU60 4.5 25.9 1.0
CG1 D:VAL109 4.5 30.1 1.0
CG D:GLU24 4.6 25.4 1.0
CB D:GLU60 4.8 26.5 1.0
O D:GLU60 4.9 24.7 1.0
CD D:GLU139 5.0 52.1 1.0
CD1 D:TYR136 5.0 29.9 1.0
CD D:GLN140 5.0 29.5 1.0
CB D:GLU24 5.0 26.1 1.0

Iron binding site 5 out of 6 in 7ek4

Go back to Iron Binding Sites List in 7ek4
Iron binding site 5 out of 6 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe202

b:45.0
occ:1.00
 OE1 E:GLU24 2.2 35.1 1.0
OE1 E:GLU60 2.4 32.7 1.0
ND1 E:HIS63 2.5 44.0 1.0
CD E:GLU24 3.1 28.9 1.0
CD E:GLU60 3.1 33.1 1.0
O E:HOH315 3.2 41.4 1.0
OE2 E:GLU60 3.2 40.8 1.0
OE2 E:GLU24 3.3 35.6 1.0
CG E:HIS63 3.4 42.9 1.0
CE1 E:HIS63 3.4 40.8 1.0
CB E:HIS63 3.6 32.0 1.0
OE1 E:GLN140 3.8 32.1 1.0
CG1 E:VAL109 4.3 26.9 1.0
OE2 E:GLU139 4.4 57.7 1.0
CG E:GLU24 4.5 27.8 1.0
CG E:GLU60 4.5 31.1 1.0
NE2 E:HIS63 4.5 42.9 1.0
CD2 E:HIS63 4.6 39.6 1.0
CA E:GLU60 4.6 32.1 1.0
CD E:GLN140 4.8 30.9 1.0
CB E:GLU60 4.8 30.4 1.0
CB E:GLU24 4.9 26.0 1.0
CD1 E:TYR136 4.9 25.8 1.0

Iron binding site 6 out of 6 in 7ek4

Go back to Iron Binding Sites List in 7ek4
Iron binding site 6 out of 6 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe202

b:40.9
occ:1.00
 OE1 F:GLU60 2.1 33.2 1.0
O F:HOH310 2.2 41.5 1.0
OE1 F:GLU24 2.2 36.8 1.0
ND1 F:HIS63 2.6 39.4 1.0
CD F:GLU60 3.0 35.2 1.0
CD F:GLU24 3.1 31.6 1.0
OE2 F:GLU60 3.2 44.1 1.0
OE2 F:GLU24 3.3 37.2 1.0
CG F:HIS63 3.4 36.0 1.0
CE1 F:HIS63 3.5 43.7 1.0
CB F:HIS63 3.6 25.7 1.0
O F:HOH305 3.9 38.8 1.0
O F:HOH304 3.9 39.1 1.0
OE1 F:GLN140 4.1 35.8 1.0
CG F:GLU60 4.3 26.4 1.0
CA F:GLU60 4.4 29.5 1.0
OE2 F:GLU139 4.4 54.0 1.0
CG1 F:VAL109 4.4 27.1 1.0
CG F:GLU24 4.4 25.6 1.0
CD2 F:HIS63 4.5 39.9 1.0
NE2 F:HIS63 4.5 50.8 1.0
CB F:GLU60 4.6 24.3 1.0
O F:GLU60 4.8 25.7 1.0
CB F:GLU24 4.9 25.3 1.0

Reference:

Y.Wang, J.Zang, C.Wang, X.Zhang, G.Zhao. Structural Insights For the Stronger Ability of Shrimp Ferritin to Coordinate with Heavy Metal Ions As Compared to Human H-Chain Ferritin. Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34360624
DOI: 10.3390/IJMS22157859
Page generated: Thu Aug 8 05:19:12 2024

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