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Iron in PDB 5u1a: Ferritin with Gc Mtre Loop 1 Inserted at HIS34

Enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34

All present enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34:
1.16.3.2;

Protein crystallography data

The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a was solved by S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 128.412, 128.412, 165.041, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.6

Other elements in 5u1a:

The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Sodium (Na) 30 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34 (pdb code 5u1a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5u1a

Go back to Iron Binding Sites List in 5u1a
Iron binding site 1 out of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:42.0
occ:1.00
 O D:HOH384 2.3 23.0 1.0
NE2 D:HIS164 2.4 32.6 1.0
NE2 A:HIS164 2.4 33.2 1.0
NE2 B:HIS164 2.6 32.7 1.0
O B:HOH378 3.2 41.8 1.0
CE1 D:HIS164 3.3 30.7 1.0
CD2 A:HIS164 3.3 32.6 1.0
CD2 D:HIS164 3.4 29.0 1.0
CE1 A:HIS164 3.4 33.8 1.0
CD2 B:HIS164 3.5 33.8 1.0
CE1 B:HIS164 3.7 34.4 1.0
ND1 D:HIS164 4.4 27.9 1.0
CG D:HIS164 4.5 29.0 1.0
CG A:HIS164 4.5 30.8 1.0
CD1 B:LEU168 4.5 26.3 1.0
ND1 A:HIS164 4.5 28.6 1.0
CD1 A:LEU168 4.6 23.2 1.0
CG B:HIS164 4.7 31.1 1.0
CD1 D:LEU168 4.7 24.6 1.0
ND1 B:HIS164 4.8 30.9 1.0
OD1 A:ASN163 5.0 40.6 1.0
OD1 B:ASN163 5.0 56.4 1.0

Iron binding site 2 out of 6 in 5u1a

Go back to Iron Binding Sites List in 5u1a
Iron binding site 2 out of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe204

b:37.9
occ:0.25
 O E:HOH390 2.2 23.8 0.2
NE2 E:HIS164 2.4 36.2 1.0
O E:HOH392 3.0 34.2 0.2
CE1 E:HIS164 3.3 36.0 1.0
CD2 E:HIS164 3.5 35.7 1.0
ND1 E:HIS164 4.4 31.7 1.0
CG E:HIS164 4.6 31.6 1.0
OD1 E:ASN163 4.6 36.5 1.0
CD1 E:LEU168 4.9 24.9 1.0

Iron binding site 3 out of 6 in 5u1a

Go back to Iron Binding Sites List in 5u1a
Iron binding site 3 out of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe206

b:37.5
occ:0.25
 O F:HOH413 2.0 13.7 0.2
O F:HOH421 2.5 50.0 0.2
NE2 F:HIS164 2.5 39.9 1.0
CE1 F:HIS164 3.4 40.4 1.0
CD2 F:HIS164 3.5 38.9 1.0
ND1 F:HIS164 4.5 34.9 1.0
CG F:HIS164 4.6 33.1 1.0
OD1 F:ASN163 4.7 47.7 1.0
CD1 F:LEU168 4.8 22.8 1.0

Iron binding site 4 out of 6 in 5u1a

Go back to Iron Binding Sites List in 5u1a
Iron binding site 4 out of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe203

b:39.6
occ:1.00
 NE2 G:HIS164 2.4 29.4 1.0
O G:HOH415 2.4 26.3 1.0
NE2 J:HIS164 2.5 33.7 1.0
NE2 H:HIS164 2.7 36.7 1.0
O J:HOH385 3.1 41.3 1.0
CD2 G:HIS164 3.3 30.9 1.0
CE1 G:HIS164 3.4 29.3 1.0
CD2 J:HIS164 3.4 32.2 1.0
CE1 J:HIS164 3.4 33.7 1.0
CD2 H:HIS164 3.5 36.0 1.0
CE1 H:HIS164 3.7 35.5 1.0
CD1 H:LEU168 4.5 26.0 1.0
CG G:HIS164 4.5 29.4 1.0
ND1 G:HIS164 4.5 29.9 1.0
ND1 J:HIS164 4.5 30.2 1.0
CG J:HIS164 4.6 30.4 1.0
CD1 G:LEU168 4.6 25.4 1.0
CG H:HIS164 4.7 30.7 1.0
CD1 J:LEU168 4.7 26.7 1.0
ND1 H:HIS164 4.8 30.6 1.0
OD1 G:ASN163 4.8 41.2 1.0
OD1 H:ASN163 5.0 51.1 1.0

Iron binding site 5 out of 6 in 5u1a

Go back to Iron Binding Sites List in 5u1a
Iron binding site 5 out of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe203

b:38.5
occ:0.25
 NE2 K:HIS164 2.4 30.6 1.0
O K:HOH420 2.5 26.3 0.2
CD2 K:HIS164 3.3 32.7 1.0
CE1 K:HIS164 3.4 32.2 1.0
ND1 K:HIS164 4.5 31.5 1.0
CG K:HIS164 4.5 28.7 1.0
CD1 K:LEU168 4.8 23.6 1.0
OD1 K:ASN163 4.8 47.8 1.0

Iron binding site 6 out of 6 in 5u1a

Go back to Iron Binding Sites List in 5u1a
Iron binding site 6 out of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe206

b:42.7
occ:0.25
 O L:HOH412 2.3 21.3 0.2
NE2 L:HIS164 2.3 34.5 1.0
O L:HOH422 2.6 48.1 0.2
CE1 L:HIS164 3.2 33.5 1.0
CD2 L:HIS164 3.4 35.1 1.0
ND1 L:HIS164 4.3 29.1 1.0
CG L:HIS164 4.4 31.0 1.0
OD1 L:ASN163 4.7 43.4 1.0
CD1 L:LEU168 4.9 25.4 1.0

Reference:

L.Wang, D.Xing, A.Le Van, A.E.Jerse, S.Wang. Structure-Based Design of Ferritin Nanoparticle Immunogens Displaying Antigenic Loops of Neisseria Gonorrhoeae. Febs Open Bio V. 7 1196 2017.
ISSN: ESSN 2211-5463
PubMed: 28781959
DOI: 10.1002/2211-5463.12267
Page generated: Tue Aug 6 09:44:20 2024

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