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Iron in PDB 7dyb: Thermotoga Maritima Ferritin Mutant-Flal-L

Enzymatic activity of Thermotoga Maritima Ferritin Mutant-Flal-L

All present enzymatic activity of Thermotoga Maritima Ferritin Mutant-Flal-L:
1.16.3.2;

Protein crystallography data

The structure of Thermotoga Maritima Ferritin Mutant-Flal-L, PDB code: 7dyb was solved by G.Zhao, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.32 / 1.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.343, 54.647, 59.91, 90, 109.94, 90
R / Rfree (%) 19.4 / 23.5

Iron Binding Sites:

The binding sites of Iron atom in the Thermotoga Maritima Ferritin Mutant-Flal-L (pdb code 7dyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Thermotoga Maritima Ferritin Mutant-Flal-L, PDB code: 7dyb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 1 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:24.4
occ:0.70
 OE1 H:GLU19 2.0 28.4 1.0
O H:HOH337 2.1 25.8 1.0
O H:HOH361 2.1 32.4 1.0
ND1 H:HIS55 2.1 22.4 1.0
OE1 H:GLU52 2.2 24.4 1.0
O H:HOH359 2.7 31.2 1.0
CE1 H:HIS55 3.0 22.6 1.0
CD H:GLU19 3.1 27.4 1.0
CG H:HIS55 3.2 21.8 1.0
CD H:GLU52 3.3 20.6 1.0
FE H:FE202 3.4 26.2 0.6
OE2 H:GLU19 3.5 33.7 1.0
CB H:HIS55 3.6 20.8 1.0
OE2 H:GLU52 3.7 22.7 1.0
NE2 H:HIS55 4.2 22.9 1.0
CD2 H:HIS55 4.3 23.0 1.0
OE1 H:GLN129 4.3 23.7 1.0
O H:HOH354 4.3 30.6 1.0
CG H:GLU19 4.4 26.5 1.0
OE2 H:GLU132 4.5 25.6 1.0
CG H:GLU52 4.5 17.7 1.0
CA H:GLU52 4.6 19.6 1.0
CB H:GLU52 4.7 19.4 1.0
CB H:GLU19 4.7 20.1 1.0
CG1 H:VAL99 4.8 22.2 1.0
OE1 H:GLU132 4.8 26.9 1.0

Iron binding site 2 out of 6 in 7dyb

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Iron binding site 2 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe202

b:26.2
occ:0.64
 O H:HOH337 2.1 25.8 1.0
OE2 H:GLU96 2.1 27.2 1.0
OE2 H:GLU52 2.2 22.7 1.0
OE1 H:GLU132 2.3 26.9 1.0
OE1 H:GLU96 2.4 24.1 1.0
CD H:GLU96 2.6 25.8 1.0
O H:HOH359 2.7 31.2 1.0
CD H:GLU52 3.0 20.6 1.0
OE1 H:GLU52 3.1 24.4 1.0
CD H:GLU132 3.3 25.2 1.0
FE H:FE201 3.4 24.4 0.7
OE2 H:GLU132 3.6 25.6 1.0
CG H:GLU96 4.1 23.1 1.0
OE1 H:GLN129 4.1 23.7 1.0
NE2 H:GLN48 4.2 24.2 1.0
CE2 H:TYR26 4.3 24.4 1.0
CG H:GLU52 4.4 17.7 1.0
O H:HOH413 4.4 29.3 1.0
OH H:TYR26 4.5 27.8 1.0
O H:HOH361 4.6 32.4 1.0
CE1 H:HIS55 4.6 22.6 1.0
CG H:GLU132 4.6 27.2 1.0
NE2 H:GLN129 4.7 21.0 1.0
ND1 H:HIS55 4.7 22.4 1.0
CD H:GLN129 4.8 20.3 1.0
CB H:GLU132 4.9 25.0 1.0
CZ H:TYR26 4.9 26.0 1.0

Iron binding site 3 out of 6 in 7dyb

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Iron binding site 3 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:29.1
occ:0.67
 OE2 A:GLU19 2.0 29.3 1.0
O A:HOH332 2.0 23.7 1.0
OE1 A:GLU52 2.1 23.7 1.0
CD2 A:HIS55 2.2 19.9 1.0
CD A:GLU19 3.0 29.9 1.0
CG A:HIS55 3.2 23.0 1.0
FE A:FE202 3.2 23.6 0.6
CD A:GLU52 3.2 24.5 1.0
O A:HOH389 3.3 32.4 1.0
NE2 A:HIS55 3.3 24.5 1.0
OE1 A:GLU19 3.3 37.4 1.0
CB A:HIS55 3.6 24.2 1.0
OE2 A:GLU52 3.7 24.7 1.0
OE1 A:GLN129 4.2 22.7 1.0
CG A:GLU19 4.3 25.4 1.0
ND1 A:HIS55 4.3 27.4 1.0
CE1 A:HIS55 4.4 24.2 1.0
CG A:GLU52 4.5 19.9 1.0
OE2 A:GLU132 4.5 38.4 1.0
CA A:GLU52 4.5 21.6 1.0
O A:HOH339 4.5 31.6 1.0
CB A:GLU19 4.6 21.4 1.0
OE1 A:GLU132 4.6 32.2 1.0
CB A:GLU52 4.7 21.0 1.0
CG1 A:VAL99 4.7 20.4 1.0
CD A:GLU132 4.9 30.7 1.0
OE1 A:GLU96 4.9 24.3 1.0
O A:GLU52 5.0 21.8 1.0

Iron binding site 4 out of 6 in 7dyb

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Iron binding site 4 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:23.6
occ:0.58
 O A:HOH332 2.0 23.7 1.0
OE2 A:GLU96 2.2 29.6 1.0
OE2 A:GLU52 2.2 24.7 1.0
OE1 A:GLU132 2.3 32.2 1.0
O A:HOH389 2.4 32.4 1.0
OE1 A:GLU96 2.5 24.3 1.0
CD A:GLU96 2.6 28.2 1.0
CD A:GLU52 2.9 24.5 1.0
OE1 A:GLU52 3.0 23.7 1.0
FE A:FE201 3.2 29.1 0.7
CD A:GLU132 3.3 30.7 1.0
OE2 A:GLU132 3.7 38.4 1.0
NE2 A:GLN48 4.1 24.3 1.0
OE1 A:GLN129 4.1 22.7 1.0
CG A:GLU96 4.1 24.6 1.0
CG A:GLU52 4.3 19.9 1.0
OH A:TYR26 4.4 29.6 1.0
CE2 A:TYR26 4.4 25.4 1.0
CD2 A:HIS55 4.4 19.9 1.0
CG A:GLU132 4.5 33.5 1.0
NE2 A:HIS55 4.6 24.5 1.0
CB A:GLU132 4.6 28.5 1.0
NE2 A:GLN129 4.7 19.7 1.0
OE2 A:GLU19 4.8 29.3 1.0
CD A:GLN129 4.9 24.6 1.0
CZ A:TYR26 4.9 29.0 1.0

Iron binding site 5 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 5 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:25.1
occ:0.78
 O B:HOH334 2.0 29.6 1.0
OE1 B:GLU52 2.1 27.6 1.0
OE1 B:GLU19 2.1 27.6 1.0
O B:HOH341 2.2 30.6 1.0
ND1 B:HIS55 2.2 24.3 1.0
O B:HOH398 2.9 36.7 1.0
CE1 B:HIS55 3.1 24.5 1.0
CD B:GLU19 3.2 26.2 1.0
CD B:GLU52 3.2 27.0 1.0
FE B:FE202 3.2 28.4 0.5
CG B:HIS55 3.3 24.7 1.0
OE2 B:GLU19 3.5 34.2 1.0
OE2 B:GLU52 3.6 28.6 1.0
CB B:HIS55 3.7 21.9 1.0
OE1 B:GLN129 4.1 29.1 1.0
NE2 B:HIS55 4.3 28.5 1.0
CD2 B:HIS55 4.4 24.1 1.0
CG B:GLU19 4.5 25.9 1.0
CG B:GLU52 4.5 18.9 1.0
CA B:GLU52 4.5 22.4 1.0
CB B:GLU52 4.6 20.1 1.0
OE1 B:GLU132 4.6 34.5 1.0
CG1 B:VAL99 4.8 24.0 1.0
CB B:GLU19 4.8 18.5 1.0
OE1 B:GLU96 5.0 27.8 1.0
CD B:GLU132 5.0 31.7 1.0

Iron binding site 6 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 6 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:28.4
occ:0.53
 O B:HOH334 1.8 29.6 1.0
OE2 B:GLU52 2.2 28.6 1.0
OE2 B:GLU96 2.3 34.5 1.0
OE1 B:GLU132 2.4 34.5 1.0
OE1 B:GLU96 2.5 27.8 1.0
O B:HOH398 2.6 36.7 1.0
CD B:GLU96 2.7 28.1 1.0
CD B:GLU52 2.9 27.0 1.0
OE1 B:GLU52 3.0 27.6 1.0
FE B:FE201 3.2 25.1 0.8
CD B:GLU132 3.4 31.7 1.0
OE1 B:GLN129 4.0 29.1 1.0
NE2 B:GLN48 4.1 24.5 1.0
CG B:GLU96 4.1 27.9 1.0
OE2 B:GLU132 4.2 40.1 1.0
CG B:GLU132 4.3 32.0 1.0
OH B:TYR26 4.3 33.0 1.0
CE2 B:TYR26 4.3 25.1 1.0
CG B:GLU52 4.4 18.9 1.0
O B:HOH341 4.4 30.6 1.0
CB B:GLU132 4.4 29.6 1.0
CE1 B:HIS55 4.5 24.5 1.0
ND1 B:HIS55 4.5 24.3 1.0
NE2 B:GLN129 4.6 24.3 1.0
CD B:GLN129 4.8 28.4 1.0
CZ B:TYR26 4.8 26.8 1.0
OE1 B:GLU19 5.0 27.6 1.0

Reference:

X.Zhang, Y.Liu, B.Zheng, J.Zang, C.Lv, T.Zhang, H.Wang, G.Zhao. Protein Interface Redesign Facilitates the Transformation of Nanocage Building Blocks to 1D and 2D Nanomaterials. Nat Commun V. 12 4849 2021.
ISSN: ESSN 2041-1723
PubMed: 34381032
DOI: 10.1038/S41467-021-25199-X
Page generated: Thu Aug 8 04:36:43 2024

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