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
Go back to
Iron Binding Sites List in 7dyb
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
Go back to
Iron Binding Sites List in 7dyb
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
Go back to
Iron Binding Sites List in 7dyb
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
|