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Iron in PDB 7dya: Crystal Structure of Tmftn with Calcium Ions

Enzymatic activity of Crystal Structure of Tmftn with Calcium Ions

All present enzymatic activity of Crystal Structure of Tmftn with Calcium Ions:
1.16.3.2;

Protein crystallography data

The structure of Crystal Structure of Tmftn with Calcium Ions, PDB code: 7dya was solved by X.Zhang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.58 / 2.20
Space group H 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.434, 175.434, 357.421, 90, 90, 120
R / Rfree (%) 17.5 / 20

Other elements in 7dya:

The structure of Crystal Structure of Tmftn with Calcium Ions also contains other interesting chemical elements:

Calcium (Ca) 9 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Tmftn with Calcium Ions (pdb code 7dya). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Tmftn with Calcium Ions, PDB code: 7dya:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 7dya

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Iron binding site 1 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:28.4
occ:0.68
 OE1 H:GLU19 2.1 31.0 1.0
O H:HOH305 2.1 32.3 1.0
OE1 H:GLU52 2.2 27.1 1.0
ND1 H:HIS55 2.2 29.4 1.0
O H:HOH309 2.4 40.7 1.0
CD H:GLU19 3.1 38.8 1.0
CE1 H:HIS55 3.1 34.2 1.0
CG H:HIS55 3.3 32.1 1.0
CD H:GLU52 3.3 28.7 1.0
FE H:FE202 3.3 35.6 1.0
OE2 H:GLU19 3.5 35.6 1.0
CB H:HIS55 3.6 28.5 1.0
OE2 H:GLU52 3.8 29.7 1.0
OE1 H:GLN129 4.0 31.0 1.0
NE2 H:HIS55 4.3 30.2 1.0
CG H:GLU19 4.4 28.6 1.0
CD2 H:HIS55 4.4 32.5 1.0
OE1 H:GLU132 4.4 32.8 1.0
CG1 H:VAL99 4.5 31.3 1.0
CA H:GLU52 4.6 28.8 1.0
CG H:GLU52 4.6 28.4 1.0
CB H:GLU19 4.7 27.2 1.0
CB H:GLU52 4.7 26.9 1.0
OE1 H:GLU96 5.0 31.9 1.0
O H:GLU52 5.0 28.3 1.0

Iron binding site 2 out of 16 in 7dya

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Iron binding site 2 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe202

b:35.6
occ:1.00
 OE1 H:GLU132 2.0 32.8 1.0
OE2 H:GLU52 2.1 29.7 1.0
O H:HOH305 2.1 32.3 1.0
OE2 H:GLU96 2.2 38.0 1.0
OE1 H:GLU96 2.5 31.9 1.0
CD H:GLU96 2.7 34.5 1.0
CD H:GLU52 2.9 28.7 1.0
OE1 H:GLU52 3.0 27.1 1.0
CD H:GLU132 3.2 32.7 1.0
FE H:FE201 3.3 28.4 0.7
CG H:GLU132 3.9 32.9 1.0
NE2 H:GLN48 3.9 32.8 1.0
OE1 H:GLN129 4.0 31.0 1.0
CG H:GLU96 4.1 30.2 1.0
OE2 H:GLU132 4.2 32.0 1.0
CE1 H:HIS55 4.3 34.2 1.0
CB H:GLU132 4.3 31.4 1.0
CG H:GLU52 4.4 28.4 1.0
ND1 H:HIS55 4.4 29.4 1.0
CE2 H:TYR26 4.5 30.3 1.0
OH H:TYR26 4.5 35.7 1.0
O H:HOH410 4.6 39.6 1.0
NE2 H:GLN129 4.7 26.0 1.0
CD H:GLN129 4.8 30.2 1.0
O H:HOH309 4.9 40.7 1.0
CZ H:TYR26 5.0 37.2 1.0
OE1 H:GLU19 5.0 31.0 1.0

Iron binding site 3 out of 16 in 7dya

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Iron binding site 3 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:39.0
occ:1.00
 OE1 A:GLU132 2.0 35.9 1.0
OE2 A:GLU52 2.2 30.1 1.0
OE2 A:GLU96 2.2 35.3 1.0
O A:HOH306 2.3 36.3 1.0
OE1 A:GLU96 2.4 32.5 1.0
CD A:GLU96 2.6 31.9 1.0
CD A:GLU52 2.9 28.8 1.0
OE1 A:GLU52 3.1 34.5 1.0
CD A:GLU132 3.2 33.9 1.0
FE A:FE202 3.4 31.4 0.6
CG A:GLU132 3.9 36.8 1.0
NE2 A:GLN48 3.9 29.5 1.0
OE1 A:GLN129 4.1 32.5 1.0
CG A:GLU96 4.1 29.6 1.0
OE2 A:GLU132 4.2 37.7 1.0
CE1 A:HIS55 4.2 37.0 1.0
ND1 A:HIS55 4.3 39.4 1.0
CB A:GLU132 4.3 33.1 1.0
CG A:GLU52 4.3 28.5 1.0
CE2 A:TYR26 4.5 26.1 1.0
OH A:TYR26 4.6 36.4 1.0
NE2 A:GLN129 4.8 27.5 1.0
CD A:GLN129 4.9 34.9 1.0
OE1 A:GLU19 4.9 35.2 1.0

Iron binding site 4 out of 16 in 7dya

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Iron binding site 4 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:31.4
occ:0.61
 O A:HOH306 2.0 36.3 1.0
OE1 A:GLU19 2.0 35.2 1.0
OE1 A:GLU52 2.2 34.5 1.0
ND1 A:HIS55 2.3 39.4 1.0
O A:HOH310 2.5 37.8 1.0
CD A:GLU19 2.9 39.8 1.0
OE2 A:GLU19 3.2 45.8 1.0
CE1 A:HIS55 3.2 37.0 1.0
CG A:HIS55 3.2 32.9 1.0
FE A:FE201 3.4 39.0 1.0
CD A:GLU52 3.4 28.8 1.0
CB A:HIS55 3.5 33.5 1.0
OE2 A:GLU52 3.8 30.1 1.0
OE1 A:GLN129 4.1 32.5 1.0
CG A:GLU19 4.3 31.8 1.0
NE2 A:HIS55 4.3 35.1 1.0
CD2 A:HIS55 4.4 34.9 1.0
CG1 A:VAL99 4.4 31.0 1.0
OE1 A:GLU132 4.5 35.9 1.0
CG A:GLU52 4.6 28.5 1.0
CA A:GLU52 4.7 31.7 1.0
CB A:GLU19 4.7 30.5 1.0
CB A:GLU52 4.8 26.9 1.0
O A:GLU52 5.0 28.8 1.0
OE1 A:GLU96 5.0 32.5 1.0

Iron binding site 5 out of 16 in 7dya

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Iron binding site 5 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:39.3
occ:1.00
 OE1 B:GLU132 2.0 36.4 1.0
OE2 B:GLU96 2.2 39.4 1.0
OE2 B:GLU52 2.2 29.9 1.0
O B:HOH309 2.3 37.0 1.0
OE1 B:GLU96 2.5 31.4 1.0
CD B:GLU96 2.7 33.3 1.0
CD B:GLU52 3.0 30.6 1.0
OE1 B:GLU52 3.1 32.0 1.0
CD B:GLU132 3.2 38.8 1.0
FE B:FE202 3.4 31.9 0.7
CG B:GLU132 3.8 35.3 1.0
NE2 B:GLN48 3.9 32.5 1.0
OE1 B:GLN129 4.1 35.5 1.0
CG B:GLU96 4.2 29.5 1.0
OE2 B:GLU132 4.2 39.6 1.0
CB B:GLU132 4.3 36.2 1.0
CE1 B:HIS55 4.4 32.9 1.0
CG B:GLU52 4.4 28.9 1.0
OH B:TYR26 4.5 36.9 1.0
CE2 B:TYR26 4.5 31.0 1.0
ND1 B:HIS55 4.5 37.9 1.0
NE2 B:GLN129 4.7 31.1 1.0
CD B:GLN129 4.9 33.0 1.0
CZ B:TYR26 5.0 38.1 1.0

Iron binding site 6 out of 16 in 7dya

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Iron binding site 6 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:31.9
occ:0.66
 O B:HOH309 2.0 37.0 1.0
OE1 B:GLU19 2.1 36.8 1.0
OE1 B:GLU52 2.2 32.0 1.0
ND1 B:HIS55 2.2 37.9 1.0
O B:HOH317 2.6 37.9 1.0
CD B:GLU19 3.0 38.3 1.0
CE1 B:HIS55 3.1 32.9 1.0
CG B:HIS55 3.3 34.2 1.0
OE2 B:GLU19 3.3 42.7 1.0
CD B:GLU52 3.4 30.6 1.0
FE B:FE201 3.4 39.3 1.0
CB B:HIS55 3.6 33.6 1.0
OE2 B:GLU52 3.9 29.9 1.0
OE1 B:GLN129 4.1 35.5 1.0
NE2 B:HIS55 4.3 33.1 1.0
CG B:GLU19 4.4 33.2 1.0
CD2 B:HIS55 4.4 33.2 1.0
CG1 B:VAL99 4.5 29.5 1.0
CA B:GLU52 4.6 29.0 1.0
OE1 B:GLU132 4.6 36.4 1.0
CG B:GLU52 4.6 28.9 1.0
CB B:GLU19 4.7 26.4 1.0
CB B:GLU52 4.7 24.2 1.0
O B:GLU52 4.9 28.3 1.0

Iron binding site 7 out of 16 in 7dya

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Iron binding site 7 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:33.0
occ:0.63
 O C:HOH324 1.9 37.9 1.0
OE1 C:GLU19 2.0 36.0 1.0
OE1 C:GLU52 2.2 31.3 1.0
ND1 C:HIS55 2.2 36.4 1.0
O C:HOH318 2.5 39.2 1.0
CD C:GLU19 3.0 40.5 1.0
CE1 C:HIS55 3.1 34.7 1.0
CG C:HIS55 3.2 30.2 1.0
CD C:GLU52 3.3 32.5 1.0
OE2 C:GLU19 3.3 42.9 1.0
FE C:FE202 3.4 36.5 1.0
CB C:HIS55 3.6 30.4 1.0
OE2 C:GLU52 3.8 34.3 1.0
OE1 C:GLN129 4.2 30.1 1.0
NE2 C:HIS55 4.2 32.1 1.0
CD2 C:HIS55 4.3 29.3 1.0
CG C:GLU19 4.3 32.2 1.0
OE1 C:GLU132 4.5 37.7 1.0
CA C:GLU52 4.5 33.2 1.0
CG1 C:VAL99 4.6 27.7 1.0
CG C:GLU52 4.6 31.1 1.0
CB C:GLU52 4.7 30.2 1.0
CB C:GLU19 4.7 29.5 1.0
O C:GLU52 4.9 32.8 1.0
OE1 C:GLU96 5.0 33.3 1.0

Iron binding site 8 out of 16 in 7dya

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Iron binding site 8 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:36.5
occ:1.00
 OE1 C:GLU132 2.1 37.7 1.0
OE2 C:GLU52 2.1 34.3 1.0
O C:HOH324 2.2 37.9 1.0
OE2 C:GLU96 2.2 37.6 1.0
OE1 C:GLU96 2.4 33.3 1.0
CD C:GLU96 2.6 35.7 1.0
CD C:GLU52 3.0 32.5 1.0
OE1 C:GLU52 3.1 31.3 1.0
CD C:GLU132 3.2 35.3 1.0
FE C:FE201 3.4 33.0 0.6
CG C:GLU132 3.8 33.4 1.0
NE2 C:GLN48 3.9 28.1 1.0
CG C:GLU96 4.1 33.8 1.0
OE1 C:GLN129 4.2 30.1 1.0
CE1 C:HIS55 4.2 34.7 1.0
OE2 C:GLU132 4.2 41.1 1.0
CB C:GLU132 4.3 33.1 1.0
ND1 C:HIS55 4.4 36.4 1.0
CG C:GLU52 4.4 31.1 1.0
CE2 C:TYR26 4.4 30.9 1.0
OH C:TYR26 4.5 36.5 1.0
NE2 C:GLN129 4.8 30.9 1.0
CZ C:TYR26 4.9 38.2 1.0
CD C:GLN129 5.0 31.1 1.0

Iron binding site 9 out of 16 in 7dya

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Iron binding site 9 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


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 Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:40.2
occ:1.00
 O D:HOH324 1.9 34.1 1.0
OE1 D:GLU132 2.1 40.7 1.0
OE2 D:GLU52 2.1 34.1 1.0
OE2 D:GLU96 2.2 40.2 1.0
OE1 D:GLU96 2.4 35.9 1.0
CD D:GLU96 2.6 38.5 1.0
CD D:GLU52 2.9 34.4 1.0
OE1 D:GLU52 3.1 34.3 1.0
CD D:GLU132 3.2 37.4 1.0
O D:HOH331 3.2 49.4 1.0
FE D:FE202 3.3 33.3 0.7
CG D:GLU132 3.7 37.7 1.0
OE1 D:GLN129 4.1 32.1 1.0
NE2 D:GLN48 4.1 31.8 1.0
CG D:GLU96 4.1 35.5 1.0
CB D:GLU132 4.2 36.0 1.0
OE2 D:GLU132 4.3 38.3 1.0
CE1 D:HIS55 4.3 38.1 1.0
CG D:GLU52 4.4 32.5 1.0
ND1 D:HIS55 4.4 38.2 1.0
CE2 D:TYR26 4.4 31.7 1.0
OH D:TYR26 4.6 36.0 1.0
NE2 D:GLN129 4.8 31.8 1.0
CD D:GLN129 4.9 31.5 1.0
OE1 D:GLU19 5.0 35.7 1.0
CZ D:TYR26 5.0 37.9 1.0

Iron binding site 10 out of 16 in 7dya

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Iron binding site 10 out of 16 in the Crystal Structure of Tmftn with Calcium Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:33.3
occ:0.68
 O D:HOH324 2.0 34.1 1.0
OE1 D:GLU19 2.1 35.7 1.0
OE1 D:GLU52 2.1 34.3 1.0
ND1 D:HIS55 2.2 38.2 1.0
CD D:GLU19 3.1 30.9 1.0
CE1 D:HIS55 3.1 38.1 1.0
CD D:GLU52 3.3 34.4 1.0
CG D:HIS55 3.3 36.5 1.0
FE D:FE201 3.3 40.2 1.0
O D:HOH331 3.4 49.4 1.0
OE2 D:GLU19 3.5 43.8 1.0
CB D:HIS55 3.6 32.6 1.0
OE2 D:GLU52 3.7 34.1 1.0
OE1 D:GLN129 4.0 32.1 1.0
NE2 D:HIS55 4.3 34.5 1.0
CD2 D:HIS55 4.4 35.6 1.0
CG D:GLU19 4.4 29.0 1.0
OE1 D:GLU132 4.4 40.7 1.0
CG D:GLU52 4.5 32.5 1.0
CG1 D:VAL99 4.6 32.9 1.0
CA D:GLU52 4.6 30.0 1.0
CB D:GLU52 4.7 31.1 1.0
CB D:GLU19 4.7 27.0 1.0
OE1 D:GLU96 4.9 35.9 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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