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Iron in PDB 5jkk: Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin

Enzymatic activity of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin

All present enzymatic activity of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin, PDB code: 5jkk was solved by M.Kuenzle, T.Beck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.37 / 1.60
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 180.980, 180.980, 180.980, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 14.3

Other elements in 5jkk:

The structure of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin also contains other interesting chemical elements:

Magnesium (Mg) 17 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin (pdb code 5jkk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin, PDB code: 5jkk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 5jkk

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Iron binding site 1 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:18.5
occ:1.00
OE1 A:GLU27 2.0 10.6 1.0
O A:HOH311 2.0 21.3 1.0
OE1 A:GLU62 2.1 14.3 1.0
O A:HOH334 2.1 10.6 1.0
ND1 A:HIS65 2.1 16.7 1.0
O A:HOH343 2.2 30.2 1.0
CE1 A:HIS65 3.0 20.4 1.0
CD A:GLU27 3.0 10.8 1.0
CD A:GLU62 3.0 17.9 1.0
CG A:HIS65 3.2 14.3 1.0
OE2 A:GLU62 3.4 19.8 1.0
OE2 A:GLU27 3.4 9.8 1.0
CB A:HIS65 3.7 10.3 1.0
OE1 A:GLN141 4.0 18.7 1.0
NE2 A:HIS65 4.2 18.8 1.0
CG A:GLU62 4.3 10.8 1.0
CD2 A:HIS65 4.3 16.5 1.0
CG A:GLU27 4.3 8.6 1.0
CG1 A:VAL110 4.4 11.7 1.0
O A:HOH441 4.6 33.2 1.0
CA A:GLU62 4.6 7.6 1.0
CB A:GLU62 4.7 8.6 1.0
CB A:GLU27 4.7 6.8 1.0
CD A:GLN141 4.9 14.3 1.0
OE1 A:GLU107 5.0 23.3 1.0
CA A:GLU27 5.0 6.7 1.0

Iron binding site 2 out of 10 in 5jkk

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Iron binding site 2 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:27.4
occ:0.50
CE1 G:HIS173 2.5 12.1 1.0
CL A:CL205 2.5 9.7 1.0
CE1 C:HIS173 2.6 12.7 1.0
NE2 G:HIS173 2.6 12.5 1.0
NE2 A:HIS173 2.6 12.3 1.0
CE1 A:HIS173 2.6 12.0 1.0
NE2 F:HIS173 2.6 10.9 1.0
CE1 F:HIS173 2.6 13.0 1.0
NE2 C:HIS173 2.6 11.8 1.0
ND1 G:HIS173 3.7 13.1 1.0
ND1 C:HIS173 3.8 13.7 1.0
ND1 A:HIS173 3.8 13.2 1.0
ND1 F:HIS173 3.8 13.5 1.0
CD2 G:HIS173 3.8 11.8 1.0
CD2 A:HIS173 3.9 12.7 1.0
CD2 C:HIS173 3.9 12.2 1.0
CD2 F:HIS173 3.9 12.1 1.0
CG G:HIS173 4.4 9.3 1.0
CG C:HIS173 4.4 9.4 1.0
CG A:HIS173 4.4 9.8 1.0
CG F:HIS173 4.5 9.6 1.0

Iron binding site 3 out of 10 in 5jkk

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Iron binding site 3 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:19.1
occ:1.00
OE1 B:GLU27 2.0 10.4 1.0
OE1 B:GLU62 2.1 15.1 1.0
ND1 B:HIS65 2.1 17.8 1.0
O B:HOH309 2.1 23.8 1.0
O B:HOH334 2.1 10.4 1.0
CE1 B:HIS65 2.9 22.9 1.0
CD B:GLU27 3.0 11.0 1.0
CD B:GLU62 3.0 18.4 1.0
CG B:HIS65 3.2 16.2 1.0
OE2 B:GLU62 3.3 19.5 1.0
OE2 B:GLU27 3.4 10.1 1.0
CB B:HIS65 3.6 9.8 1.0
OE1 B:GLN141 4.0 19.5 1.0
NE2 B:HIS65 4.1 21.3 1.0
CD2 B:HIS65 4.3 18.6 1.0
CG B:GLU27 4.3 9.0 1.0
CG B:GLU62 4.3 10.7 1.0
CG1 B:VAL110 4.4 11.4 1.0
O B:HOH443 4.5 37.3 1.0
CA B:GLU62 4.6 7.7 1.0
CB B:GLU27 4.7 8.0 1.0
CB B:GLU62 4.7 8.6 1.0
CD B:GLN141 4.9 14.2 1.0
CA B:GLU27 4.9 6.3 1.0

Iron binding site 4 out of 10 in 5jkk

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Iron binding site 4 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:18.4
occ:1.00
OE1 C:GLU27 2.0 10.6 1.0
OE1 C:GLU62 2.0 13.8 1.0
O C:HOH331 2.0 29.2 1.0
ND1 C:HIS65 2.1 15.1 1.0
O C:HOH344 2.1 11.3 1.0
O C:HOH313 2.2 24.1 1.0
CE1 C:HIS65 3.0 19.3 1.0
CD C:GLU62 3.0 16.1 1.0
CD C:GLU27 3.0 9.9 1.0
CG C:HIS65 3.2 14.6 1.0
OE2 C:GLU62 3.3 19.9 1.0
OE2 C:GLU27 3.4 10.8 1.0
CB C:HIS65 3.7 9.4 1.0
O C:HOH343 3.9 25.7 1.0
OE1 C:GLN141 4.0 19.3 1.0
NE2 C:HIS65 4.2 20.4 1.0
CG C:GLU62 4.3 11.0 1.0
CD2 C:HIS65 4.3 18.8 1.0
CG C:GLU27 4.3 9.0 1.0
CG1 C:VAL110 4.4 12.3 1.0
CA C:GLU62 4.6 7.3 1.0
CB C:GLU62 4.6 8.7 1.0
CB C:GLU27 4.7 7.0 1.0
O C:HOH404 4.9 26.6 1.0
OE1 C:GLU107 4.9 23.2 1.0
CD C:GLN141 4.9 14.3 1.0
CA C:GLU27 4.9 6.7 1.0

Iron binding site 5 out of 10 in 5jkk

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Iron binding site 5 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:18.0
occ:1.00
OE1 D:GLU27 2.0 9.8 1.0
OE1 D:GLU62 2.1 14.1 1.0
O D:HOH312 2.1 23.8 1.0
ND1 D:HIS65 2.1 16.1 1.0
O D:HOH325 2.1 11.7 1.0
CE1 D:HIS65 3.0 19.6 1.0
CD D:GLU62 3.0 16.2 1.0
CD D:GLU27 3.0 9.8 1.0
CG D:HIS65 3.3 13.8 1.0
OE2 D:GLU62 3.3 22.2 1.0
OE2 D:GLU27 3.4 9.7 1.0
CB D:HIS65 3.7 10.2 1.0
OE1 D:GLN141 4.0 20.9 1.0
NE2 D:HIS65 4.2 19.5 1.0
CG D:GLU27 4.3 7.6 1.0
CG D:GLU62 4.3 10.2 1.0
CD2 D:HIS65 4.3 15.8 1.0
CG1 D:VAL110 4.4 12.9 1.0
CB D:GLU62 4.6 7.8 1.0
CA D:GLU62 4.6 7.9 1.0
CB D:GLU27 4.7 6.4 1.0
OE1 D:GLU107 4.9 23.3 1.0
CD D:GLN141 4.9 14.2 1.0
CA D:GLU27 5.0 5.8 1.0

Iron binding site 6 out of 10 in 5jkk

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Iron binding site 6 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:12.1
occ:0.25
NE2 E:HIS173 2.6 12.6 1.0
CL D:CL205 2.6 2.0 0.2
CE1 D:HIS173 2.6 13.6 1.0
NE2 D:HIS173 2.6 12.9 1.0
CE1 E:HIS173 2.6 12.7 1.0
ND1 D:HIS173 3.8 13.1 1.0
ND1 E:HIS173 3.8 12.6 1.0
CD2 E:HIS173 3.9 11.7 1.0
CD2 D:HIS173 3.9 11.2 1.0
CG E:HIS173 4.4 9.3 1.0
CG D:HIS173 4.4 10.0 1.0

Iron binding site 7 out of 10 in 5jkk

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Iron binding site 7 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:18.4
occ:1.00
OE1 E:GLU27 2.0 10.5 1.0
OE1 E:GLU62 2.0 14.5 1.0
ND1 E:HIS65 2.1 18.1 1.0
O E:HOH314 2.1 25.6 1.0
O E:HOH323 2.2 12.1 1.0
CE1 E:HIS65 2.9 22.5 1.0
CD E:GLU62 3.0 17.4 1.0
CD E:GLU27 3.1 10.3 1.0
CG E:HIS65 3.2 15.8 1.0
OE2 E:GLU62 3.3 21.6 1.0
OE2 E:GLU27 3.4 9.5 1.0
CB E:HIS65 3.7 10.0 1.0
OE1 E:GLN141 3.9 18.7 1.0
NE2 E:HIS65 4.1 20.3 1.0
CD2 E:HIS65 4.3 18.0 1.0
CG E:GLU62 4.3 10.7 1.0
CG E:GLU27 4.4 8.3 1.0
CG1 E:VAL110 4.5 12.4 1.0
CA E:GLU62 4.6 7.7 1.0
CB E:GLU62 4.6 8.6 1.0
CB E:GLU27 4.7 7.2 1.0
CD E:GLN141 5.0 14.1 1.0
OE1 E:GLU107 5.0 23.7 1.0
CA E:GLU27 5.0 6.7 1.0

Iron binding site 8 out of 10 in 5jkk

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Iron binding site 8 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:18.6
occ:1.00
OE1 F:GLU27 2.0 10.1 1.0
OE1 F:GLU62 2.1 14.7 1.0
O F:HOH308 2.1 23.8 1.0
ND1 F:HIS65 2.1 16.7 1.0
O F:HOH345 2.1 12.2 1.0
CE1 F:HIS65 3.0 21.5 1.0
CD F:GLU27 3.0 10.4 1.0
CD F:GLU62 3.0 16.1 1.0
CG F:HIS65 3.3 15.0 1.0
OE2 F:GLU62 3.3 20.5 1.0
OE2 F:GLU27 3.4 10.7 1.0
CB F:HIS65 3.7 10.4 1.0
OE1 F:GLN141 3.9 19.7 1.0
NE2 F:HIS65 4.2 17.8 1.0
CG F:GLU27 4.3 9.1 1.0
CD2 F:HIS65 4.3 16.6 1.0
CG F:GLU62 4.3 11.6 1.0
CG1 F:VAL110 4.4 10.8 1.0
CB F:GLU62 4.6 8.6 1.0
CA F:GLU62 4.7 7.3 1.0
CB F:GLU27 4.7 7.6 1.0
CD F:GLN141 4.9 14.2 1.0
OE1 F:GLU107 5.0 23.9 1.0
CA F:GLU27 5.0 6.9 1.0
O F:HOH355 5.0 29.5 1.0

Iron binding site 9 out of 10 in 5jkk

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Iron binding site 9 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:18.8
occ:1.00
OE1 G:GLU27 2.0 9.6 1.0
OE1 G:GLU62 2.1 14.0 1.0
O G:HOH315 2.1 24.4 1.0
ND1 G:HIS65 2.1 17.8 1.0
O G:HOH334 2.1 11.1 1.0
CE1 G:HIS65 3.0 21.6 1.0
CD G:GLU62 3.0 16.9 1.0
CD G:GLU27 3.1 10.5 1.0
CG G:HIS65 3.2 15.5 1.0
OE2 G:GLU62 3.3 20.9 1.0
OE2 G:GLU27 3.4 10.1 1.0
CB G:HIS65 3.7 10.9 1.0
OE1 G:GLN141 4.0 18.8 1.0
NE2 G:HIS65 4.1 20.7 1.0
CG G:GLU62 4.3 10.6 1.0
CD2 G:HIS65 4.3 17.5 1.0
CG G:GLU27 4.3 9.2 1.0
CG1 G:VAL110 4.4 10.7 1.0
CA G:GLU62 4.6 8.1 1.0
CB G:GLU62 4.7 9.2 1.0
CB G:GLU27 4.7 7.0 1.0
CD G:GLN141 4.9 14.6 1.0
OE1 G:GLU107 4.9 22.4 1.0
CA G:GLU27 5.0 6.3 1.0

Iron binding site 10 out of 10 in 5jkk

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Iron binding site 10 out of 10 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:18.2
occ:1.00
O H:HOH329 2.0 24.6 1.0
OE1 H:GLU27 2.0 10.1 1.0
OE1 H:GLU62 2.0 13.9 1.0
O H:HOH333 2.1 11.3 1.0
ND1 H:HIS65 2.1 16.3 1.0
CE1 H:HIS65 3.0 20.9 1.0
CD H:GLU62 3.0 16.9 1.0
CD H:GLU27 3.0 10.8 1.0
CG H:HIS65 3.2 14.9 1.0
OE2 H:GLU62 3.3 21.2 1.0
OE2 H:GLU27 3.4 10.1 1.0
CB H:HIS65 3.6 10.6 1.0
O H:HOH320 3.9 27.9 1.0
OE1 H:GLN141 4.0 20.2 1.0
NE2 H:HIS65 4.1 19.5 1.0
CD2 H:HIS65 4.3 16.3 1.0
CG H:GLU62 4.3 10.6 1.0
CG H:GLU27 4.3 8.7 1.0
CG1 H:VAL110 4.4 11.9 1.0
O H:HOH416 4.5 31.5 1.0
CB H:GLU62 4.6 8.4 1.0
CA H:GLU62 4.7 7.6 1.0
CB H:GLU27 4.7 7.6 1.0
OE1 H:GLU107 4.9 23.7 1.0
CD H:GLN141 4.9 12.9 1.0
O H:HOH358 5.0 29.4 1.0
CA H:GLU27 5.0 6.4 1.0

Reference:

M.Kuenzle, T.Eckert, T.Beck. Self-Assembly of Charged Protein Containers Enables Positioning of Nanoparticles in A 3-D Lattice to Form Biohybrid Materials To Be Published.
Page generated: Sun Dec 13 16:04:18 2020

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