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Iron in PDB 5jkm: Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)

Enzymatic activity of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)

All present enzymatic activity of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition):
1.16.3.1;

Protein crystallography data

The structure of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition), PDB code: 5jkm 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) 47.60 / 1.80
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 126.840, 126.840, 175.020, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.1

Other elements in 5jkm:

The structure of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) also contains other interesting chemical elements:

Magnesium (Mg) 17 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) (pdb code 5jkm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition), PDB code: 5jkm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 5jkm

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Iron binding site 1 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:33.2
occ:1.00
OE1 A:GLU27 2.1 16.6 1.0
OE1 A:GLU62 2.1 18.7 1.0
O A:HOH315 2.2 15.7 1.0
ND1 A:HIS65 2.2 20.6 1.0
O A:HOH307 2.2 21.0 1.0
CD A:GLU62 3.0 21.2 1.0
CD A:GLU27 3.0 17.1 1.0
CE1 A:HIS65 3.1 22.0 1.0
CG A:HIS65 3.3 18.8 1.0
OE2 A:GLU62 3.3 22.7 1.0
OE2 A:GLU27 3.4 17.3 1.0
CB A:HIS65 3.7 16.0 1.0
OE1 A:GLN141 4.0 25.9 1.0
CG1 A:VAL110 4.2 18.3 1.0
NE2 A:HIS65 4.3 22.1 1.0
CG A:GLU27 4.3 15.3 1.0
CG A:GLU62 4.3 16.4 1.0
CD2 A:HIS65 4.4 20.1 1.0
CA A:GLU62 4.6 14.2 1.0
CB A:GLU27 4.6 14.7 1.0
CB A:GLU62 4.6 14.7 1.0
CD A:GLN141 4.9 18.7 1.0
OE1 A:GLU107 4.9 33.1 1.0
CA A:GLU27 5.0 14.1 1.0

Iron binding site 2 out of 12 in 5jkm

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Iron binding site 2 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:29.8
occ:1.00
OE1 B:GLU27 2.0 15.4 1.0
OE1 B:GLU62 2.0 18.8 1.0
O B:HOH317 2.2 17.4 1.0
O B:HOH321 2.2 24.5 1.0
ND1 B:HIS65 2.2 21.1 1.0
CD B:GLU62 3.0 20.7 1.0
CD B:GLU27 3.0 15.5 1.0
CE1 B:HIS65 3.1 24.0 1.0
CG B:HIS65 3.2 20.7 1.0
OE2 B:GLU62 3.3 25.0 1.0
OE2 B:GLU27 3.4 16.1 1.0
CB B:HIS65 3.6 17.5 1.0
O B:HOH376 4.0 27.5 1.0
OE1 B:GLN141 4.0 24.7 1.0
CG1 B:VAL110 4.2 15.4 1.0
NE2 B:HIS65 4.3 21.1 1.0
CD2 B:HIS65 4.3 20.4 1.0
CG B:GLU62 4.4 16.0 1.0
CG B:GLU27 4.4 14.9 1.0
CA B:GLU62 4.6 15.2 1.0
CB B:GLU62 4.7 15.3 1.0
CB B:GLU27 4.7 14.9 1.0
CD B:GLN141 4.9 21.3 1.0
CA B:GLU27 5.0 13.7 1.0

Iron binding site 3 out of 12 in 5jkm

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Iron binding site 3 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:27.1
occ:1.00
OE1 C:GLU27 2.0 17.2 1.0
O C:HOH336 2.1 19.3 1.0
OE1 C:GLU62 2.1 23.2 1.0
ND1 C:HIS65 2.2 17.2 1.0
O C:HOH339 2.2 13.5 1.0
CD C:GLU62 3.0 23.2 1.0
CE1 C:HIS65 3.0 21.9 1.0
CD C:GLU27 3.1 16.3 1.0
CG C:HIS65 3.2 15.9 1.0
OE2 C:GLU62 3.3 28.6 1.0
OE2 C:GLU27 3.5 17.1 1.0
CB C:HIS65 3.6 14.8 1.0
O C:HOH360 4.1 28.1 1.0
OE1 C:GLN141 4.1 23.4 1.0
NE2 C:HIS65 4.2 19.7 1.0
CG1 C:VAL110 4.3 18.0 1.0
CD2 C:HIS65 4.3 17.5 1.0
CG C:GLU62 4.4 17.4 1.0
CG C:GLU27 4.4 14.6 1.0
CA C:GLU62 4.5 14.6 1.0
CB C:GLU62 4.6 15.1 1.0
CB C:GLU27 4.7 13.5 1.0
O C:HOH334 4.9 51.4 1.0
CD C:GLN141 4.9 21.3 1.0
OE1 C:GLU107 5.0 32.8 1.0
CA C:GLU27 5.0 13.3 1.0

Iron binding site 4 out of 12 in 5jkm

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Iron binding site 4 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:28.4
occ:1.00
OE1 D:GLU27 2.0 17.0 1.0
OE1 D:GLU62 2.0 21.4 1.0
O D:HOH333 2.1 23.9 1.0
ND1 D:HIS65 2.1 18.1 1.0
O D:HOH331 2.1 16.3 1.0
CD D:GLU27 3.0 17.2 1.0
CD D:GLU62 3.0 22.2 1.0
CE1 D:HIS65 3.0 22.8 1.0
CG D:HIS65 3.2 19.5 1.0
OE2 D:GLU62 3.4 30.2 1.0
OE2 D:GLU27 3.4 17.1 1.0
CB D:HIS65 3.6 16.1 1.0
OE1 D:GLN141 4.0 22.0 1.0
NE2 D:HIS65 4.2 22.1 1.0
CG D:GLU27 4.3 15.7 1.0
CD2 D:HIS65 4.3 19.4 1.0
CG1 D:VAL110 4.3 17.6 1.0
CG D:GLU62 4.3 17.5 1.0
CA D:GLU62 4.5 13.9 1.0
CB D:GLU62 4.6 14.6 1.0
CB D:GLU27 4.7 15.2 1.0

Iron binding site 5 out of 12 in 5jkm

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Iron binding site 5 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:29.7
occ:1.00
OE1 E:GLU27 2.0 16.6 1.0
O E:HOH315 2.1 23.1 1.0
OE1 E:GLU62 2.1 22.2 1.0
O E:HOH310 2.1 16.4 1.0
ND1 E:HIS65 2.2 22.7 1.0
O E:HOH313 2.3 38.1 1.0
CE1 E:HIS65 3.0 25.7 1.0
CD E:GLU62 3.0 23.6 1.0
CD E:GLU27 3.0 16.8 1.0
CG E:HIS65 3.3 21.0 1.0
OE2 E:GLU62 3.3 24.7 1.0
OE2 E:GLU27 3.4 17.7 1.0
CB E:HIS65 3.7 16.9 1.0
O E:HOH351 3.9 32.8 1.0
OE1 E:GLN141 4.0 21.0 1.0
NE2 E:HIS65 4.2 23.2 1.0
CD2 E:HIS65 4.3 24.0 1.0
CG1 E:VAL110 4.3 18.7 1.0
CG E:GLU62 4.3 17.5 1.0
CG E:GLU27 4.4 14.5 1.0
CA E:GLU62 4.6 15.0 1.0
CB E:GLU62 4.7 15.1 1.0
CB E:GLU27 4.8 14.7 1.0
CD E:GLN141 4.9 18.2 1.0
OE1 E:GLU107 4.9 31.8 1.0

Iron binding site 6 out of 12 in 5jkm

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Iron binding site 6 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:27.5
occ:1.00
OE1 F:GLU27 2.0 15.8 1.0
OE1 F:GLU62 2.0 18.6 1.0
O F:HOH345 2.1 15.7 1.0
O F:HOH314 2.1 24.6 1.0
ND1 F:HIS65 2.2 20.8 1.0
CD F:GLU62 3.0 22.2 1.0
CD F:GLU27 3.1 16.4 1.0
CE1 F:HIS65 3.1 22.5 1.0
CG F:HIS65 3.2 19.8 1.0
OE2 F:GLU62 3.3 23.9 1.0
OE2 F:GLU27 3.5 18.7 1.0
CB F:HIS65 3.6 16.1 1.0
OE1 F:GLN141 4.1 24.4 1.0
O F:HOH394 4.1 28.0 1.0
NE2 F:HIS65 4.2 22.2 1.0
CG1 F:VAL110 4.3 16.4 1.0
CG F:GLU62 4.3 15.9 1.0
CG F:GLU27 4.3 14.0 1.0
CD2 F:HIS65 4.3 20.0 1.0
CA F:GLU62 4.5 13.2 1.0
CB F:GLU62 4.6 13.2 1.0
CB F:GLU27 4.7 14.1 1.0
CD F:GLN141 4.9 21.0 1.0
CA F:GLU27 5.0 12.5 1.0

Iron binding site 7 out of 12 in 5jkm

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Iron binding site 7 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:40.0
occ:1.00
OE1 G:GLU27 2.0 20.9 1.0
O G:HOH324 2.0 41.6 1.0
OE1 G:GLU62 2.1 25.5 1.0
O G:HOH330 2.2 21.4 1.0
ND1 G:HIS65 2.2 29.9 1.0
CD G:GLU27 3.0 21.2 1.0
CD G:GLU62 3.0 24.4 1.0
CE1 G:HIS65 3.1 33.1 1.0
OE2 G:GLU62 3.3 27.6 1.0
CG G:HIS65 3.3 27.0 1.0
OE2 G:GLU27 3.4 22.2 1.0
CB G:HIS65 3.7 21.0 1.0
OE1 G:GLN141 3.8 29.0 1.0
NE2 G:HIS65 4.3 31.5 1.0
CG G:GLU27 4.3 20.5 1.0
CD2 G:HIS65 4.4 28.8 1.0
CG G:GLU62 4.4 20.9 1.0
CG1 G:VAL110 4.4 21.3 1.0
CA G:GLU62 4.7 20.5 1.0
CB G:GLU27 4.7 19.3 1.0
CB G:GLU62 4.7 19.6 1.0
CD G:GLN141 4.8 28.5 1.0
OE1 G:GLU107 4.8 38.3 1.0
CA G:GLU27 5.0 19.4 1.0

Iron binding site 8 out of 12 in 5jkm

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Iron binding site 8 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:35.3
occ:1.00
OE1 H:GLU27 2.0 21.3 1.0
OE1 H:GLU62 2.1 24.0 1.0
O H:HOH335 2.1 29.3 1.0
O H:HOH356 2.2 22.2 1.0
ND1 H:HIS65 2.2 30.2 1.0
CD H:GLU62 3.0 24.4 1.0
CD H:GLU27 3.1 22.6 1.0
CE1 H:HIS65 3.1 32.5 1.0
OE2 H:GLU62 3.3 26.9 1.0
CG H:HIS65 3.3 25.7 1.0
OE2 H:GLU27 3.4 22.2 1.0
CB H:HIS65 3.7 21.0 1.0
OE1 H:GLN141 3.9 30.0 1.0
NE2 H:HIS65 4.3 27.4 1.0
CG H:GLU62 4.4 19.8 1.0
CG H:GLU27 4.4 18.8 1.0
CD2 H:HIS65 4.4 29.9 1.0
CG1 H:VAL110 4.4 19.3 1.0
CA H:GLU62 4.6 18.7 1.0
CB H:GLU62 4.7 18.5 1.0
CB H:GLU27 4.7 20.1 1.0
OE1 H:GLU107 4.9 36.7 1.0
CD H:GLN141 4.9 25.1 1.0
CA H:GLU27 5.0 19.5 1.0

Iron binding site 9 out of 12 in 5jkm

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Iron binding site 9 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:37.8
occ:1.00
OE1 I:GLU27 2.0 23.0 1.0
O I:HOH332 2.2 21.5 1.0
OE1 I:GLU62 2.2 26.9 1.0
ND1 I:HIS65 2.2 25.6 1.0
O I:HOH312 2.3 31.9 1.0
O I:HOH348 2.4 41.0 1.0
CD I:GLU27 3.0 20.6 1.0
CE1 I:HIS65 3.1 26.8 1.0
CD I:GLU62 3.2 23.6 1.0
CG I:HIS65 3.2 26.5 1.0
OE2 I:GLU27 3.4 23.3 1.0
OE2 I:GLU62 3.5 29.4 1.0
CB I:HIS65 3.6 20.3 1.0
OE1 I:GLN141 3.9 28.6 1.0
NE2 I:HIS65 4.2 27.6 1.0
CG I:GLU27 4.3 18.7 1.0
CD2 I:HIS65 4.3 25.0 1.0
CG1 I:VAL110 4.5 22.4 1.0
CG I:GLU62 4.5 23.2 1.0
CB I:GLU27 4.7 17.8 1.0
CA I:GLU62 4.7 17.8 1.0
CB I:GLU62 4.8 19.5 1.0
CD I:GLN141 4.9 24.1 1.0
OE1 I:GLU107 5.0 32.2 1.0

Iron binding site 10 out of 12 in 5jkm

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Iron binding site 10 out of 12 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:36.2
occ:1.00
OE1 J:GLU62 2.0 28.6 1.0
OE1 J:GLU27 2.0 22.6 1.0
O J:HOH304 2.1 18.3 1.0
O J:HOH330 2.2 30.6 1.0
ND1 J:HIS65 2.2 24.0 1.0
CD J:GLU27 3.0 20.9 1.0
CD J:GLU62 3.0 26.1 1.0
CE1 J:HIS65 3.1 26.8 1.0
CG J:HIS65 3.3 23.3 1.0
OE2 J:GLU27 3.3 22.4 1.0
OE2 J:GLU62 3.3 29.7 1.0
CB J:HIS65 3.6 21.4 1.0
OE1 J:GLN141 4.0 29.9 1.0
NE2 J:HIS65 4.3 22.2 1.0
CG J:GLU27 4.3 17.6 1.0
CG1 J:VAL110 4.4 21.1 1.0
CG J:GLU62 4.4 23.2 1.0
CD2 J:HIS65 4.4 23.4 1.0
CA J:GLU62 4.6 18.0 1.0
CB J:GLU27 4.7 17.5 1.0
CB J:GLU62 4.7 19.1 1.0
OE1 J:GLU107 4.8 34.1 1.0
CD J:GLN141 4.9 26.2 1.0
CA J:GLU27 5.0 18.0 1.0

Reference:

M.Kunzle, T.Eckert, T.Beck. Binary Protein Crystals For the Assembly of Inorganic Nanoparticle Superlattices. J.Am.Chem.Soc. V. 138 12731 2016.
ISSN: ESSN 1520-5126
PubMed: 27617514
DOI: 10.1021/JACS.6B07260
Page generated: Tue Aug 6 02:31:37 2024

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