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Iron in PDB 5c6f: Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen

Enzymatic activity of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen

All present enzymatic activity of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen:
1.16.3.2;

Protein crystallography data

The structure of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen, PDB code: 5c6f was solved by S.Kim, K.H.Kim, J.H.Seok, Y.H.Park, S.W.Jung, Y.B.Chung, D.B.Lee, J.H.Lee, K.R.Han, A.E.Cho, C.Lee, M.S.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 128.051, 128.051, 165.103, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 19.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen (pdb code 5c6f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen, PDB code: 5c6f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 5c6f

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Iron binding site 1 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:41.9
occ:0.50
 CE1 A:HIS149 2.2 38.2 0.5
CE1 D:HIS149 2.4 34.0 0.5
CE1 B:HIS149 2.6 29.1 0.5
FE A:FE202 2.7 53.7 0.5
NE2 A:HIS149 3.0 37.1 0.5
NE2 D:HIS149 3.1 35.3 0.5
ND1 A:HIS149 3.3 37.8 0.5
ND1 D:HIS149 3.5 34.8 0.5
ND1 B:HIS149 3.5 28.6 0.5
NE2 B:HIS149 3.5 30.6 0.5
CD2 A:HIS149 4.2 36.7 0.5
ND1 A:HIS149 4.2 28.7 0.5
ND1 D:HIS149 4.4 25.8 0.5
CD2 D:HIS149 4.4 34.1 0.5
CG A:HIS149 4.4 37.6 0.5
ND1 B:HIS149 4.5 28.2 0.5
CG D:HIS149 4.6 33.2 0.5
CD1 A:LEU153 4.6 23.2 1.0
CD1 D:LEU153 4.6 30.2 1.0
CG B:HIS149 4.7 29.0 0.5
CD2 B:HIS149 4.7 28.2 0.5
OD1 D:ASN148 4.8 58.9 1.0
CD1 B:LEU153 4.8 31.2 1.0

Iron binding site 2 out of 9 in 5c6f

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Iron binding site 2 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:53.7
occ:0.50
 FE A:FE201 2.7 41.9 0.5
CE1 A:HIS149 3.7 38.2 0.5
CE1 D:HIS149 3.9 34.0 0.5
CD2 B:LEU153 4.0 28.9 1.0
CD1 B:LEU153 4.1 31.2 1.0
CD2 A:LEU153 4.1 26.9 1.0
CE1 B:HIS149 4.2 29.1 0.5
ND1 A:HIS149 4.2 37.8 0.5
CD2 D:LEU153 4.2 28.4 1.0
CD1 A:LEU153 4.3 23.2 1.0
CD1 D:LEU153 4.3 30.2 1.0
ND1 D:HIS149 4.5 34.8 0.5
ND1 B:HIS149 4.6 28.6 0.5
CG B:LEU153 4.6 28.2 1.0
CG A:LEU153 4.7 22.9 1.0
NE2 A:HIS149 4.8 37.1 0.5
CG D:LEU153 4.9 27.0 1.0
NE2 D:HIS149 4.9 35.3 0.5

Iron binding site 3 out of 9 in 5c6f

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Iron binding site 3 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:22.4
occ:0.50
 OE2 A:GLU50 2.2 32.5 1.0
OE1 A:GLU130 2.3 18.5 1.0
O A:HOH358 2.5 27.9 1.0
OE2 A:GLU94 2.5 21.1 1.0
OE1 A:GLN127 2.6 21.3 1.0
CD A:GLU50 3.0 28.0 1.0
OE1 A:GLU50 3.0 36.6 1.0
CD A:GLU94 3.2 20.6 1.0
OE1 A:GLU94 3.3 20.2 1.0
CD A:GLU130 3.5 19.6 1.0
CD A:GLN127 3.5 19.8 1.0
NE2 A:GLN127 3.9 20.1 1.0
CE1 A:HIS46 4.0 19.1 1.0
CD1 A:ILE97 4.0 15.3 0.5
NE2 A:HIS46 4.1 20.1 1.0
CB A:GLU130 4.2 19.9 1.0
CG2 A:ILE97 4.3 16.1 0.5
OE2 A:GLU130 4.3 20.0 1.0
CG A:GLU50 4.4 26.5 1.0
CG A:GLU130 4.4 21.3 1.0
CG2 A:ILE97 4.6 17.0 0.5
CG A:GLU94 4.7 19.6 1.0
CD2 A:HIS53 4.7 23.4 1.0
NE2 A:HIS53 4.8 26.5 1.0
CB A:ILE97 4.8 16.4 0.5
CB A:ILE97 4.9 17.5 0.5
CG A:GLN127 4.9 19.9 1.0
OE2 A:GLU17 4.9 22.3 1.0
OE1 A:GLU17 5.0 29.4 1.0

Iron binding site 4 out of 9 in 5c6f

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Iron binding site 4 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:19.0
occ:0.50
 OE2 B:GLU50 2.3 33.8 1.0
OE1 B:GLU130 2.3 23.1 1.0
OE2 B:GLU94 2.4 22.2 1.0
OE1 B:GLN127 2.5 20.4 1.0
O B:HOH355 2.6 31.8 1.0
CD B:GLU50 3.0 31.9 1.0
OE1 B:GLU50 3.1 39.2 1.0
CD B:GLU94 3.2 22.0 1.0
OE1 B:GLU94 3.2 24.0 1.0
CD B:GLU130 3.5 25.7 1.0
CD B:GLN127 3.5 23.4 1.0
NE2 B:GLN127 3.8 23.0 1.0
CE1 B:HIS46 4.0 18.1 1.0
CB B:GLU130 4.0 22.7 1.0
NE2 B:HIS46 4.2 20.1 1.0
CD1 B:ILE97 4.2 18.2 0.5
OE2 B:GLU130 4.3 25.0 1.0
CG B:GLU130 4.3 23.5 1.0
CG2 B:ILE97 4.4 20.6 0.5
CG B:GLU50 4.4 28.9 1.0
CG2 B:ILE97 4.5 19.4 0.5
CD2 B:HIS53 4.6 23.3 1.0
CG B:GLU94 4.7 21.2 1.0
NE2 B:HIS53 4.7 25.0 1.0
CG B:GLN127 4.8 23.4 1.0
OE2 B:GLU17 4.8 20.7 1.0
CB B:ILE97 4.8 20.5 0.5
OE1 B:GLU17 4.9 26.0 1.0
CB B:ILE97 4.9 19.2 0.5

Iron binding site 5 out of 9 in 5c6f

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Iron binding site 5 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:59.8
occ:0.25
 O F:HOH493 2.0 28.1 0.2
CE1 F:HIS149 2.8 28.1 0.5
ND1 F:HIS149 3.6 28.2 0.5
NE2 F:HIS149 3.7 28.2 0.5
O F:HOH317 3.8 40.8 0.2
ND1 F:HIS149 4.4 22.6 0.5
CD1 F:LEU153 4.5 24.8 1.0
O F:HOH511 4.6 35.7 0.2
OD1 F:ASN148 4.7 34.8 0.5
CG F:HIS149 4.9 27.9 0.5
CD2 F:HIS149 4.9 28.6 0.5

Iron binding site 6 out of 9 in 5c6f

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Iron binding site 6 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:36.1
occ:0.50
 CE1 G:HIS149 2.2 25.9 0.5
FE I:FE201 2.3 42.0 0.5
CE1 I:HIS149 2.4 27.5 0.5
CE1 K:HIS149 2.4 27.7 0.5
O I:HOH312 2.9 45.1 1.0
NE2 I:HIS149 3.0 27.6 0.5
ND1 G:HIS149 3.1 28.6 0.5
NE2 K:HIS149 3.2 27.9 0.5
NE2 G:HIS149 3.3 27.0 0.5
ND1 K:HIS149 3.5 29.7 0.5
ND1 I:HIS149 3.5 30.1 0.5
ND1 K:HIS149 4.2 22.7 0.5
ND1 I:HIS149 4.3 22.3 0.5
CD2 I:HIS149 4.3 27.2 0.5
CG G:HIS149 4.3 27.7 0.5
CD2 G:HIS149 4.4 26.0 0.5
CD2 K:HIS149 4.4 27.9 0.5
ND1 G:HIS149 4.5 19.4 0.5
CG I:HIS149 4.6 28.1 0.5
CG K:HIS149 4.6 28.4 0.5
CD1 G:LEU153 4.7 23.1 1.0
CD1 K:LEU153 4.7 26.3 1.0
ND2 I:ASN148 4.7 67.4 1.0
OD1 G:ASN148 4.8 64.5 1.0
CD1 I:LEU153 4.8 22.5 1.0
CB G:HIS149 5.0 22.1 0.5
CB K:HIS149 5.0 24.0 0.5

Iron binding site 7 out of 9 in 5c6f

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Iron binding site 7 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:42.0
occ:0.50
 FE G:FE201 2.3 36.1 0.5
CE1 I:HIS149 3.5 27.5 0.5
CE1 K:HIS149 3.5 27.7 0.5
CE1 G:HIS149 3.7 25.9 0.5
ND1 G:HIS149 4.0 28.6 0.5
CD2 K:LEU153 4.1 25.2 1.0
ND1 K:HIS149 4.1 29.7 0.5
CD1 K:LEU153 4.1 26.3 1.0
ND1 I:HIS149 4.1 30.1 0.5
CD1 G:LEU153 4.2 23.1 1.0
CD2 G:LEU153 4.2 22.1 1.0
CD1 I:LEU153 4.2 22.5 1.0
CD2 I:LEU153 4.5 21.6 1.0
NE2 I:HIS149 4.6 27.6 0.5
NE2 K:HIS149 4.6 27.9 0.5
CG K:LEU153 4.6 23.4 1.0
CG G:LEU153 4.7 20.6 1.0
CG I:LEU153 4.8 19.4 1.0
NE2 G:HIS149 4.9 27.0 0.5

Iron binding site 8 out of 9 in 5c6f

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Iron binding site 8 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:19.4
occ:0.50
 OE1 J:GLU130 2.2 17.2 1.0
OE2 J:GLU50 2.4 30.2 1.0
O J:HOH359 2.5 24.5 1.0
OE2 J:GLU94 2.5 16.9 1.0
OE1 J:GLN127 2.5 18.5 1.0
OE1 J:GLU50 3.0 37.2 1.0
CD J:GLU50 3.1 32.6 1.0
OE1 J:GLU94 3.2 20.4 1.0
CD J:GLU94 3.2 17.7 1.0
CD J:GLU130 3.4 20.9 1.0
CD J:GLN127 3.5 15.9 1.0
NE2 J:GLN127 3.8 16.1 1.0
NE2 J:HIS46 4.0 16.4 1.0
CE1 J:HIS46 4.0 15.6 1.0
CB J:GLU130 4.1 16.6 1.0
OE2 J:GLU130 4.3 18.6 1.0
CG J:GLU130 4.3 17.5 1.0
CG J:GLU50 4.5 27.4 1.0
CG2 J:ILE97 4.5 19.4 1.0
CG J:GLU94 4.7 15.4 1.0
CD2 J:HIS53 4.7 24.1 1.0
NE2 J:HIS53 4.8 21.7 1.0
CB J:ILE97 4.9 19.4 1.0
OE2 J:GLU17 4.9 18.9 1.0
CG J:GLN127 4.9 16.7 1.0
OE1 J:GLU17 4.9 25.9 1.0
CG1 J:ILE97 4.9 22.8 1.0

Iron binding site 9 out of 9 in 5c6f

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Iron binding site 9 out of 9 in the Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structures of Ferritin Mutants Reveal Side-on Binding to Diiron and End-on Cleavage of Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe201

b:18.1
occ:0.50
 OE1 K:GLU130 2.2 24.0 1.0
O K:HOH331 2.4 27.7 1.0
OE1 K:GLN127 2.5 17.7 1.0
OE2 K:GLU94 2.5 18.3 1.0
OE1 K:GLU50 2.7 29.1 1.0
OE2 K:GLU50 2.8 22.4 1.0
CD K:GLU50 3.1 26.1 1.0
OE1 K:GLU94 3.2 18.7 1.0
CD K:GLU94 3.3 17.6 1.0
CD K:GLU130 3.4 21.6 1.0
CD K:GLN127 3.6 20.2 1.0
NE2 K:GLN127 3.9 19.6 1.0
CE1 K:HIS46 4.0 16.1 1.0
NE2 K:HIS46 4.1 17.0 1.0
CB K:GLU130 4.1 18.6 1.0
CD1 K:ILE97 4.1 17.4 1.0
OE2 K:GLU130 4.3 23.2 1.0
CG K:GLU130 4.3 19.8 1.0
CG2 K:ILE97 4.4 15.7 1.0
CD2 K:HIS53 4.7 26.2 1.0
CG K:GLU50 4.7 22.7 1.0
NE2 K:HIS53 4.7 26.5 1.0
CG K:GLU94 4.7 14.4 1.0
OE1 K:GLU17 4.8 23.1 1.0
OE2 K:GLU17 4.9 18.2 1.0
CB K:ILE97 4.9 15.3 1.0
CG K:GLN127 4.9 19.0 1.0

Reference:

S.Kim, J.H.Lee, J.H.Seok, Y.H.Park, S.W.Jung, A.E.Cho, C.Lee, M.S.Chung, K.H.Kim. Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins From Gram-Negative Bacteria. J. Mol. Biol. V. 428 5007 2016.
ISSN: ESSN 1089-8638
PubMed: 27777002
DOI: 10.1016/J.JMB.2016.10.022
Page generated: Mon Aug 5 20:48:05 2024

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