Atomistry » Iron » PDB 5c2i-5cnd » 5c6f
Atomistry »
  Iron »
    PDB 5c2i-5cnd »
      5c6f »

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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Go back to Iron Binding Sites List in 5c6f
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy