Atomistry » Iron » PDB 4lm8-4m6y » 4lyu
Atomistry »
  Iron »
    PDB 4lm8-4m6y »
      4lyu »

Iron in PDB 4lyu: Fifteen Minutes Iron Loaded Frog M Ferritin

Enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin

All present enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Fifteen Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyu was solved by S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.08 / 1.75
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.843, 183.843, 183.843, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 20.4

Other elements in 4lyu:

The structure of Fifteen Minutes Iron Loaded Frog M Ferritin also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Fifteen Minutes Iron Loaded Frog M Ferritin (pdb code 4lyu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Fifteen Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 1 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:17.5
occ:0.70
 OE1 A:GLU23 2.0 15.9 1.0
OE1 A:GLU58 2.0 19.7 1.0
O A:HOH301 2.1 22.7 1.0
O A:HOH302 2.1 18.4 1.0
ND1 A:HIS61 2.4 18.0 1.0
CD A:GLU23 2.9 14.9 1.0
CD A:GLU58 3.1 19.3 1.0
OE2 A:GLU23 3.1 16.7 1.0
CE1 A:HIS61 3.2 18.6 1.0
CG A:HIS61 3.4 16.5 1.0
OE2 A:GLU58 3.6 21.6 1.0
O A:HOH464 3.6 30.6 0.7
CB A:HIS61 3.7 15.0 1.0
FE A:FE2203 3.8 28.4 0.7
CG1 A:VAL106 4.0 11.1 1.0
OE1 A:GLN137 4.1 18.1 1.0
O A:HOH424 4.3 20.5 1.0
CG A:GLU23 4.3 13.3 1.0
CG A:GLU58 4.4 16.8 1.0
NE2 A:HIS61 4.4 18.5 1.0
O A:HOH413 4.4 25.4 1.0
CA A:GLU58 4.5 13.8 1.0
CD2 A:HIS61 4.5 17.8 1.0
CB A:GLU58 4.6 15.1 1.0
CB A:GLU23 4.8 11.4 1.0
CD A:GLN137 5.0 16.6 1.0

Iron binding site 2 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 2 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:42.4
occ:0.40
 ND1 A:HIS54 2.5 21.9 1.0
FE A:FE2203 2.5 28.4 0.7
O A:HOH413 2.8 25.4 1.0
OE2 A:GLU58 2.9 21.6 1.0
OE2 A:GLU103 3.0 19.9 1.0
CE1 A:HIS54 3.1 22.7 1.0
OD2 A:ASP140 3.4 21.9 1.0
OE2 A:GLU57 3.4 28.9 1.0
CG A:HIS54 3.6 19.6 1.0
CD A:GLU103 3.6 17.8 1.0
OE1 A:GLU103 3.8 19.1 1.0
CD A:GLU57 3.9 26.7 1.0
CD A:GLU58 3.9 19.3 1.0
CE2 A:TYR30 4.0 14.7 1.0
OE1 A:GLU57 4.0 30.6 1.0
CG A:ASP140 4.1 18.4 1.0
OH A:TYR30 4.1 18.2 1.0
CB A:HIS54 4.1 16.2 1.0
CZ A:TYR30 4.3 15.8 1.0
O A:HOH301 4.3 22.7 1.0
NE2 A:HIS54 4.4 23.6 1.0
FE A:FE2205 4.4 36.4 0.5
CG A:GLU58 4.5 16.8 1.0
CB A:ASP140 4.5 15.4 1.0
O A:HIS54 4.6 12.6 1.0
CD2 A:HIS54 4.6 21.3 1.0
CA A:HIS54 4.6 14.3 1.0
OE1 A:GLU58 4.8 19.7 1.0
CG A:GLU57 4.8 22.8 1.0
CD2 A:TYR30 4.8 13.3 1.0
O A:HOH464 4.9 30.6 0.7
OD1 A:ASP140 4.9 19.7 1.0
CG A:GLU103 4.9 15.2 1.0

Iron binding site 3 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 3 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:28.4
occ:0.70
 OE2 A:GLU58 1.8 21.6 1.0
O A:HOH413 1.9 25.4 1.0
O A:HOH301 2.1 22.7 1.0
OE2 A:GLU103 2.1 19.9 1.0
OE1 A:GLU103 2.4 19.1 1.0
FE A:FE2202 2.5 42.4 0.4
O A:HOH464 2.5 30.6 0.7
CD A:GLU103 2.6 17.8 1.0
CD A:GLU58 2.8 19.3 1.0
OE1 A:GLU58 3.3 19.7 1.0
FE A:FE2201 3.8 17.5 0.7
NE2 A:GLN137 4.0 17.9 1.0
OE1 A:GLN137 4.1 18.1 1.0
CG A:GLU58 4.1 16.8 1.0
CG A:GLU103 4.1 15.2 1.0
OD2 A:ASP140 4.2 21.9 1.0
CE2 A:TYR30 4.3 14.7 1.0
CD A:GLN137 4.4 16.6 1.0
OE2 A:GLU57 4.5 28.9 1.0
OH A:TYR30 4.5 18.2 1.0
CE1 A:HIS61 4.7 18.6 1.0
ND1 A:HIS54 4.8 21.9 1.0
ND1 A:HIS61 4.8 18.0 1.0
O A:HOH302 4.8 18.4 1.0
CZ A:TYR30 4.9 15.8 1.0
CB A:GLU103 4.9 13.4 1.0

Iron binding site 4 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 4 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:37.1
occ:0.50
 OE2 A:GLU136 2.2 26.9 1.0
OE1 A:GLU136 2.2 27.9 1.0
CD A:GLU136 2.5 25.5 1.0
NE2 A:HIS61 2.9 18.5 1.0
CD2 A:HIS61 3.6 17.8 1.0
O A:HOH434 3.7 29.7 1.0
CG A:GLU57 3.8 22.8 1.0
CG A:GLU136 4.0 23.3 1.0
CE1 A:HIS61 4.1 18.6 1.0
CD A:GLU57 4.2 26.7 1.0
OE2 A:GLU57 4.2 28.9 1.0
CB A:GLU136 4.9 19.6 1.0
CG A:HIS61 4.9 16.5 1.0

Iron binding site 5 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 5 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:36.4
occ:0.50
 O A:HOH303 2.2 50.3 1.0
OD1 A:ASP140 2.4 19.7 1.0
OD2 A:ASP140 2.4 21.9 1.0
OE1 A:GLU57 2.5 30.6 1.0
OE2 A:GLU57 2.6 28.9 1.0
CG A:ASP140 2.7 18.4 1.0
CD A:GLU57 2.8 26.7 1.0
OE1 A:GLU136 3.3 27.9 1.0
CG A:GLU136 3.7 23.3 1.0
CD A:GLU136 4.0 25.5 1.0
CB A:ASP140 4.2 15.4 1.0
CG A:GLU57 4.3 22.8 1.0
CE1 A:HIS54 4.4 22.7 1.0
FE A:FE2202 4.4 42.4 0.4
O A:GLU136 4.6 14.9 1.0
O A:HOH413 4.7 25.4 1.0
O A:HOH438 4.7 31.5 1.0
ND1 A:HIS54 4.9 21.9 1.0
NE2 A:HIS54 4.9 23.6 1.0

Iron binding site 6 out of 6 in 4lyu

Go back to Iron Binding Sites List in 4lyu
Iron binding site 6 out of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:10.7
occ:0.25
 CL A:CL215 2.2 14.2 0.2
NE2 A:HIS169 2.3 9.9 1.0
O A:HOH304 2.4 16.5 0.2
CE1 A:HIS169 3.1 10.1 1.0
CD2 A:HIS169 3.3 10.5 1.0
ND1 A:HIS169 4.3 10.3 1.0
CG A:HIS169 4.4 10.1 1.0

Reference:

S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli. Crystallographic Snapshots of Iron in Frog M Ferritin To Be Published.
Page generated: Mon Aug 5 06:29:35 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy