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Iron in PDB 4cmy: Chlorobium Tepidum Ferritin

Protein crystallography data

The structure of Chlorobium Tepidum Ferritin, PDB code: 4cmy was solved by E.Pohl, M.Arenas, P.D.Townsend, A.Yevenes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.71 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.310, 190.370, 242.070, 90.00, 90.00, 90.00
R / Rfree (%) 19.297 / 21.788

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the Chlorobium Tepidum Ferritin (pdb code 4cmy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Chlorobium Tepidum Ferritin, PDB code: 4cmy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in 4cmy

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Iron binding site 1 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1164

b:27.4
occ:1.00
 OE1 A:GLU17 2.0 29.6 1.0
OE1 A:GLU50 2.1 27.1 1.0
ND1 A:HIS53 2.2 38.3 1.0
O A:HOH2006 2.2 23.1 1.0
CD A:GLU17 3.0 31.1 1.0
CE1 A:HIS53 3.0 39.2 1.0
FE A:FE1165 3.1 35.9 1.0
CD A:GLU50 3.1 28.3 1.0
OE2 A:GLU17 3.2 31.9 1.0
CG A:HIS53 3.3 38.1 1.0
OE2 A:GLU50 3.4 27.9 1.0
OE1 A:GLN127 3.6 36.3 1.0
CB A:HIS53 3.7 34.7 1.0
NE2 A:HIS53 4.2 38.5 1.0
CD2 A:HIS53 4.3 36.1 1.0
CG A:GLU17 4.4 26.7 1.0
OE1 A:GLU130 4.4 44.9 1.0
CG A:GLU50 4.4 28.1 1.0
CG2 A:ILE97 4.5 24.2 1.0
CD1 A:ILE97 4.5 26.9 1.0
CA A:GLU50 4.7 29.6 1.0
CB A:GLU50 4.8 26.9 1.0
CD A:GLN127 4.8 36.3 1.0
CB A:GLU17 4.9 25.8 1.0
OE2 A:GLU94 4.9 27.6 1.0

Iron binding site 2 out of 48 in 4cmy

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Iron binding site 2 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1165

b:35.9
occ:1.00
 OE2 A:GLU50 1.9 27.9 1.0
OE1 A:GLU130 1.9 44.9 1.0
OE2 A:GLU94 2.0 27.6 1.0
OE1 A:GLU94 2.7 29.1 1.0
CD A:GLU94 2.7 29.8 1.0
CD A:GLU50 2.9 28.3 1.0
CD A:GLU130 3.0 47.3 1.0
FE A:FE1164 3.1 27.4 1.0
OE1 A:GLU50 3.2 27.1 1.0
OE1 A:GLN127 3.5 36.3 1.0
CG A:GLU130 3.6 39.5 1.0
CE1 A:HIS53 4.1 39.2 1.0
CD1 A:ILE97 4.1 26.9 1.0
OE2 A:GLU130 4.1 47.2 1.0
CG A:GLU94 4.2 30.4 1.0
NE2 A:HIS46 4.2 30.6 1.0
ND1 A:HIS53 4.2 38.3 1.0
CB A:GLU130 4.3 39.0 1.0
CG A:GLU50 4.3 28.1 1.0
CD A:GLN127 4.5 36.3 1.0
O A:HOH2006 4.6 23.1 1.0
OH A:TYR24 4.6 36.2 1.0
NE2 A:GLN127 4.6 35.5 1.0
CD2 A:HIS46 4.7 28.9 1.0
CE2 A:TYR24 4.7 35.1 1.0
OE1 A:GLU17 4.8 29.6 1.0

Iron binding site 3 out of 48 in 4cmy

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Iron binding site 3 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1165

b:39.1
occ:1.00
 OE1 B:GLU130 1.9 49.6 1.0
OE2 B:GLU50 2.0 29.3 1.0
OE2 B:GLU94 2.0 33.5 1.0
OE1 B:GLU94 2.6 26.6 1.0
CD B:GLU94 2.6 33.2 1.0
CD B:GLU50 2.9 34.3 1.0
CD B:GLU130 3.0 47.4 1.0
FE B:FE1166 3.0 27.8 1.0
OE1 B:GLU50 3.2 31.3 1.0
OE1 B:GLN127 3.5 32.3 1.0
CG B:GLU130 3.5 45.9 1.0
CE1 B:HIS53 4.1 42.1 1.0
OE2 B:GLU130 4.1 51.3 1.0
CG B:GLU94 4.1 34.9 1.0
CD1 B:ILE97 4.2 49.0 1.0
CB B:GLU130 4.2 42.1 1.0
NE2 B:HIS46 4.2 38.2 1.0
ND1 B:HIS53 4.3 44.5 1.0
CG B:GLU50 4.4 32.6 1.0
CD B:GLN127 4.4 36.6 1.0
O B:HOH2004 4.5 48.0 1.0
NE2 B:GLN127 4.5 39.4 1.0
OH B:TYR24 4.6 39.9 1.0
CD2 B:HIS46 4.7 35.9 1.0
CE2 B:TYR24 4.7 30.9 1.0
OE1 B:GLU17 4.8 43.0 1.0

Iron binding site 4 out of 48 in 4cmy

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Iron binding site 4 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1166

b:27.8
occ:1.00
 OE1 B:GLU17 2.1 43.0 1.0
OE1 B:GLU50 2.1 31.3 1.0
ND1 B:HIS53 2.2 44.5 1.0
O B:HOH2004 2.3 48.0 1.0
CE1 B:HIS53 3.0 42.1 1.0
CD B:GLU17 3.0 39.2 1.0
FE B:FE1165 3.0 39.1 1.0
CD B:GLU50 3.1 34.3 1.0
OE2 B:GLU17 3.2 40.0 1.0
CG B:HIS53 3.3 41.3 1.0
OE2 B:GLU50 3.4 29.3 1.0
OE1 B:GLN127 3.5 32.3 1.0
CB B:HIS53 3.8 38.6 1.0
NE2 B:HIS53 4.2 43.5 1.0
CD2 B:HIS53 4.4 42.5 1.0
OE1 B:GLU130 4.4 49.6 1.0
CG B:GLU17 4.4 39.7 1.0
CG2 B:ILE97 4.4 38.7 1.0
CD1 B:ILE97 4.5 49.0 1.0
CG B:GLU50 4.5 32.6 1.0
CD B:GLN127 4.7 36.6 1.0
CA B:GLU50 4.7 37.5 1.0
OE2 B:GLU94 4.8 33.5 1.0
CB B:GLU50 4.8 34.5 1.0
CB B:GLU17 5.0 35.5 1.0
OE1 B:GLU94 5.0 26.6 1.0

Iron binding site 5 out of 48 in 4cmy

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Iron binding site 5 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1164

b:30.9
occ:1.00
 OE1 C:GLU17 2.1 33.7 1.0
OE1 C:GLU50 2.1 32.6 1.0
ND1 C:HIS53 2.2 39.4 1.0
O C:HOH2006 2.6 41.3 1.0
CD C:GLU17 3.0 36.4 1.0
FE C:FE1165 3.0 38.6 1.0
CE1 C:HIS53 3.0 38.2 1.0
CD C:GLU50 3.1 35.8 1.0
OE2 C:GLU17 3.2 39.0 1.0
CG C:HIS53 3.3 35.4 1.0
OE2 C:GLU50 3.4 38.2 1.0
OE1 C:GLN127 3.5 45.5 1.0
CB C:HIS53 3.8 37.5 1.0
NE2 C:HIS53 4.2 36.9 1.0
OE1 C:GLU130 4.4 38.7 1.0
CD2 C:HIS53 4.4 33.6 1.0
CG C:GLU17 4.4 34.1 1.0
CG2 C:ILE97 4.4 38.5 1.0
CG C:GLU50 4.5 37.4 1.0
CD1 C:ILE97 4.5 48.6 1.0
CD C:GLN127 4.7 41.3 1.0
CA C:GLU50 4.7 36.4 1.0
CB C:GLU50 4.8 35.0 1.0
OE2 C:GLU94 4.9 29.2 1.0
CB C:GLU17 4.9 32.5 1.0
OE1 C:GLU94 5.0 32.4 1.0

Iron binding site 6 out of 48 in 4cmy

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Iron binding site 6 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1165

b:38.6
occ:1.00
 OE2 C:GLU50 1.8 38.2 1.0
OE1 C:GLU130 1.9 38.7 1.0
OE2 C:GLU94 2.0 29.2 1.0
CD C:GLU94 2.7 34.3 1.0
OE1 C:GLU94 2.7 32.4 1.0
CD C:GLU50 2.8 35.8 1.0
FE C:FE1164 3.0 30.9 1.0
CD C:GLU130 3.0 39.6 1.0
OE1 C:GLU50 3.1 32.6 1.0
CG C:GLU130 3.6 40.0 1.0
OE1 C:GLN127 3.6 45.5 1.0
CE1 C:HIS53 4.1 38.2 1.0
OE2 C:GLU130 4.1 39.4 1.0
NE2 C:HIS46 4.2 45.4 1.0
CD1 C:ILE97 4.2 48.6 1.0
CG C:GLU50 4.2 37.4 1.0
ND1 C:HIS53 4.2 39.4 1.0
CG C:GLU94 4.2 33.9 1.0
CB C:GLU130 4.3 38.7 1.0
OH C:TYR24 4.5 40.2 1.0
CD C:GLN127 4.6 41.3 1.0
CD2 C:HIS46 4.6 41.0 1.0
CE2 C:TYR24 4.6 36.8 1.0
NE2 C:GLN127 4.7 41.9 1.0
OE1 C:GLU17 4.7 33.7 1.0
O C:HOH2006 4.9 41.3 1.0

Iron binding site 7 out of 48 in 4cmy

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Iron binding site 7 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1164

b:29.7
occ:1.00
 OE1 D:GLU50 2.1 30.3 1.0
OE1 D:GLU17 2.1 31.0 1.0
ND1 D:HIS53 2.2 41.9 1.0
O D:HOH2005 2.4 41.3 1.0
FE D:FE1165 2.8 38.0 1.0
CE1 D:HIS53 3.0 42.5 1.0
CD D:GLU50 3.0 36.0 1.0
CD D:GLU17 3.0 36.5 1.0
OE2 D:GLU17 3.3 37.7 1.0
OE2 D:GLU50 3.3 38.0 1.0
CG D:HIS53 3.4 39.6 1.0
NE2 D:GLN127 3.6 38.6 1.0
CB D:HIS53 3.8 38.3 1.0
NE2 D:HIS53 4.2 41.6 1.0
OE1 D:GLU130 4.3 43.8 1.0
CD1 D:ILE97 4.4 45.0 1.0
CD2 D:HIS53 4.4 41.5 1.0
CG2 D:ILE97 4.4 37.5 1.0
CG D:GLU50 4.4 35.2 1.0
CG D:GLU17 4.5 37.4 1.0
CA D:GLU50 4.7 35.6 1.0
OE2 D:GLU94 4.8 27.7 1.0
CB D:GLU50 4.8 33.6 1.0
CD D:GLN127 4.8 36.8 1.0
OE1 D:GLU94 4.9 32.2 1.0
CB D:GLU17 5.0 35.5 1.0

Iron binding site 8 out of 48 in 4cmy

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Iron binding site 8 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1165

b:38.0
occ:1.00
 OE2 D:GLU50 2.0 38.0 1.0
OE1 D:GLU130 2.0 43.8 1.0
OE2 D:GLU94 2.1 27.7 1.0
OE1 D:GLU94 2.7 32.2 1.0
CD D:GLU94 2.7 36.8 1.0
FE D:FE1164 2.8 29.7 1.0
CD D:GLU50 2.9 36.0 1.0
OE1 D:GLU50 3.1 30.3 1.0
CD D:GLU130 3.1 47.4 1.0
NE2 D:GLN127 3.5 38.6 1.0
CG D:GLU130 3.6 44.6 1.0
CE1 D:HIS53 4.0 42.5 1.0
CD1 D:ILE97 4.0 45.0 1.0
ND1 D:HIS53 4.2 41.9 1.0
OE2 D:GLU130 4.2 50.4 1.0
CG D:GLU94 4.2 36.2 1.0
CB D:GLU130 4.3 39.5 1.0
CG D:GLU50 4.3 35.2 1.0
NE2 D:HIS46 4.3 38.8 1.0
CD D:GLN127 4.4 36.8 1.0
OE1 D:GLN127 4.6 40.7 1.0
O D:HOH2005 4.6 41.3 1.0
OH D:TYR24 4.6 49.9 1.0
OE1 D:GLU17 4.7 31.0 1.0
CE2 D:TYR24 4.8 54.5 1.0
CD2 D:HIS46 4.8 38.3 1.0

Iron binding site 9 out of 48 in 4cmy

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Iron binding site 9 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1164

b:35.5
occ:1.00
 OE2 E:GLU50 1.9 33.9 1.0
OE1 E:GLU130 2.0 41.0 1.0
OE2 E:GLU94 2.0 31.5 1.0
CD E:GLU94 2.7 29.7 1.0
OE1 E:GLU94 2.7 29.5 1.0
CD E:GLU50 2.8 38.6 1.0
FE E:FE1165 3.0 30.3 1.0
CD E:GLU130 3.1 42.0 1.0
OE1 E:GLU50 3.1 32.7 1.0
OE1 E:GLN127 3.6 35.9 1.0
CG E:GLU130 3.6 46.8 1.0
CD1 E:ILE97 4.1 41.1 1.0
CE1 E:HIS53 4.1 36.0 1.0
OE2 E:GLU130 4.2 39.9 1.0
CG E:GLU94 4.2 29.3 1.0
ND1 E:HIS53 4.2 39.8 1.0
NE2 E:HIS46 4.2 42.8 1.0
CG E:GLU50 4.2 34.8 1.0
CB E:GLU130 4.3 42.7 1.0
CD E:GLN127 4.5 33.8 1.0
OH E:TYR24 4.5 38.6 1.0
NE2 E:GLN127 4.6 36.5 1.0
CE2 E:TYR24 4.6 34.9 1.0
CD2 E:HIS46 4.7 44.0 1.0
O E:HOH2005 4.7 46.7 1.0
OE1 E:GLU17 4.7 26.7 1.0

Iron binding site 10 out of 48 in 4cmy

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Iron binding site 10 out of 48 in the Chlorobium Tepidum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Chlorobium Tepidum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1165

b:30.3
occ:1.00
 OE1 E:GLU17 2.1 26.7 1.0
OE1 E:GLU50 2.1 32.7 1.0
ND1 E:HIS53 2.2 39.8 1.0
O E:HOH2005 2.3 46.7 1.0
CD E:GLU17 3.0 27.3 1.0
FE E:FE1164 3.0 35.5 1.0
CE1 E:HIS53 3.0 36.0 1.0
CD E:GLU50 3.1 38.6 1.0
OE2 E:GLU17 3.2 25.8 1.0
CG E:HIS53 3.3 35.4 1.0
OE2 E:GLU50 3.4 33.9 1.0
OE1 E:GLN127 3.5 35.9 1.0
CB E:HIS53 3.8 33.1 1.0
NE2 E:HIS53 4.2 33.4 1.0
CD2 E:HIS53 4.4 34.0 1.0
OE1 E:GLU130 4.4 41.0 1.0
CG E:GLU17 4.4 29.7 1.0
CG2 E:ILE97 4.4 34.7 1.0
CD1 E:ILE97 4.5 41.1 1.0
CG E:GLU50 4.5 34.8 1.0
CD E:GLN127 4.7 33.8 1.0
CA E:GLU50 4.7 37.7 1.0
CB E:GLU50 4.9 35.4 1.0
OE2 E:GLU94 4.9 31.5 1.0
CB E:GLU17 4.9 30.6 1.0
OE1 E:GLU94 5.0 29.5 1.0

Reference:

M.Arenas, P.D.Townsend, C.Brito, V.Marquez, V.Marabolli, F.Gonzalez-Nilo, C.Matias, R.K.Watt, J.D.Lopez-Castro, J.Dominguez-Vera, E.Pohl, A.Yevenes. The Crystal Structure of Ferritin From Chlorobium Tepidum Reveals A New Conformation of the 4-Fold Channel For This Protein Family. Biochimie 2014.
ISSN: ESSN 1638-6183
DOI: 10.1016/J.BIOCHI.2014.07.019
Page generated: Mon Aug 5 00:37:54 2024

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