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Iron in PDB 4fvc: Hmob Structure with Heme

Protein crystallography data

The structure of Hmob Structure with Heme, PDB code: 4fvc was solved by S.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.58 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.821, 117.519, 70.847, 90.00, 91.22, 90.00
R / Rfree (%) 19.9 / 23.3

Iron Binding Sites:

The binding sites of Iron atom in the Hmob Structure with Heme (pdb code 4fvc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Hmob Structure with Heme, PDB code: 4fvc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4fvc

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Iron binding site 1 out of 6 in the Hmob Structure with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hmob Structure with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:27.0
occ:1.00
FE A:HEM201 0.0 27.0 1.0
NB A:HEM201 2.0 23.6 1.0
NA A:HEM201 2.0 24.5 1.0
ND A:HEM201 2.1 28.6 1.0
NC A:HEM201 2.1 27.7 1.0
OH A:TYR134 2.3 39.0 1.0
C4A A:HEM201 3.0 19.9 1.0
C1B A:HEM201 3.0 21.8 1.0
C4B A:HEM201 3.0 25.3 1.0
C1A A:HEM201 3.1 25.5 1.0
C1C A:HEM201 3.1 27.1 1.0
C4D A:HEM201 3.1 30.8 1.0
C1D A:HEM201 3.1 29.8 1.0
C4C A:HEM201 3.1 27.5 1.0
CZ A:TYR134 3.2 39.4 1.0
CHB A:HEM201 3.4 20.9 1.0
CHC A:HEM201 3.4 25.9 1.0
CHA A:HEM201 3.4 27.4 1.0
CHD A:HEM201 3.4 28.3 1.0
CD1 A:ILE115 3.5 22.7 1.0
CE1 A:TYR134 3.9 37.2 1.0
CE2 A:TYR134 4.0 39.8 1.0
C3A A:HEM201 4.2 23.0 1.0
C3B A:HEM201 4.2 25.5 1.0
C2B A:HEM201 4.3 20.9 1.0
C2A A:HEM201 4.3 24.4 1.0
C3C A:HEM201 4.3 28.3 1.0
C2C A:HEM201 4.3 27.3 1.0
C3D A:HEM201 4.3 34.2 1.0
C2D A:HEM201 4.3 33.7 1.0
CD1 A:ILE72 4.9 19.4 1.0

Iron binding site 2 out of 6 in 4fvc

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Iron binding site 2 out of 6 in the Hmob Structure with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hmob Structure with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:29.1
occ:1.00
FE B:HEM201 0.0 29.1 1.0
ND B:HEM201 2.0 33.2 1.0
NA B:HEM201 2.0 26.7 1.0
NB B:HEM201 2.0 24.9 1.0
NC B:HEM201 2.1 30.3 1.0
OH B:TYR134 2.2 43.0 1.0
C4D B:HEM201 3.0 34.4 1.0
C1D B:HEM201 3.0 33.7 1.0
C1A B:HEM201 3.0 28.2 1.0
C4B B:HEM201 3.0 25.8 1.0
C4A B:HEM201 3.1 25.5 1.0
C1B B:HEM201 3.1 24.9 1.0
C1C B:HEM201 3.1 28.6 1.0
C4C B:HEM201 3.1 29.1 1.0
CZ B:TYR134 3.2 44.3 1.0
CHA B:HEM201 3.3 32.1 1.0
CHC B:HEM201 3.4 27.4 1.0
CHD B:HEM201 3.4 33.3 1.0
CHB B:HEM201 3.5 25.5 1.0
CD1 B:ILE115 3.5 25.9 1.0
CE1 B:TYR134 3.9 45.9 1.0
CE2 B:TYR134 4.0 44.7 1.0
O B:HOH400 4.1 42.7 1.0
C3D B:HEM201 4.2 37.1 1.0
C2D B:HEM201 4.2 36.9 1.0
C2A B:HEM201 4.3 27.3 1.0
C3B B:HEM201 4.3 28.4 1.0
C3A B:HEM201 4.3 26.6 1.0
C2B B:HEM201 4.3 24.9 1.0
C2C B:HEM201 4.3 29.2 1.0
C3C B:HEM201 4.3 29.0 1.0

Iron binding site 3 out of 6 in 4fvc

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Iron binding site 3 out of 6 in the Hmob Structure with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hmob Structure with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:26.3
occ:1.00
FE C:HEM201 0.0 26.3 1.0
NB C:HEM201 2.0 24.0 1.0
NC C:HEM201 2.0 29.7 1.0
NA C:HEM201 2.0 25.1 1.0
ND C:HEM201 2.1 30.1 1.0
OH C:TYR134 2.2 36.9 1.0
C4B C:HEM201 3.0 27.1 1.0
C1C C:HEM201 3.0 28.9 1.0
C4C C:HEM201 3.0 30.2 1.0
C4A C:HEM201 3.0 21.8 1.0
C1B C:HEM201 3.1 22.1 1.0
C1A C:HEM201 3.1 26.8 1.0
C1D C:HEM201 3.1 32.2 1.0
C4D C:HEM201 3.1 32.9 1.0
CZ C:TYR134 3.2 38.4 1.0
CHC C:HEM201 3.4 27.0 1.0
CHA C:HEM201 3.4 28.4 1.0
CHD C:HEM201 3.4 31.3 1.0
CHB C:HEM201 3.5 22.5 1.0
CD1 C:ILE115 3.5 25.5 1.0
CE1 C:TYR134 4.0 39.4 1.0
CE2 C:TYR134 4.0 35.9 1.0
C3B C:HEM201 4.2 25.0 1.0
C3C C:HEM201 4.2 30.3 1.0
C2C C:HEM201 4.3 29.7 1.0
C3A C:HEM201 4.3 23.4 1.0
C2B C:HEM201 4.3 22.8 1.0
C2A C:HEM201 4.3 26.1 1.0
C2D C:HEM201 4.3 35.1 1.0
C3D C:HEM201 4.3 36.5 1.0
CD1 C:ILE72 4.8 21.0 1.0

Iron binding site 4 out of 6 in 4fvc

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Iron binding site 4 out of 6 in the Hmob Structure with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hmob Structure with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:21.7
occ:1.00
FE D:HEM201 0.0 21.7 1.0
NB D:HEM201 2.0 20.4 1.0
ND D:HEM201 2.0 21.0 1.0
NA D:HEM201 2.1 20.2 1.0
NC D:HEM201 2.1 22.5 1.0
OH D:TYR134 2.1 28.8 1.0
C4B D:HEM201 3.0 21.8 1.0
C4D D:HEM201 3.0 22.3 1.0
C1B D:HEM201 3.0 20.8 1.0
C1D D:HEM201 3.0 21.9 1.0
C1A D:HEM201 3.1 21.5 1.0
C1C D:HEM201 3.1 22.4 1.0
C4A D:HEM201 3.1 21.3 1.0
C4C D:HEM201 3.1 24.1 1.0
CZ D:TYR134 3.2 30.9 1.0
CHA D:HEM201 3.4 23.2 1.0
CHC D:HEM201 3.4 21.4 1.0
CHB D:HEM201 3.4 20.8 1.0
CHD D:HEM201 3.5 20.6 1.0
CD1 D:ILE115 3.5 20.2 1.0
O D:HOH322 3.9 31.8 1.0
CE1 D:TYR134 3.9 31.9 1.0
O D:HOH364 4.0 36.9 1.0
CE2 D:TYR134 4.1 32.2 1.0
C3B D:HEM201 4.2 23.2 1.0
C2B D:HEM201 4.2 22.8 1.0
C3D D:HEM201 4.2 26.5 1.0
C2D D:HEM201 4.3 22.1 1.0
C2A D:HEM201 4.3 21.6 1.0
C3A D:HEM201 4.3 21.4 1.0
C3C D:HEM201 4.3 24.3 1.0
C2C D:HEM201 4.3 24.2 1.0
CD1 D:ILE72 4.8 18.0 1.0
CG1 D:ILE115 5.0 17.8 1.0

Iron binding site 5 out of 6 in 4fvc

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Iron binding site 5 out of 6 in the Hmob Structure with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hmob Structure with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:29.1
occ:1.00
FE E:HEM201 0.0 29.1 1.0
ND E:HEM201 2.0 33.1 1.0
NA E:HEM201 2.0 26.8 1.0
NB E:HEM201 2.1 26.8 1.0
NC E:HEM201 2.1 30.0 1.0
OH E:TYR134 2.1 38.9 1.0
C4D E:HEM201 3.0 35.5 1.0
C1A E:HEM201 3.0 29.5 1.0
C1D E:HEM201 3.0 34.1 1.0
C4B E:HEM201 3.0 26.3 1.0
C1C E:HEM201 3.1 29.2 1.0
C4A E:HEM201 3.1 26.4 1.0
C1B E:HEM201 3.1 26.3 1.0
C4C E:HEM201 3.1 30.2 1.0
CZ E:TYR134 3.2 42.2 1.0
CHA E:HEM201 3.3 32.0 1.0
CHC E:HEM201 3.4 26.6 1.0
CHD E:HEM201 3.4 33.3 1.0
CHB E:HEM201 3.5 26.2 1.0
CD1 E:ILE115 3.5 24.5 1.0
CE2 E:TYR134 3.9 41.8 1.0
CE1 E:TYR134 4.0 43.9 1.0
C3D E:HEM201 4.2 38.1 1.0
C2D E:HEM201 4.2 37.3 1.0
C3B E:HEM201 4.3 28.8 1.0
C2A E:HEM201 4.3 27.3 1.0
C3A E:HEM201 4.3 27.8 1.0
C2C E:HEM201 4.3 29.8 1.0
C2B E:HEM201 4.3 26.7 1.0
C3C E:HEM201 4.3 31.1 1.0
CG1 E:ILE115 5.0 21.3 1.0

Iron binding site 6 out of 6 in 4fvc

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Iron binding site 6 out of 6 in the Hmob Structure with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hmob Structure with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:21.7
occ:1.00
FE F:HEM201 0.0 21.7 1.0
NB F:HEM201 2.0 20.7 1.0
ND F:HEM201 2.1 21.9 1.0
NA F:HEM201 2.1 20.1 1.0
NC F:HEM201 2.1 22.5 1.0
OH F:TYR134 2.2 28.1 1.0
C4B F:HEM201 3.0 21.4 1.0
C4D F:HEM201 3.0 23.6 1.0
C1B F:HEM201 3.0 20.9 1.0
C1A F:HEM201 3.1 22.4 1.0
C4A F:HEM201 3.1 20.4 1.0
C1D F:HEM201 3.1 22.9 1.0
C1C F:HEM201 3.1 21.2 1.0
CZ F:TYR134 3.1 30.3 1.0
C4C F:HEM201 3.1 23.6 1.0
CHA F:HEM201 3.4 23.3 1.0
CHC F:HEM201 3.4 21.8 1.0
CHB F:HEM201 3.5 20.2 1.0
CD1 F:ILE115 3.5 18.4 1.0
CHD F:HEM201 3.5 20.5 1.0
CE1 F:TYR134 3.8 32.5 1.0
O F:HOH345 4.0 36.6 1.0
CE2 F:TYR134 4.0 32.1 1.0
C3B F:HEM201 4.2 24.9 1.0
C2B F:HEM201 4.2 20.2 1.0
C3D F:HEM201 4.3 26.9 1.0
C2A F:HEM201 4.3 22.0 1.0
C2D F:HEM201 4.3 25.0 1.0
C3A F:HEM201 4.3 21.3 1.0
C3C F:HEM201 4.3 24.5 1.0
C2C F:HEM201 4.3 22.4 1.0
O F:HOH362 4.5 46.9 1.0
CD1 F:ILE72 4.8 19.3 1.0
CG1 F:ILE115 5.0 16.6 1.0

Reference:

S.Park, S.Park. N/A N/A.
Page generated: Sun Dec 13 15:34:33 2020

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