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Iron in PDB 2gtl: Lumbricus Erythrocruorin at 3.5A Resolution

Protein crystallography data

The structure of Lumbricus Erythrocruorin at 3.5A Resolution, PDB code: 2gtl was solved by W.E.Royer Jr., H.Sharma, K.Strand, J.E.Knapp, B.Bhyravbhatla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 3.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 176.080, 257.960, 436.530, 89.69, 97.15, 90.98
R / Rfree (%) 28.8 / 29.7

Other elements in 2gtl:

The structure of Lumbricus Erythrocruorin at 3.5A Resolution also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Zinc (Zn) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Lumbricus Erythrocruorin at 3.5A Resolution (pdb code 2gtl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Lumbricus Erythrocruorin at 3.5A Resolution, PDB code: 2gtl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 2gtl

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Iron binding site 1 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe160

b:60.6
occ:1.00
FE A:HEM160 0.0 60.6 1.0
C A:CMO161 1.8 82.2 1.0
NA A:HEM160 1.9 60.6 1.0
NE2 A:HIS101 1.9 55.7 1.0
NB A:HEM160 1.9 60.6 1.0
ND A:HEM160 2.0 60.6 1.0
NC A:HEM160 2.0 60.6 1.0
CE1 A:HIS101 2.8 55.7 1.0
C4A A:HEM160 3.0 60.6 1.0
C1A A:HEM160 3.0 60.6 1.0
C1B A:HEM160 3.0 60.6 1.0
C4D A:HEM160 3.0 60.6 1.0
C4B A:HEM160 3.0 60.6 1.0
O A:CMO161 3.0 82.2 1.0
C1D A:HEM160 3.0 60.6 1.0
C1C A:HEM160 3.0 60.6 1.0
CD2 A:HIS101 3.1 55.7 1.0
C4C A:HEM160 3.1 60.6 1.0
CHB A:HEM160 3.3 60.6 1.0
CHA A:HEM160 3.4 60.6 1.0
CHC A:HEM160 3.4 60.6 1.0
CHD A:HEM160 3.5 60.6 1.0
ND1 A:HIS101 4.0 55.7 1.0
CG A:HIS101 4.1 55.7 1.0
C3A A:HEM160 4.2 60.6 1.0
C2A A:HEM160 4.2 60.6 1.0
C2B A:HEM160 4.2 60.6 1.0
C2D A:HEM160 4.2 60.6 1.0
C3D A:HEM160 4.2 60.6 1.0
C3B A:HEM160 4.2 60.6 1.0
C2C A:HEM160 4.3 60.6 1.0
C3C A:HEM160 4.3 60.6 1.0

Iron binding site 2 out of 12 in 2gtl

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Iron binding site 2 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe160

b:26.1
occ:1.00
FE B:HEM160 0.0 26.1 1.0
C B:CMO161 1.7 46.6 1.0
ND B:HEM160 1.9 26.1 1.0
NA B:HEM160 1.9 26.1 1.0
NC B:HEM160 2.0 26.1 1.0
NE2 B:HIS96 2.0 60.0 1.0
NB B:HEM160 2.0 26.1 1.0
O B:CMO161 2.9 46.6 1.0
CE1 B:HIS96 2.9 60.0 1.0
C4D B:HEM160 2.9 26.1 1.0
C1D B:HEM160 2.9 26.1 1.0
C1A B:HEM160 3.0 26.1 1.0
C4C B:HEM160 3.0 26.1 1.0
C4A B:HEM160 3.0 26.1 1.0
C1C B:HEM160 3.0 26.1 1.0
C4B B:HEM160 3.0 26.1 1.0
C1B B:HEM160 3.0 26.1 1.0
CD2 B:HIS96 3.1 60.0 1.0
CHA B:HEM160 3.4 26.1 1.0
CHD B:HEM160 3.4 26.1 1.0
CHC B:HEM160 3.4 26.1 1.0
CHB B:HEM160 3.4 26.1 1.0
ND1 B:HIS96 4.1 60.0 1.0
C3D B:HEM160 4.2 26.1 1.0
C2D B:HEM160 4.2 26.1 1.0
CG B:HIS96 4.2 60.0 1.0
C2A B:HEM160 4.2 26.1 1.0
C3A B:HEM160 4.2 26.1 1.0
C3C B:HEM160 4.2 26.1 1.0
C2C B:HEM160 4.2 26.1 1.0
C2B B:HEM160 4.3 26.1 1.0
C3B B:HEM160 4.3 26.1 1.0
CG1 B:VAL68 4.9 43.4 1.0

Iron binding site 3 out of 12 in 2gtl

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Iron binding site 3 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe160

b:39.2
occ:1.00
FE C:HEM160 0.0 39.2 1.0
C C:CMO161 1.8 46.5 1.0
ND C:HEM160 1.9 39.2 1.0
NA C:HEM160 2.0 39.2 1.0
NE2 C:HIS102 2.0 39.4 1.0
NB C:HEM160 2.0 39.2 1.0
NC C:HEM160 2.0 39.2 1.0
CE1 C:HIS102 2.7 39.4 1.0
C4D C:HEM160 3.0 39.2 1.0
C1A C:HEM160 3.0 39.2 1.0
C4A C:HEM160 3.0 39.2 1.0
C1D C:HEM160 3.0 39.2 1.0
C1B C:HEM160 3.0 39.2 1.0
C4B C:HEM160 3.0 39.2 1.0
C1C C:HEM160 3.0 39.2 1.0
O C:CMO161 3.0 46.5 1.0
C4C C:HEM160 3.0 39.2 1.0
CD2 C:HIS102 3.2 39.4 1.0
CHA C:HEM160 3.4 39.2 1.0
CHC C:HEM160 3.4 39.2 1.0
CHB C:HEM160 3.4 39.2 1.0
CHD C:HEM160 3.4 39.2 1.0
ND1 C:HIS102 3.9 39.4 1.0
CG C:HIS102 4.2 39.4 1.0
C3D C:HEM160 4.2 39.2 1.0
C2D C:HEM160 4.2 39.2 1.0
C2A C:HEM160 4.2 39.2 1.0
C3A C:HEM160 4.2 39.2 1.0
C2B C:HEM160 4.3 39.2 1.0
C3C C:HEM160 4.3 39.2 1.0
C2C C:HEM160 4.3 39.2 1.0
C3B C:HEM160 4.3 39.2 1.0

Iron binding site 4 out of 12 in 2gtl

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Iron binding site 4 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe160

b:38.7
occ:1.00
FE D:HEM160 0.0 38.7 1.0
C D:CMO161 1.8 74.4 1.0
ND D:HEM160 1.9 38.7 1.0
NC D:HEM160 1.9 38.7 1.0
NA D:HEM160 2.0 38.7 1.0
NB D:HEM160 2.0 38.7 1.0
NE2 D:HIS101 2.0 81.9 1.0
CE1 D:HIS101 2.8 81.9 1.0
C4D D:HEM160 3.0 38.7 1.0
C1D D:HEM160 3.0 38.7 1.0
O D:CMO161 3.0 74.4 1.0
C1C D:HEM160 3.0 38.7 1.0
C4C D:HEM160 3.0 38.7 1.0
C1A D:HEM160 3.0 38.7 1.0
C4B D:HEM160 3.0 38.7 1.0
C4A D:HEM160 3.0 38.7 1.0
C1B D:HEM160 3.1 38.7 1.0
CD2 D:HIS101 3.2 81.9 1.0
CHA D:HEM160 3.4 38.7 1.0
CHD D:HEM160 3.4 38.7 1.0
CHC D:HEM160 3.4 38.7 1.0
CHB D:HEM160 3.4 38.7 1.0
ND1 D:HIS101 4.0 81.9 1.0
C3D D:HEM160 4.2 38.7 1.0
C2D D:HEM160 4.2 38.7 1.0
C3C D:HEM160 4.2 38.7 1.0
CG D:HIS101 4.2 81.9 1.0
C2C D:HEM160 4.2 38.7 1.0
C2A D:HEM160 4.2 38.7 1.0
C3A D:HEM160 4.3 38.7 1.0
C3B D:HEM160 4.3 38.7 1.0
C2B D:HEM160 4.3 38.7 1.0
CG1 D:VAL73 4.9 41.0 1.0
CG2 D:VAL73 5.0 41.0 1.0

Iron binding site 5 out of 12 in 2gtl

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Iron binding site 5 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe160

b:71.4
occ:1.00
FE E:HEM160 0.0 71.4 1.0
C E:CMO161 1.8 54.5 1.0
NE2 E:HIS101 1.9 56.4 1.0
ND E:HEM160 1.9 71.4 1.0
NA E:HEM160 2.0 71.4 1.0
NC E:HEM160 2.0 71.4 1.0
NB E:HEM160 2.0 71.4 1.0
CE1 E:HIS101 2.8 56.4 1.0
C4D E:HEM160 2.9 71.4 1.0
C1D E:HEM160 3.0 71.4 1.0
C1A E:HEM160 3.0 71.4 1.0
C1C E:HEM160 3.0 71.4 1.0
CD2 E:HIS101 3.0 56.4 1.0
C4C E:HEM160 3.0 71.4 1.0
C4A E:HEM160 3.0 71.4 1.0
O E:CMO161 3.1 54.5 1.0
C4B E:HEM160 3.1 71.4 1.0
C1B E:HEM160 3.1 71.4 1.0
CHA E:HEM160 3.3 71.4 1.0
CHD E:HEM160 3.4 71.4 1.0
CHC E:HEM160 3.4 71.4 1.0
CHB E:HEM160 3.4 71.4 1.0
ND1 E:HIS101 4.0 56.4 1.0
CG E:HIS101 4.1 56.4 1.0
C2D E:HEM160 4.1 71.4 1.0
C3D E:HEM160 4.2 71.4 1.0
C3A E:HEM160 4.2 71.4 1.0
C2A E:HEM160 4.2 71.4 1.0
C2C E:HEM160 4.2 71.4 1.0
C3C E:HEM160 4.2 71.4 1.0
C2B E:HEM160 4.3 71.4 1.0
C3B E:HEM160 4.3 71.4 1.0

Iron binding site 6 out of 12 in 2gtl

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Iron binding site 6 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe160

b:38.0
occ:1.00
FE F:HEM160 0.0 38.0 1.0
C F:CMO161 1.8 64.9 1.0
NA F:HEM160 1.9 38.0 1.0
NE2 F:HIS96 1.9 54.4 1.0
ND F:HEM160 1.9 38.0 1.0
NC F:HEM160 2.0 38.0 1.0
NB F:HEM160 2.0 38.0 1.0
CE1 F:HIS96 2.8 54.4 1.0
C1A F:HEM160 2.9 38.0 1.0
C4D F:HEM160 3.0 38.0 1.0
O F:CMO161 3.0 64.9 1.0
C4A F:HEM160 3.0 38.0 1.0
C1D F:HEM160 3.0 38.0 1.0
CD2 F:HIS96 3.0 54.4 1.0
C4C F:HEM160 3.0 38.0 1.0
C1B F:HEM160 3.0 38.0 1.0
C1C F:HEM160 3.0 38.0 1.0
C4B F:HEM160 3.0 38.0 1.0
CHA F:HEM160 3.4 38.0 1.0
CHB F:HEM160 3.4 38.0 1.0
CHD F:HEM160 3.4 38.0 1.0
CHC F:HEM160 3.4 38.0 1.0
ND1 F:HIS96 4.0 54.4 1.0
CG F:HIS96 4.1 54.4 1.0
C3D F:HEM160 4.2 38.0 1.0
C2A F:HEM160 4.2 38.0 1.0
C3A F:HEM160 4.2 38.0 1.0
C2D F:HEM160 4.2 38.0 1.0
C2C F:HEM160 4.3 38.0 1.0
C3C F:HEM160 4.3 38.0 1.0
C2B F:HEM160 4.3 38.0 1.0
C3B F:HEM160 4.3 38.0 1.0
CG1 F:VAL68 4.9 30.4 1.0

Iron binding site 7 out of 12 in 2gtl

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Iron binding site 7 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe160

b:66.3
occ:1.00
FE G:HEM160 0.0 66.3 1.0
C G:CMO161 1.8 38.4 1.0
NB G:HEM160 2.0 66.3 1.0
ND G:HEM160 2.0 66.3 1.0
NA G:HEM160 2.0 66.3 1.0
NC G:HEM160 2.0 66.3 1.0
NE2 G:HIS102 2.0 42.1 1.0
CE1 G:HIS102 2.7 42.1 1.0
C1B G:HEM160 3.0 66.3 1.0
C4D G:HEM160 3.0 66.3 1.0
C4B G:HEM160 3.0 66.3 1.0
C4A G:HEM160 3.0 66.3 1.0
C1A G:HEM160 3.0 66.3 1.0
C1C G:HEM160 3.0 66.3 1.0
O G:CMO161 3.0 38.4 1.0
C1D G:HEM160 3.0 66.3 1.0
C4C G:HEM160 3.0 66.3 1.0
CD2 G:HIS102 3.2 42.1 1.0
CHB G:HEM160 3.4 66.3 1.0
CHA G:HEM160 3.4 66.3 1.0
CHC G:HEM160 3.4 66.3 1.0
CHD G:HEM160 3.4 66.3 1.0
ND1 G:HIS102 4.0 42.1 1.0
CG G:HIS102 4.2 42.1 1.0
C2B G:HEM160 4.2 66.3 1.0
C3B G:HEM160 4.2 66.3 1.0
C3A G:HEM160 4.2 66.3 1.0
C2C G:HEM160 4.2 66.3 1.0
C2A G:HEM160 4.2 66.3 1.0
C2D G:HEM160 4.3 66.3 1.0
C3D G:HEM160 4.3 66.3 1.0
C3C G:HEM160 4.3 66.3 1.0

Iron binding site 8 out of 12 in 2gtl

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Iron binding site 8 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe160

b:52.5
occ:1.00
FE H:HEM160 0.0 52.5 1.0
C H:CMO161 1.8 68.9 1.0
ND H:HEM160 1.9 52.5 1.0
NA H:HEM160 2.0 52.5 1.0
NC H:HEM160 2.0 52.5 1.0
NB H:HEM160 2.0 52.5 1.0
NE2 H:HIS101 2.0 80.9 1.0
CE1 H:HIS101 2.7 80.9 1.0
C4D H:HEM160 3.0 52.5 1.0
C1D H:HEM160 3.0 52.5 1.0
C1A H:HEM160 3.0 52.5 1.0
C1C H:HEM160 3.0 52.5 1.0
C4A H:HEM160 3.0 52.5 1.0
C4C H:HEM160 3.0 52.5 1.0
C4B H:HEM160 3.0 52.5 1.0
O H:CMO161 3.0 68.9 1.0
C1B H:HEM160 3.0 52.5 1.0
CD2 H:HIS101 3.2 80.9 1.0
CHA H:HEM160 3.4 52.5 1.0
CHD H:HEM160 3.4 52.5 1.0
CHC H:HEM160 3.4 52.5 1.0
CHB H:HEM160 3.4 52.5 1.0
ND1 H:HIS101 3.9 80.9 1.0
CG H:HIS101 4.2 80.9 1.0
C3D H:HEM160 4.2 52.5 1.0
C2D H:HEM160 4.2 52.5 1.0
C3C H:HEM160 4.2 52.5 1.0
C2A H:HEM160 4.2 52.5 1.0
C2C H:HEM160 4.2 52.5 1.0
C3A H:HEM160 4.2 52.5 1.0
C3B H:HEM160 4.3 52.5 1.0
C2B H:HEM160 4.3 52.5 1.0
CG1 H:VAL73 5.0 57.3 1.0

Iron binding site 9 out of 12 in 2gtl

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Iron binding site 9 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe160

b:64.3
occ:1.00
FE I:HEM160 0.0 64.3 1.0
C I:CMO161 1.8 80.6 1.0
ND I:HEM160 1.9 64.3 1.0
NA I:HEM160 1.9 64.3 1.0
NE2 I:HIS101 2.0 52.9 1.0
NC I:HEM160 2.0 64.3 1.0
NB I:HEM160 2.0 64.3 1.0
CE1 I:HIS101 2.8 52.9 1.0
C1D I:HEM160 3.0 64.3 1.0
C4D I:HEM160 3.0 64.3 1.0
C1A I:HEM160 3.0 64.3 1.0
C4A I:HEM160 3.0 64.3 1.0
O I:CMO161 3.0 80.6 1.0
C4C I:HEM160 3.0 64.3 1.0
C1C I:HEM160 3.0 64.3 1.0
C1B I:HEM160 3.0 64.3 1.0
C4B I:HEM160 3.1 64.3 1.0
CD2 I:HIS101 3.1 52.9 1.0
CHA I:HEM160 3.4 64.3 1.0
CHD I:HEM160 3.4 64.3 1.0
CHB I:HEM160 3.4 64.3 1.0
CHC I:HEM160 3.4 64.3 1.0
ND1 I:HIS101 4.0 52.9 1.0
CG I:HIS101 4.2 52.9 1.0
C2D I:HEM160 4.2 64.3 1.0
C3D I:HEM160 4.2 64.3 1.0
C3A I:HEM160 4.2 64.3 1.0
C2A I:HEM160 4.2 64.3 1.0
C2C I:HEM160 4.2 64.3 1.0
C3C I:HEM160 4.2 64.3 1.0
C2B I:HEM160 4.3 64.3 1.0
C3B I:HEM160 4.3 64.3 1.0

Iron binding site 10 out of 12 in 2gtl

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Iron binding site 10 out of 12 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe160

b:54.3
occ:1.00
FE J:HEM160 0.0 54.3 1.0
C J:CMO161 1.8 70.0 1.0
NE2 J:HIS96 1.9 71.2 1.0
NB J:HEM160 1.9 54.3 1.0
NA J:HEM160 1.9 54.3 1.0
NC J:HEM160 2.0 54.3 1.0
ND J:HEM160 2.0 54.3 1.0
CE1 J:HIS96 2.9 71.2 1.0
O J:CMO161 3.0 70.0 1.0
C1B J:HEM160 3.0 54.3 1.0
C1A J:HEM160 3.0 54.3 1.0
C4B J:HEM160 3.0 54.3 1.0
C1C J:HEM160 3.0 54.3 1.0
C4D J:HEM160 3.0 54.3 1.0
C4A J:HEM160 3.0 54.3 1.0
C1D J:HEM160 3.0 54.3 1.0
C4C J:HEM160 3.0 54.3 1.0
CD2 J:HIS96 3.0 71.2 1.0
CHB J:HEM160 3.4 54.3 1.0
CHC J:HEM160 3.4 54.3 1.0
CHA J:HEM160 3.4 54.3 1.0
CHD J:HEM160 3.4 54.3 1.0
ND1 J:HIS96 4.0 71.2 1.0
CG J:HIS96 4.1 71.2 1.0
C3A J:HEM160 4.2 54.3 1.0
C2A J:HEM160 4.2 54.3 1.0
C2B J:HEM160 4.2 54.3 1.0
C3B J:HEM160 4.2 54.3 1.0
C3D J:HEM160 4.2 54.3 1.0
C2C J:HEM160 4.2 54.3 1.0
C3C J:HEM160 4.2 54.3 1.0
C2D J:HEM160 4.3 54.3 1.0
CG1 J:VAL68 4.9 31.0 1.0

Reference:

W.E.Royer Jr., H.Sharma, K.Strand, J.E.Knapp, B.Bhyravbhatla. Lumbricus Erythrocruorin at 3.5 A Resolution: Architecture of A Megadalton Respiratory Complex. Structure V. 14 1167 2006.
ISSN: ISSN 0969-2126
PubMed: 16843898
DOI: 10.1016/J.STR.2006.05.011
Page generated: Sun Dec 13 14:45:44 2020

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