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Iron in PDB 2d2m: Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi

Protein crystallography data

The structure of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi, PDB code: 2d2m was solved by N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.85
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 111.498, 111.498, 276.835, 90.00, 90.00, 120.00
R / Rfree (%) 23.6 / 27.7

Iron Binding Sites:

The binding sites of Iron atom in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi (pdb code 2d2m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi, PDB code: 2d2m:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2d2m

Go back to Iron Binding Sites List in 2d2m
Iron binding site 1 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:36.8
occ:1.00
FE A:HEM200 0.0 36.8 1.0
O1 A:OXY201 1.8 97.2 1.0
NE2 A:HIS94 2.0 66.8 1.0
ND A:HEM200 2.0 53.2 1.0
NA A:HEM200 2.0 53.2 1.0
NB A:HEM200 2.1 53.2 1.0
NC A:HEM200 2.1 53.2 1.0
O2 A:OXY201 2.9 97.6 1.0
CD2 A:HIS94 2.9 66.8 1.0
CE1 A:HIS94 3.0 66.8 1.0
C4D A:HEM200 3.0 53.2 1.0
C1A A:HEM200 3.0 53.2 1.0
C1D A:HEM200 3.0 53.2 1.0
C4A A:HEM200 3.1 53.2 1.0
C4C A:HEM200 3.1 53.2 1.0
C4B A:HEM200 3.1 53.2 1.0
C1C A:HEM200 3.1 53.2 1.0
C1B A:HEM200 3.1 53.2 1.0
CHA A:HEM200 3.4 53.2 1.0
CHD A:HEM200 3.4 53.2 1.0
CHC A:HEM200 3.4 53.2 1.0
CHB A:HEM200 3.4 53.2 1.0
ND1 A:HIS94 4.1 66.8 1.0
CG A:HIS94 4.1 66.8 1.0
C3D A:HEM200 4.3 53.2 1.0
C2D A:HEM200 4.3 53.2 1.0
C2A A:HEM200 4.3 53.2 1.0
C3A A:HEM200 4.3 53.2 1.0
C3C A:HEM200 4.3 53.2 1.0
C3B A:HEM200 4.3 53.2 1.0
C2C A:HEM200 4.3 53.2 1.0
C2B A:HEM200 4.4 53.2 1.0
CG2 A:VAL66 4.9 28.6 1.0

Iron binding site 2 out of 4 in 2d2m

Go back to Iron Binding Sites List in 2d2m
Iron binding site 2 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:40.7
occ:1.00
FE B:HEM200 0.0 40.7 1.0
O1 B:OXY1201 1.8 99.8 1.0
NE2 B:HIS94 2.0 50.8 1.0
NA B:HEM200 2.0 42.2 1.0
ND B:HEM200 2.0 42.2 1.0
NB B:HEM200 2.1 42.2 1.0
NC B:HEM200 2.1 42.2 1.0
O2 B:OXY1201 2.8 0.1 1.0
CD2 B:HIS94 2.9 50.8 1.0
CE1 B:HIS94 3.0 50.8 1.0
C4A B:HEM200 3.0 42.2 1.0
C1A B:HEM200 3.1 42.2 1.0
C1D B:HEM200 3.1 42.2 1.0
C4D B:HEM200 3.1 42.2 1.0
C1B B:HEM200 3.1 42.2 1.0
C4C B:HEM200 3.1 42.2 1.0
C4B B:HEM200 3.1 42.2 1.0
C1C B:HEM200 3.1 42.2 1.0
CHA B:HEM200 3.4 42.2 1.0
CHB B:HEM200 3.4 42.2 1.0
CHD B:HEM200 3.4 42.2 1.0
CHC B:HEM200 3.5 42.2 1.0
CG B:HIS94 4.1 50.8 1.0
ND1 B:HIS94 4.1 50.8 1.0
C2D B:HEM200 4.3 42.2 1.0
C3D B:HEM200 4.3 42.2 1.0
C3A B:HEM200 4.3 42.2 1.0
C2A B:HEM200 4.3 42.2 1.0
C3B B:HEM200 4.3 42.2 1.0
C2B B:HEM200 4.3 42.2 1.0
C2C B:HEM200 4.3 42.2 1.0
C3C B:HEM200 4.3 42.2 1.0
CG2 B:VAL66 4.8 23.4 1.0

Iron binding site 3 out of 4 in 2d2m

Go back to Iron Binding Sites List in 2d2m
Iron binding site 3 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:37.1
occ:1.00
FE C:HEM200 0.0 37.1 1.0
O1 C:OXY2201 1.8 75.3 1.0
NE2 C:HIS98 2.0 34.1 1.0
ND C:HEM200 2.0 60.4 1.0
NA C:HEM200 2.1 60.4 1.0
NB C:HEM200 2.1 60.4 1.0
NC C:HEM200 2.1 60.4 1.0
CD2 C:HIS98 2.9 34.1 1.0
O2 C:OXY2201 3.0 75.7 1.0
CE1 C:HIS98 3.0 34.1 1.0
C1D C:HEM200 3.1 60.4 1.0
C4A C:HEM200 3.1 60.4 1.0
C4D C:HEM200 3.1 60.4 1.0
C4B C:HEM200 3.1 60.4 1.0
C1B C:HEM200 3.1 60.4 1.0
C1A C:HEM200 3.1 60.4 1.0
C4C C:HEM200 3.1 60.4 1.0
C1C C:HEM200 3.1 60.4 1.0
CHD C:HEM200 3.4 60.4 1.0
CHB C:HEM200 3.4 60.4 1.0
CHA C:HEM200 3.4 60.4 1.0
CHC C:HEM200 3.4 60.4 1.0
ND1 C:HIS98 4.1 34.1 1.0
CG C:HIS98 4.1 34.1 1.0
C2D C:HEM200 4.3 60.4 1.0
C3D C:HEM200 4.3 60.4 1.0
C3B C:HEM200 4.3 60.4 1.0
C2B C:HEM200 4.3 60.4 1.0
C3A C:HEM200 4.3 60.4 1.0
C2A C:HEM200 4.3 60.4 1.0
C3C C:HEM200 4.3 60.4 1.0
C2C C:HEM200 4.3 60.4 1.0
CG2 C:VAL70 4.8 43.5 1.0

Iron binding site 4 out of 4 in 2d2m

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Iron binding site 4 out of 4 in the Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:76.0
occ:1.00
FE D:HEM200 0.0 76.0 1.0
O1 D:OXY3201 1.8 90.4 1.0
NE2 D:HIS96 2.0 59.8 1.0
ND D:HEM200 2.1 87.8 1.0
NA D:HEM200 2.1 87.8 1.0
NB D:HEM200 2.1 87.8 1.0
NC D:HEM200 2.1 87.8 1.0
O2 D:OXY3201 2.9 90.7 1.0
CD2 D:HIS96 3.0 59.8 1.0
CE1 D:HIS96 3.0 59.8 1.0
C1D D:HEM200 3.1 87.8 1.0
C4C D:HEM200 3.1 87.8 1.0
C4D D:HEM200 3.1 87.8 1.0
C1A D:HEM200 3.1 87.8 1.0
C4A D:HEM200 3.1 87.8 1.0
C1B D:HEM200 3.1 87.8 1.0
C4B D:HEM200 3.1 87.8 1.0
C1C D:HEM200 3.1 87.8 1.0
CHD D:HEM200 3.4 87.8 1.0
CHA D:HEM200 3.4 87.8 1.0
CHC D:HEM200 3.5 87.8 1.0
CHB D:HEM200 3.5 87.8 1.0
ND1 D:HIS96 4.1 59.8 1.0
CG D:HIS96 4.1 59.8 1.0
C3D D:HEM200 4.3 87.8 1.0
C2D D:HEM200 4.3 87.8 1.0
C2B D:HEM200 4.3 87.8 1.0
C3B D:HEM200 4.3 87.8 1.0
C3C D:HEM200 4.3 87.8 1.0
C3A D:HEM200 4.3 87.8 1.0
C2A D:HEM200 4.3 87.8 1.0
C2C D:HEM200 4.4 87.8 1.0

Reference:

N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, K.Miki. Structure of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi. Proc.Natl.Acad.Sci.Usa V. 102 14521 2005.
ISSN: ISSN 0027-8424
PubMed: 16204001
DOI: 10.1073/PNAS.0501541102
Page generated: Thu Jul 17 00:35:31 2025

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