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Iron in PDB 1s5y: The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide

Protein crystallography data

The structure of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide, PDB code: 1s5y was solved by L.Vitagliano, G.Bonomi, A.Riccio, G.Di Prisco, G.Smulevich, L.Mazzarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.993, 62.980, 63.502, 77.06, 69.79, 84.17
R / Rfree (%) 19.9 / 24.7

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide (pdb code 1s5y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide, PDB code: 1s5y:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1s5y

Go back to Iron Binding Sites List in 1s5y
Iron binding site 1 out of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:21.5
occ:1.00
FE A:HEM200 0.0 21.5 1.0
NC A:HEM200 2.0 20.3 1.0
NE2 A:HIS88 2.0 16.4 1.0
ND A:HEM200 2.0 23.7 1.0
NA A:HEM200 2.0 23.7 1.0
NB A:HEM200 2.0 21.3 1.0
O A:HOH850 2.1 17.8 1.0
CE1 A:HIS88 2.9 14.3 1.0
C4C A:HEM200 3.0 20.2 1.0
C1C A:HEM200 3.0 19.9 1.0
C1D A:HEM200 3.1 22.9 1.0
C4A A:HEM200 3.1 24.4 1.0
C4D A:HEM200 3.1 24.5 1.0
C1A A:HEM200 3.1 25.6 1.0
C4B A:HEM200 3.1 20.4 1.0
C1B A:HEM200 3.1 21.4 1.0
CD2 A:HIS88 3.1 14.2 1.0
CHD A:HEM200 3.3 22.2 1.0
CHC A:HEM200 3.4 19.5 1.0
CHA A:HEM200 3.4 25.2 1.0
CHB A:HEM200 3.4 22.8 1.0
NE2 A:HIS59 4.1 31.0 1.0
ND1 A:HIS88 4.1 13.9 1.0
CG A:HIS88 4.2 15.4 1.0
C3C A:HEM200 4.3 21.5 1.0
C2C A:HEM200 4.3 21.4 1.0
C3A A:HEM200 4.3 25.4 1.0
CE1 A:HIS59 4.4 29.8 1.0
C2A A:HEM200 4.4 27.1 1.0
C3D A:HEM200 4.4 25.4 1.0
C2D A:HEM200 4.4 23.7 1.0
C3B A:HEM200 4.4 20.4 1.0
C2B A:HEM200 4.4 20.7 1.0
CG2 A:VAL63 4.9 25.0 1.0
CD1 A:LEU92 4.9 37.6 1.0

Iron binding site 2 out of 4 in 1s5y

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Iron binding site 2 out of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:31.0
occ:1.00
FE B:HEM400 0.0 31.0 1.0
NE2 B:HIS92 2.0 35.0 1.0
ND B:HEM400 2.0 33.8 1.0
NA B:HEM400 2.0 35.4 1.0
NC B:HEM400 2.0 32.8 1.0
NB B:HEM400 2.0 31.1 1.0
NE2 B:HIS63 2.1 27.8 1.0
CE1 B:HIS63 2.9 26.4 1.0
C4D B:HEM400 3.0 35.1 1.0
CE1 B:HIS92 3.0 37.8 1.0
CD2 B:HIS92 3.0 38.0 1.0
C1A B:HEM400 3.0 36.2 1.0
C1D B:HEM400 3.1 33.5 1.0
C4B B:HEM400 3.1 29.4 1.0
C4A B:HEM400 3.1 34.2 1.0
C1C B:HEM400 3.1 30.8 1.0
C4C B:HEM400 3.1 32.5 1.0
C1B B:HEM400 3.1 30.5 1.0
CHA B:HEM400 3.3 35.4 1.0
CD2 B:HIS63 3.4 25.6 1.0
CHC B:HEM400 3.4 30.1 1.0
CHD B:HEM400 3.4 33.6 1.0
CHB B:HEM400 3.4 32.1 1.0
ND1 B:HIS63 4.1 25.4 1.0
ND1 B:HIS92 4.1 38.9 1.0
CG B:HIS92 4.2 39.1 1.0
C3D B:HEM400 4.3 35.8 1.0
C2A B:HEM400 4.3 37.3 1.0
C3A B:HEM400 4.3 35.9 1.0
C3C B:HEM400 4.3 32.0 1.0
C2D B:HEM400 4.3 35.1 1.0
C3B B:HEM400 4.4 28.9 1.0
CG B:HIS63 4.4 23.4 1.0
C2C B:HEM400 4.4 31.1 1.0
C2B B:HEM400 4.4 30.8 1.0
CG2 B:VAL67 4.9 17.8 1.0

Iron binding site 3 out of 4 in 1s5y

Go back to Iron Binding Sites List in 1s5y
Iron binding site 3 out of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe600

b:18.5
occ:1.00
FE C:HEM600 0.0 18.5 1.0
ND C:HEM600 2.0 18.4 1.0
NB C:HEM600 2.0 14.6 1.0
NA C:HEM600 2.0 19.2 1.0
NC C:HEM600 2.0 16.6 1.0
NE2 C:HIS88 2.1 18.8 1.0
O C:HOH900 2.1 21.1 1.0
CE1 C:HIS88 2.8 17.7 1.0
C4D C:HEM600 3.0 20.6 1.0
C1D C:HEM600 3.0 19.6 1.0
C4A C:HEM600 3.0 18.4 1.0
C1A C:HEM600 3.1 20.6 1.0
C1B C:HEM600 3.1 14.8 1.0
C4C C:HEM600 3.1 16.2 1.0
C4B C:HEM600 3.1 16.0 1.0
C1C C:HEM600 3.1 13.9 1.0
CD2 C:HIS88 3.3 18.9 1.0
CHD C:HEM600 3.3 18.1 1.0
CHA C:HEM600 3.4 18.5 1.0
CHB C:HEM600 3.4 15.7 1.0
CHC C:HEM600 3.4 13.6 1.0
ND1 C:HIS88 4.1 17.8 1.0
NE2 C:HIS59 4.1 23.5 1.0
C2D C:HEM600 4.3 20.4 1.0
C3D C:HEM600 4.3 22.8 1.0
C2A C:HEM600 4.3 24.4 1.0
C3A C:HEM600 4.3 22.0 1.0
CG C:HIS88 4.3 19.1 1.0
C2B C:HEM600 4.4 16.0 1.0
C3C C:HEM600 4.4 13.9 1.0
C3B C:HEM600 4.4 17.1 1.0
CE1 C:HIS59 4.4 24.9 1.0
C2C C:HEM600 4.4 12.4 1.0
CG2 C:VAL63 4.8 21.5 1.0

Iron binding site 4 out of 4 in 1s5y

Go back to Iron Binding Sites List in 1s5y
Iron binding site 4 out of 4 in the The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Trematomus Bernacchii Hemoglobin Oxidized By Ferricyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe800

b:46.3
occ:1.00
FE D:HEM800 0.0 46.3 1.0
ND D:HEM800 2.0 48.8 1.0
NE2 D:HIS92 2.0 37.0 1.0
NC D:HEM800 2.0 48.7 1.0
NA D:HEM800 2.0 50.2 1.0
NB D:HEM800 2.1 47.5 1.0
NE2 D:HIS63 2.1 35.0 1.0
CE1 D:HIS63 2.8 30.9 1.0
CE1 D:HIS92 2.9 36.7 1.0
C1D D:HEM800 3.0 50.3 1.0
C4D D:HEM800 3.0 49.8 1.0
C4C D:HEM800 3.1 49.5 1.0
C1A D:HEM800 3.1 51.8 1.0
CD2 D:HIS92 3.1 38.1 1.0
C1C D:HEM800 3.1 48.0 1.0
C4A D:HEM800 3.1 50.1 1.0
C4B D:HEM800 3.1 47.2 1.0
C1B D:HEM800 3.2 46.9 1.0
CHD D:HEM800 3.3 50.7 1.0
CHA D:HEM800 3.4 51.0 1.0
CD2 D:HIS63 3.4 30.7 1.0
CHC D:HEM800 3.4 47.8 1.0
CHB D:HEM800 3.5 48.4 1.0
ND1 D:HIS63 4.1 30.2 1.0
ND1 D:HIS92 4.1 36.3 1.0
CG D:HIS92 4.2 38.5 1.0
C3D D:HEM800 4.2 51.5 1.0
C2D D:HEM800 4.3 51.1 1.0
C3C D:HEM800 4.3 49.5 1.0
C2A D:HEM800 4.3 54.1 1.0
C3A D:HEM800 4.3 52.5 1.0
C2C D:HEM800 4.4 49.5 1.0
CG D:HIS63 4.4 28.3 1.0
C3B D:HEM800 4.4 46.9 1.0
C2B D:HEM800 4.4 47.2 1.0
CG2 D:VAL67 4.5 13.9 1.0

Reference:

L.Vitagliano, G.Bonomi, A.Riccio, G.Di Prisco, G.Smulevich, L.Mazzarella. The Oxidation Process of Antarctic Fish Hemoglobins Eur.J.Biochem. V. 271 1651 2004.
ISSN: ISSN 0014-2956
PubMed: 15096204
DOI: 10.1111/J.1432-1033.2004.04054.X
Page generated: Wed Jul 16 20:34:01 2025

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