Atomistry » Iron » PDB 1rte-1sdk » 1s5y
Atomistry »
  Iron »
    PDB 1rte-1sdk »
      1s5y »

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

Go back to Iron Binding Sites List in 1s5y
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: Sat Aug 3 14:34:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy