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Iron in PDB 2dn3: 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form

Protein crystallography data

The structure of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form, PDB code: 2dn3 was solved by S.-Y.Park, T.Yokoyama, N.Shibayama, Y.Shiro, J.R.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.25
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.270, 53.270, 189.780, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / n/a

Iron Binding Sites:

The binding sites of Iron atom in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form (pdb code 2dn3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form, PDB code: 2dn3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2dn3

Go back to Iron Binding Sites List in 2dn3
Iron binding site 1 out of 2 in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe142

b:12.5
occ:1.00
FE A:HEM142 0.0 12.5 1.0
C A:CMO143 1.7 14.9 1.0
NC A:HEM142 2.0 13.7 1.0
NB A:HEM142 2.0 13.7 1.0
NA A:HEM142 2.0 13.1 1.0
ND A:HEM142 2.1 13.2 1.0
NE2 A:HIS87 2.1 13.1 1.0
O A:CMO143 2.9 14.9 1.0
C4B A:HEM142 3.0 13.2 1.0
C4C A:HEM142 3.0 13.8 1.0
C1D A:HEM142 3.0 13.8 1.0
C1C A:HEM142 3.0 12.7 1.0
C1B A:HEM142 3.0 13.4 1.0
C4D A:HEM142 3.1 14.3 1.0
CE1 A:HIS87 3.1 13.4 1.0
C1A A:HEM142 3.1 13.4 1.0
C4A A:HEM142 3.1 13.0 1.0
CD2 A:HIS87 3.1 14.3 1.0
CHB A:HEM142 3.4 14.1 1.0
CHC A:HEM142 3.4 13.6 1.0
CHD A:HEM142 3.4 13.7 1.0
CHA A:HEM142 3.5 14.3 1.0
C2C A:HEM142 4.2 13.4 1.0
ND1 A:HIS87 4.2 13.6 1.0
C3C A:HEM142 4.2 13.6 1.0
C2B A:HEM142 4.3 13.5 1.0
C3A A:HEM142 4.3 13.9 1.0
CG A:HIS87 4.3 13.7 1.0
C3B A:HEM142 4.3 13.3 1.0
C2D A:HEM142 4.3 14.9 1.0
C2A A:HEM142 4.3 14.9 1.0
C3D A:HEM142 4.3 15.5 1.0
NE2 A:HIS58 4.4 18.2 1.0
CG2 A:VAL62 5.0 15.7 1.0

Iron binding site 2 out of 2 in 2dn3

Go back to Iron Binding Sites List in 2dn3
Iron binding site 2 out of 2 in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Carbonmonoxy Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe147

b:15.3
occ:1.00
FE B:HEM147 0.0 15.3 1.0
C B:CMO148 1.7 14.8 1.0
NA B:HEM147 2.0 16.0 1.0
ND B:HEM147 2.0 17.0 1.0
NB B:HEM147 2.0 16.3 1.0
NC B:HEM147 2.0 16.3 1.0
NE2 B:HIS92 2.1 16.6 1.0
O B:CMO148 2.9 17.3 1.0
C1A B:HEM147 3.0 16.6 1.0
C1D B:HEM147 3.0 17.3 1.0
C4C B:HEM147 3.1 16.3 1.0
C1C B:HEM147 3.1 16.8 1.0
C4B B:HEM147 3.1 17.0 1.0
C4A B:HEM147 3.1 16.7 1.0
CE1 B:HIS92 3.1 16.4 1.0
C1B B:HEM147 3.1 16.7 1.0
C4D B:HEM147 3.1 17.6 1.0
CD2 B:HIS92 3.1 17.0 1.0
CHD B:HEM147 3.4 17.0 1.0
CHC B:HEM147 3.4 17.5 1.0
CHB B:HEM147 3.5 17.4 1.0
CHA B:HEM147 3.5 16.5 1.0
ND1 B:HIS92 4.2 16.1 1.0
C2C B:HEM147 4.3 16.1 1.0
C3C B:HEM147 4.3 16.7 1.0
CG B:HIS92 4.3 15.2 1.0
C3A B:HEM147 4.3 16.4 1.0
C3B B:HEM147 4.3 16.9 1.0
C2A B:HEM147 4.3 16.6 1.0
C2D B:HEM147 4.3 17.2 1.0
C2B B:HEM147 4.4 16.4 1.0
C3D B:HEM147 4.4 16.3 1.0
NE2 B:HIS63 4.5 19.7 1.0
CG2 B:VAL67 4.6 18.5 1.0

Reference:

S.-Y.Park, T.Yokoyama, N.Shibayama, Y.Shiro, J.R.Tame. 1.25 A Resolution Crystal Structures of Human Haemoglobin in the Oxy, Deoxy and Carbonmonoxy Forms. J.Mol.Biol. V. 360 690 2006.
ISSN: ISSN 0022-2836
PubMed: 16765986
DOI: 10.1016/J.JMB.2006.05.036
Page generated: Sun Dec 13 14:42:45 2020

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