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Iron in PDB 2d5z: Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules

Protein crystallography data

The structure of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules, PDB code: 2d5z was solved by T.Yokoyama, S.Neya, A.Tsuneshige, T.Yonetani, S.Y.Park, J.R.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.028, 82.697, 110.343, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.5

Other elements in 2d5z:

The structure of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules (pdb code 2d5z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules, PDB code: 2d5z:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2d5z

Go back to Iron Binding Sites List in 2d5z
Iron binding site 1 out of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe142

b:13.9
occ:1.00
FE A:HEM142 0.0 13.9 1.0
NA A:HEM142 2.1 12.4 1.0
NC A:HEM142 2.1 12.5 1.0
NB A:HEM142 2.1 14.1 1.0
ND A:HEM142 2.1 15.1 1.0
NE2 A:HIS87 2.2 14.0 1.0
CE1 A:HIS87 3.0 14.6 1.0
C4A A:HEM142 3.1 13.8 1.0
C4C A:HEM142 3.1 13.2 1.0
C1A A:HEM142 3.1 13.6 1.0
C1D A:HEM142 3.1 13.7 1.0
C1B A:HEM142 3.1 14.0 1.0
C1C A:HEM142 3.1 12.7 1.0
C4D A:HEM142 3.1 14.3 1.0
C4B A:HEM142 3.1 15.1 1.0
O A:HOH1238 3.1 22.4 1.0
CD2 A:HIS87 3.3 13.4 1.0
CHB A:HEM142 3.4 13.9 1.0
CHD A:HEM142 3.5 13.3 1.0
CHA A:HEM142 3.5 13.4 1.0
CHC A:HEM142 3.5 13.4 1.0
ND1 A:HIS87 4.2 13.3 1.0
C3A A:HEM142 4.3 14.1 1.0
C2A A:HEM142 4.3 15.1 1.0
C3C A:HEM142 4.3 13.0 1.0
C2C A:HEM142 4.3 11.0 1.0
C2B A:HEM142 4.3 13.9 1.0
C2D A:HEM142 4.3 15.0 1.0
C3B A:HEM142 4.3 13.7 1.0
C3D A:HEM142 4.3 14.7 1.0
CG A:HIS87 4.4 13.4 1.0
CE1 A:HIS58 4.5 20.5 1.0
NE2 A:HIS58 4.5 20.5 1.0
CD1 A:LEU91 4.6 13.5 1.0

Iron binding site 2 out of 4 in 2d5z

Go back to Iron Binding Sites List in 2d5z
Iron binding site 2 out of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe147

b:18.0
occ:1.00
FE B:HEM147 0.0 18.0 1.0
NC B:HEM147 2.0 18.0 1.0
NB B:HEM147 2.1 14.8 1.0
ND B:HEM147 2.1 17.4 1.0
NA B:HEM147 2.1 19.9 1.0
NE2 B:HIS92 2.1 17.2 1.0
O B:HOH196 2.6 29.2 1.0
CE1 B:HIS92 3.0 17.2 1.0
C1B B:HEM147 3.1 17.6 1.0
C1D B:HEM147 3.1 18.1 1.0
C4D B:HEM147 3.1 19.0 1.0
C4C B:HEM147 3.1 16.8 1.0
C1A B:HEM147 3.1 20.2 1.0
C4A B:HEM147 3.1 19.1 1.0
C1C B:HEM147 3.1 16.7 1.0
C4B B:HEM147 3.1 17.6 1.0
CD2 B:HIS92 3.2 16.4 1.0
CHB B:HEM147 3.4 18.8 1.0
CHA B:HEM147 3.4 19.7 1.0
CHD B:HEM147 3.4 17.9 1.0
CHC B:HEM147 3.5 17.5 1.0
ND1 B:HIS92 4.1 16.9 1.0
NE2 B:HIS63 4.2 19.4 1.0
C2B B:HEM147 4.3 17.4 1.0
CG B:HIS92 4.3 17.4 1.0
C3D B:HEM147 4.3 18.8 1.0
C2C B:HEM147 4.3 16.7 1.0
C2D B:HEM147 4.3 18.6 1.0
C3C B:HEM147 4.3 16.8 1.0
C2A B:HEM147 4.3 21.2 1.0
C3B B:HEM147 4.3 17.9 1.0
C3A B:HEM147 4.3 20.6 1.0
CG2 B:VAL67 4.5 18.6 1.0
CE1 B:HIS63 4.9 20.7 1.0

Iron binding site 3 out of 4 in 2d5z

Go back to Iron Binding Sites List in 2d5z
Iron binding site 3 out of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe142

b:16.4
occ:1.00
FE C:HEM142 0.0 16.4 1.0
NA C:HEM142 2.1 14.2 1.0
NB C:HEM142 2.1 16.8 1.0
NC C:HEM142 2.1 14.6 1.0
ND C:HEM142 2.1 16.8 1.0
NE2 C:HIS87 2.2 17.8 1.0
CE1 C:HIS87 3.0 17.1 1.0
C4A C:HEM142 3.1 16.3 1.0
C1B C:HEM142 3.1 15.8 1.0
C1C C:HEM142 3.1 14.9 1.0
C4B C:HEM142 3.1 14.1 1.0
C1A C:HEM142 3.1 17.8 1.0
C4D C:HEM142 3.1 16.8 1.0
C4C C:HEM142 3.1 14.1 1.0
C1D C:HEM142 3.1 15.8 1.0
O C:HOH1258 3.3 27.3 1.0
CD2 C:HIS87 3.3 18.1 1.0
CHB C:HEM142 3.4 16.4 1.0
CHA C:HEM142 3.5 16.5 1.0
CHC C:HEM142 3.5 15.3 1.0
CHD C:HEM142 3.5 15.7 1.0
ND1 C:HIS87 4.2 17.9 1.0
C2C C:HEM142 4.3 13.7 1.0
C2B C:HEM142 4.3 14.8 1.0
C3A C:HEM142 4.3 18.4 1.0
C2A C:HEM142 4.3 18.5 1.0
C3B C:HEM142 4.3 15.1 1.0
C3C C:HEM142 4.3 14.3 1.0
C3D C:HEM142 4.4 16.6 1.0
CG C:HIS87 4.4 17.5 1.0
C2D C:HEM142 4.4 15.6 1.0
CE1 C:HIS58 4.4 22.8 1.0
CD1 C:LEU91 4.4 18.1 1.0
NE2 C:HIS58 4.4 22.8 1.0

Iron binding site 4 out of 4 in 2d5z

Go back to Iron Binding Sites List in 2d5z
Iron binding site 4 out of 4 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe147

b:13.2
occ:1.00
FE D:HEM147 0.0 13.2 1.0
NA D:HEM147 2.1 12.8 1.0
ND D:HEM147 2.1 12.7 1.0
NC D:HEM147 2.1 12.2 1.0
NB D:HEM147 2.1 12.9 1.0
NE2 D:HIS92 2.2 11.1 1.0
CE1 D:HIS92 3.0 11.1 1.0
C4A D:HEM147 3.1 13.4 1.0
C4D D:HEM147 3.1 13.0 1.0
C1A D:HEM147 3.1 13.8 1.0
C1B D:HEM147 3.1 12.6 1.0
C1D D:HEM147 3.1 12.6 1.0
C4B D:HEM147 3.1 12.8 1.0
C1C D:HEM147 3.1 12.5 1.0
C4C D:HEM147 3.1 12.1 1.0
CD2 D:HIS92 3.2 11.1 1.0
CHB D:HEM147 3.4 13.9 1.0
CHA D:HEM147 3.4 13.8 1.0
CHC D:HEM147 3.5 12.2 1.0
CHD D:HEM147 3.5 12.2 1.0
CG2 D:VAL67 3.9 14.9 1.0
NE2 D:HIS63 4.2 18.1 1.0
ND1 D:HIS92 4.2 11.6 1.0
C3A D:HEM147 4.3 14.9 1.0
C2A D:HEM147 4.3 14.5 1.0
C2B D:HEM147 4.3 12.2 1.0
C3B D:HEM147 4.3 12.3 1.0
C3D D:HEM147 4.3 14.6 1.0
CG D:HIS92 4.3 12.4 1.0
C2D D:HEM147 4.3 14.0 1.0
C2C D:HEM147 4.3 9.8 1.0
C3C D:HEM147 4.4 12.9 1.0
CE1 D:HIS63 4.5 19.3 1.0
CD1 D:LEU96 4.8 15.6 1.0

Reference:

T.Yokoyama, S.Neya, A.Tsuneshige, T.Yonetani, S.Y.Park, J.R.Tame. R-State Haemoglobin with Low Oxygen Affinity: Crystal Structures of Deoxy Human and Carbonmonoxy Horse Haemoglobin Bound to the Effector Molecule L35 J.Mol.Biol. V. 356 790 2006.
ISSN: ISSN 0022-2836
PubMed: 16403522
DOI: 10.1016/J.JMB.2005.12.018
Page generated: Sat Aug 3 20:43:20 2024

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