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Iron in PDB 1yvq: The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5)

Protein crystallography data

The structure of The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5), PDB code: 1yvq was solved by V.N.Malashkevich, T.C.Balazs, S.C.Almo, R.E.Hirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.38 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.621, 96.018, 101.368, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23

Iron Binding Sites:

The binding sites of Iron atom in the The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5) (pdb code 1yvq). 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 Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5), PDB code: 1yvq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1yvq

Go back to Iron Binding Sites List in 1yvq
Iron binding site 1 out of 4 in the The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.9
occ:1.00
 FE A:HEM701 0.0 18.9 1.0
C A:CMO801 1.8 16.1 1.0
ND A:HEM701 2.0 16.7 1.0
NC A:HEM701 2.0 16.1 1.0
NB A:HEM701 2.1 17.3 1.0
NA A:HEM701 2.1 16.6 1.0
NE2 A:HIS87 2.1 15.0 1.0
O A:CMO801 2.9 25.1 1.0
C1D A:HEM701 3.0 17.3 1.0
C4C A:HEM701 3.0 17.4 1.0
C4D A:HEM701 3.1 18.0 1.0
C1C A:HEM701 3.1 15.9 1.0
C4B A:HEM701 3.1 16.8 1.0
C1A A:HEM701 3.1 18.1 1.0
C1B A:HEM701 3.1 17.5 1.0
CE1 A:HIS87 3.1 18.3 1.0
C4A A:HEM701 3.1 18.0 1.0
CD2 A:HIS87 3.1 16.4 1.0
CHD A:HEM701 3.4 15.9 1.0
CHC A:HEM701 3.4 13.9 1.0
CHA A:HEM701 3.4 16.9 1.0
CHB A:HEM701 3.5 15.4 1.0
ND1 A:HIS87 4.2 16.3 1.0
CG A:HIS87 4.3 15.9 1.0
C2D A:HEM701 4.3 17.4 1.0
NE2 A:HIS58 4.3 23.9 1.0
C3D A:HEM701 4.3 16.9 1.0
C3C A:HEM701 4.3 16.8 1.0
C2C A:HEM701 4.3 15.2 1.0
C3B A:HEM701 4.3 16.8 1.0
C2A A:HEM701 4.3 19.4 1.0
C2B A:HEM701 4.3 15.7 1.0
C3A A:HEM701 4.3 18.7 1.0
CG2 A:VAL62 4.9 18.5 1.0

Iron binding site 2 out of 4 in 1yvq

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Iron binding site 2 out of 4 in the The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:19.6
occ:1.00
 FE B:HEM702 0.0 19.6 1.0
C B:CMO802 1.8 16.4 1.0
NA B:HEM702 2.0 18.4 1.0
ND B:HEM702 2.1 19.3 1.0
NB B:HEM702 2.1 18.7 1.0
NC B:HEM702 2.1 17.8 1.0
NE2 B:HIS92 2.2 15.3 1.0
O B:CMO802 2.9 22.3 1.0
C4A B:HEM702 3.1 17.8 1.0
C4B B:HEM702 3.1 17.7 1.0
C1A B:HEM702 3.1 19.6 1.0
C1C B:HEM702 3.1 18.0 1.0
C4D B:HEM702 3.1 18.2 1.0
C1B B:HEM702 3.1 16.6 1.0
C1D B:HEM702 3.1 18.2 1.0
C4C B:HEM702 3.1 17.8 1.0
CD2 B:HIS92 3.1 17.2 1.0
CE1 B:HIS92 3.2 19.7 1.0
CHC B:HEM702 3.4 17.5 1.0
CHB B:HEM702 3.4 17.2 1.0
CHA B:HEM702 3.4 18.1 1.0
CHD B:HEM702 3.5 18.6 1.0
CG B:HIS92 4.3 17.3 1.0
ND1 B:HIS92 4.3 17.3 1.0
C3A B:HEM702 4.3 17.6 1.0
C3D B:HEM702 4.3 20.3 1.0
C2D B:HEM702 4.3 19.1 1.0
C2A B:HEM702 4.3 18.0 1.0
C2B B:HEM702 4.3 18.0 1.0
C3B B:HEM702 4.3 18.4 1.0
C2C B:HEM702 4.3 18.0 1.0
C3C B:HEM702 4.3 19.5 1.0
NE2 B:HIS63 4.4 21.9 1.0
CG2 B:VAL67 4.8 16.5 1.0

Iron binding site 3 out of 4 in 1yvq

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Iron binding site 3 out of 4 in the The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe703

b:18.3
occ:1.00
 FE C:HEM703 0.0 18.3 1.0
C C:CMO803 1.8 18.6 1.0
ND C:HEM703 2.0 18.3 1.0
NA C:HEM703 2.0 16.2 1.0
NC C:HEM703 2.1 17.4 1.0
NB C:HEM703 2.1 17.5 1.0
NE2 C:HIS87 2.2 17.1 1.0
O C:CMO803 2.9 22.2 1.0
C4D C:HEM703 3.0 18.1 1.0
C1A C:HEM703 3.0 18.9 1.0
C1C C:HEM703 3.1 15.1 1.0
C1D C:HEM703 3.1 18.5 1.0
C4A C:HEM703 3.1 15.8 1.0
C4B C:HEM703 3.1 15.2 1.0
C4C C:HEM703 3.1 14.9 1.0
C1B C:HEM703 3.1 17.9 1.0
CD2 C:HIS87 3.1 16.9 1.0
CE1 C:HIS87 3.2 17.6 1.0
CHA C:HEM703 3.4 16.1 1.0
CHC C:HEM703 3.4 16.0 1.0
CHD C:HEM703 3.5 15.6 1.0
CHB C:HEM703 3.5 16.6 1.0
ND1 C:HIS87 4.3 16.1 1.0
C3D C:HEM703 4.3 18.9 1.0
C2D C:HEM703 4.3 17.8 1.0
CG C:HIS87 4.3 17.8 1.0
C2A C:HEM703 4.3 19.9 1.0
C2C C:HEM703 4.3 14.8 1.0
C3C C:HEM703 4.3 14.7 1.0
C3B C:HEM703 4.3 16.4 1.0
C3A C:HEM703 4.3 16.5 1.0
C2B C:HEM703 4.3 16.3 1.0
NE2 C:HIS58 4.4 23.2 1.0
CG2 C:VAL62 4.9 15.5 1.0

Iron binding site 4 out of 4 in 1yvq

Go back to Iron Binding Sites List in 1yvq
Iron binding site 4 out of 4 in the The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Low Salt (Peg) Crystal Structure of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe704

b:25.0
occ:1.00
 FE D:HEM704 0.0 25.0 1.0
C D:CMO804 1.8 19.6 1.0
ND D:HEM704 2.0 24.8 1.0
NA D:HEM704 2.0 23.3 1.0
NB D:HEM704 2.1 23.4 1.0
NC D:HEM704 2.1 23.9 1.0
NE2 D:HIS92 2.2 22.4 1.0
O D:CMO804 2.8 23.1 1.0
C1D D:HEM704 3.0 25.3 1.0
C4D D:HEM704 3.0 26.7 1.0
C1A D:HEM704 3.1 24.7 1.0
C4A D:HEM704 3.1 22.8 1.0
CD2 D:HIS92 3.1 25.8 1.0
C4C D:HEM704 3.1 23.2 1.0
C1B D:HEM704 3.1 23.7 1.0
C4B D:HEM704 3.1 23.4 1.0
C1C D:HEM704 3.1 23.7 1.0
CE1 D:HIS92 3.3 25.6 1.0
CHA D:HEM704 3.4 24.2 1.0
CHD D:HEM704 3.4 23.7 1.0
CHB D:HEM704 3.4 23.3 1.0
CHC D:HEM704 3.4 23.8 1.0
C2D D:HEM704 4.3 26.1 1.0
CG D:HIS92 4.3 25.7 1.0
C3D D:HEM704 4.3 26.5 1.0
C2A D:HEM704 4.3 25.0 1.0
C3A D:HEM704 4.3 23.5 1.0
ND1 D:HIS92 4.3 23.2 1.0
NE2 D:HIS63 4.3 26.9 1.0
C3B D:HEM704 4.3 22.1 1.0
C2B D:HEM704 4.3 23.3 1.0
C3C D:HEM704 4.3 24.2 1.0
C2C D:HEM704 4.4 24.3 1.0
CG2 D:VAL67 4.9 25.8 1.0

Reference:

V.N.Malashkevich, T.C.Balazs, S.C.Almo, R.E.Hirsch. Crystal Structures of Co Hemoglobin E (BETAE26K) Approaching Physiological pH (pH 7.5) To Be Published.
Page generated: Sat Aug 3 18:04:58 2024

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