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Iron in PDB 7dy3: High Resolution Crystal Structure of Hemoglobin M Iwate.

Protein crystallography data

The structure of High Resolution Crystal Structure of Hemoglobin M Iwate., PDB code: 7dy3 was solved by M.Ohki, S.-Y.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.08 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.494, 86.275, 121.005, 90, 99.25, 90
R / Rfree (%) 16.8 / 19.3

Iron Binding Sites:

The binding sites of Iron atom in the High Resolution Crystal Structure of Hemoglobin M Iwate. (pdb code 7dy3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the High Resolution Crystal Structure of Hemoglobin M Iwate., PDB code: 7dy3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7dy3

Go back to Iron Binding Sites List in 7dy3
Iron binding site 1 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:7.1
occ:1.00
FE A:HEM201 0.0 7.1 1.0
OH A:TYR87 2.0 13.9 1.0
NC A:HEM201 2.1 5.6 1.0
NB A:HEM201 2.1 6.4 1.0
ND A:HEM201 2.1 6.1 1.0
NA A:HEM201 2.1 8.7 1.0
C4B A:HEM201 3.1 6.8 1.0
C1C A:HEM201 3.1 6.5 1.0
C1B A:HEM201 3.1 7.2 1.0
C4C A:HEM201 3.1 5.5 1.0
C1A A:HEM201 3.1 7.6 1.0
C4D A:HEM201 3.1 7.1 1.0
C1D A:HEM201 3.1 6.5 1.0
C4A A:HEM201 3.1 8.7 1.0
CZ A:TYR87 3.2 7.5 1.0
CHC A:HEM201 3.4 5.2 1.0
CHA A:HEM201 3.5 7.7 1.0
CHD A:HEM201 3.5 6.3 1.0
CHB A:HEM201 3.5 7.0 1.0
NE2 A:HIS58 3.9 11.4 1.0
CE2 A:TYR87 4.0 7.3 1.0
CE1 A:TYR87 4.1 7.3 1.0
C3B A:HEM201 4.3 6.8 1.0
C2C A:HEM201 4.3 5.5 1.0
CE1 A:HIS58 4.3 11.4 1.0
C2B A:HEM201 4.3 7.2 1.0
C3C A:HEM201 4.3 6.0 1.0
C2A A:HEM201 4.3 7.6 1.0
C3A A:HEM201 4.3 7.8 1.0
C2D A:HEM201 4.3 7.0 1.0
C3D A:HEM201 4.3 8.2 1.0
CD1 A:LEU91 4.8 9.4 1.0
CG2 A:VAL62 4.8 6.9 1.0

Iron binding site 2 out of 8 in 7dy3

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Iron binding site 2 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:8.3
occ:1.00
FE B:HEM201 0.0 8.3 1.0
NC B:HEM201 2.0 6.7 1.0
NA B:HEM201 2.1 8.8 1.0
ND B:HEM201 2.1 6.5 1.0
NB B:HEM201 2.1 6.5 1.0
NE2 B:HIS92 2.2 6.5 1.0
O B:HOH321 2.3 17.7 1.0
C1C B:HEM201 3.0 6.6 1.0
C4D B:HEM201 3.1 8.4 1.0
C4C B:HEM201 3.1 5.4 1.0
C1A B:HEM201 3.1 8.4 1.0
C4B B:HEM201 3.1 8.2 1.0
C4A B:HEM201 3.1 7.8 1.0
C1B B:HEM201 3.1 7.1 1.0
C1D B:HEM201 3.1 7.4 1.0
CE1 B:HIS92 3.1 7.0 1.0
CD2 B:HIS92 3.2 5.0 1.0
CHA B:HEM201 3.4 8.9 1.0
CHC B:HEM201 3.4 8.2 1.0
CHB B:HEM201 3.4 9.1 1.0
CHD B:HEM201 3.5 6.5 1.0
ND1 B:HIS92 4.2 6.8 1.0
C2C B:HEM201 4.3 5.3 1.0
NE2 B:HIS63 4.3 15.5 1.0
C3C B:HEM201 4.3 7.2 1.0
C3D B:HEM201 4.3 8.1 1.0
C2D B:HEM201 4.3 9.4 1.0
C3A B:HEM201 4.3 8.0 1.0
C2A B:HEM201 4.3 8.0 1.0
C3B B:HEM201 4.3 7.2 1.0
C2B B:HEM201 4.3 8.2 1.0
CG B:HIS92 4.3 5.7 1.0
CG2 B:VAL67 4.5 15.4 1.0
CE1 B:HIS63 4.8 15.5 1.0
CD1 B:LEU96 5.0 7.6 1.0

Iron binding site 3 out of 8 in 7dy3

Go back to Iron Binding Sites List in 7dy3
Iron binding site 3 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:7.8
occ:1.00
FE C:HEM201 0.0 7.8 1.0
OH C:TYR87 2.0 13.2 1.0
NC C:HEM201 2.1 6.6 1.0
ND C:HEM201 2.1 7.6 1.0
NA C:HEM201 2.1 7.8 1.0
NB C:HEM201 2.1 7.4 1.0
C4B C:HEM201 3.1 5.9 1.0
C4C C:HEM201 3.1 6.6 1.0
C1C C:HEM201 3.1 6.2 1.0
C1D C:HEM201 3.1 5.9 1.0
C1A C:HEM201 3.1 10.4 1.0
C4D C:HEM201 3.1 8.6 1.0
C1B C:HEM201 3.1 7.9 1.0
C4A C:HEM201 3.1 8.7 1.0
CZ C:TYR87 3.2 8.2 1.0
CHD C:HEM201 3.4 5.8 1.0
CHC C:HEM201 3.4 6.9 1.0
CHA C:HEM201 3.5 8.5 1.0
CHB C:HEM201 3.5 7.2 1.0
CE2 C:TYR87 3.9 8.3 1.0
NE2 C:HIS58 4.0 13.2 1.0
CE1 C:TYR87 4.2 9.3 1.0
C3B C:HEM201 4.3 8.1 1.0
C3C C:HEM201 4.3 6.8 1.0
C2C C:HEM201 4.3 6.7 1.0
C2B C:HEM201 4.3 6.1 1.0
C2D C:HEM201 4.3 10.0 1.0
C3D C:HEM201 4.3 9.1 1.0
CE1 C:HIS58 4.3 11.1 1.0
C2A C:HEM201 4.3 8.7 1.0
C3A C:HEM201 4.3 7.9 1.0
CG2 C:VAL62 4.8 7.7 1.0
CD1 C:LEU91 4.9 10.1 1.0

Iron binding site 4 out of 8 in 7dy3

Go back to Iron Binding Sites List in 7dy3
Iron binding site 4 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:8.8
occ:1.00
FE D:HEM201 0.0 8.8 1.0
NC D:HEM201 2.0 7.5 1.0
ND D:HEM201 2.0 9.3 1.0
NB D:HEM201 2.1 6.9 1.0
NA D:HEM201 2.1 8.3 1.0
NE2 D:HIS92 2.1 7.8 1.0
O D:HOH315 2.2 11.0 1.0
CE1 D:HIS92 3.0 6.9 1.0
C4C D:HEM201 3.0 7.8 1.0
C1C D:HEM201 3.0 5.5 1.0
C1D D:HEM201 3.1 8.4 1.0
C4D D:HEM201 3.1 8.7 1.0
C4B D:HEM201 3.1 8.1 1.0
C4A D:HEM201 3.1 8.0 1.0
C1A D:HEM201 3.1 9.1 1.0
C1B D:HEM201 3.1 8.2 1.0
CD2 D:HIS92 3.2 7.4 1.0
CHD D:HEM201 3.4 8.9 1.0
CHC D:HEM201 3.4 7.1 1.0
CHB D:HEM201 3.5 7.7 1.0
CHA D:HEM201 3.5 9.4 1.0
ND1 D:HIS92 4.2 6.7 1.0
NE2 D:HIS63 4.2 11.9 1.0
C2C D:HEM201 4.3 6.7 1.0
C3C D:HEM201 4.3 6.8 1.0
C3D D:HEM201 4.3 9.5 1.0
C2D D:HEM201 4.3 10.9 1.0
CG D:HIS92 4.3 6.4 1.0
C3B D:HEM201 4.3 7.8 1.0
C2B D:HEM201 4.3 8.7 1.0
C3A D:HEM201 4.3 9.5 1.0
C2A D:HEM201 4.3 10.7 1.0
CG2 D:VAL67 4.7 10.3 1.0
CE1 D:HIS63 4.7 14.7 1.0

Iron binding site 5 out of 8 in 7dy3

Go back to Iron Binding Sites List in 7dy3
Iron binding site 5 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:6.6
occ:1.00
FE E:HEM201 0.0 6.6 1.0
OH E:TYR87 2.0 10.9 1.0
NC E:HEM201 2.1 6.1 1.0
NB E:HEM201 2.1 6.4 1.0
NA E:HEM201 2.1 9.0 1.0
ND E:HEM201 2.1 6.4 1.0
C4B E:HEM201 3.1 6.6 1.0
C1C E:HEM201 3.1 6.9 1.0
C1B E:HEM201 3.1 6.7 1.0
C4C E:HEM201 3.1 5.2 1.0
C1D E:HEM201 3.1 6.4 1.0
C1A E:HEM201 3.1 6.8 1.0
C4A E:HEM201 3.1 8.3 1.0
C4D E:HEM201 3.1 7.3 1.0
CZ E:TYR87 3.2 6.5 1.0
CHC E:HEM201 3.4 5.9 1.0
CHB E:HEM201 3.5 6.5 1.0
CHD E:HEM201 3.5 5.8 1.0
CHA E:HEM201 3.5 6.9 1.0
CE1 E:TYR87 4.0 6.6 1.0
CE2 E:TYR87 4.1 8.3 1.0
NE2 E:HIS58 4.1 12.4 1.0
C3B E:HEM201 4.3 7.1 1.0
C2C E:HEM201 4.3 7.2 1.0
C2B E:HEM201 4.3 6.1 1.0
C3C E:HEM201 4.3 5.1 1.0
C3A E:HEM201 4.3 8.0 1.0
C2D E:HEM201 4.3 6.9 1.0
C3D E:HEM201 4.3 7.4 1.0
C2A E:HEM201 4.3 8.8 1.0
CE1 E:HIS58 4.8 14.3 1.0
CD1 E:LEU91 4.9 9.3 1.0
CG2 E:VAL62 4.9 7.4 1.0

Iron binding site 6 out of 8 in 7dy3

Go back to Iron Binding Sites List in 7dy3
Iron binding site 6 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:9.0
occ:1.00
FE F:HEM201 0.0 9.0 1.0
NC F:HEM201 2.0 7.8 1.0
ND F:HEM201 2.0 8.3 1.0
NA F:HEM201 2.0 8.9 1.0
NB F:HEM201 2.1 7.5 1.0
NE2 F:HIS92 2.2 6.5 1.0
O F:HOH326 2.2 16.6 1.0
C1C F:HEM201 3.0 7.2 1.0
C4C F:HEM201 3.0 8.4 1.0
C1D F:HEM201 3.1 8.4 1.0
C4A F:HEM201 3.1 8.1 1.0
C4D F:HEM201 3.1 10.2 1.0
C1A F:HEM201 3.1 9.1 1.0
C4B F:HEM201 3.1 7.8 1.0
C1B F:HEM201 3.1 7.5 1.0
CE1 F:HIS92 3.1 7.4 1.0
CD2 F:HIS92 3.2 8.9 1.0
CHC F:HEM201 3.4 6.8 1.0
CHD F:HEM201 3.4 8.2 1.0
CHA F:HEM201 3.4 8.1 1.0
CHB F:HEM201 3.4 7.4 1.0
C2C F:HEM201 4.3 6.7 1.0
C3C F:HEM201 4.3 8.1 1.0
ND1 F:HIS92 4.3 8.2 1.0
C2D F:HEM201 4.3 8.5 1.0
C3D F:HEM201 4.3 9.1 1.0
C2A F:HEM201 4.3 9.7 1.0
C3A F:HEM201 4.3 10.0 1.0
C3B F:HEM201 4.3 9.7 1.0
C2B F:HEM201 4.3 8.6 1.0
NE2 F:HIS63 4.3 13.7 1.0
CG F:HIS92 4.3 9.3 1.0
CG2 F:VAL67 4.5 11.8 1.0
CE1 F:HIS63 4.8 13.7 1.0
CD1 F:LEU96 4.9 8.7 1.0

Iron binding site 7 out of 8 in 7dy3

Go back to Iron Binding Sites List in 7dy3
Iron binding site 7 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:10.8
occ:1.00
FE G:HEM201 0.0 10.8 1.0
OH G:TYR87 2.1 14.2 1.0
NB G:HEM201 2.1 11.2 1.0
NA G:HEM201 2.1 10.2 1.0
NC G:HEM201 2.1 8.6 1.0
ND G:HEM201 2.1 10.4 1.0
C1B G:HEM201 3.1 10.7 1.0
C4B G:HEM201 3.1 9.4 1.0
C4A G:HEM201 3.1 11.4 1.0
C1D G:HEM201 3.1 9.1 1.0
C4C G:HEM201 3.1 8.0 1.0
C1C G:HEM201 3.1 8.4 1.0
C1A G:HEM201 3.1 14.1 1.0
C4D G:HEM201 3.1 10.7 1.0
CZ G:TYR87 3.3 10.3 1.0
CHB G:HEM201 3.4 11.6 1.0
CHD G:HEM201 3.4 10.7 1.0
CHC G:HEM201 3.4 9.8 1.0
CHA G:HEM201 3.5 13.2 1.0
CE2 G:TYR87 3.9 11.6 1.0
NE2 G:HIS58 4.1 18.0 1.0
CE1 G:HIS58 4.2 17.0 1.0
CE1 G:TYR87 4.2 10.3 1.0
C2B G:HEM201 4.3 10.7 1.0
C3B G:HEM201 4.3 9.5 1.0
C3A G:HEM201 4.3 12.6 1.0
C3C G:HEM201 4.3 9.9 1.0
C2C G:HEM201 4.3 9.2 1.0
C2A G:HEM201 4.3 14.0 1.0
C2D G:HEM201 4.3 10.9 1.0
C3D G:HEM201 4.3 11.5 1.0
CG2 G:VAL62 4.8 10.1 1.0
CD1 G:LEU91 4.8 12.3 1.0

Iron binding site 8 out of 8 in 7dy3

Go back to Iron Binding Sites List in 7dy3
Iron binding site 8 out of 8 in the High Resolution Crystal Structure of Hemoglobin M Iwate.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of High Resolution Crystal Structure of Hemoglobin M Iwate. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:8.3
occ:1.00
FE H:HEM201 0.0 8.3 1.0
NB H:HEM201 2.0 5.9 1.0
NC H:HEM201 2.0 7.6 1.0
ND H:HEM201 2.0 8.4 1.0
NA H:HEM201 2.0 6.8 1.0
NE2 H:HIS92 2.1 7.6 1.0
O H:HOH326 2.2 11.7 1.0
C1C H:HEM201 3.0 6.7 1.0
C4B H:HEM201 3.0 6.6 1.0
C4D H:HEM201 3.1 8.2 1.0
C1A H:HEM201 3.1 9.4 1.0
C1B H:HEM201 3.1 7.7 1.0
C4A H:HEM201 3.1 7.7 1.0
C1D H:HEM201 3.1 8.5 1.0
C4C H:HEM201 3.1 6.8 1.0
CE1 H:HIS92 3.1 6.5 1.0
CD2 H:HIS92 3.2 6.0 1.0
CHC H:HEM201 3.4 6.5 1.0
CHA H:HEM201 3.4 9.3 1.0
CHB H:HEM201 3.5 8.0 1.0
CHD H:HEM201 3.5 7.6 1.0
ND1 H:HIS92 4.2 7.2 1.0
NE2 H:HIS63 4.2 12.8 1.0
C3B H:HEM201 4.3 7.8 1.0
C2C H:HEM201 4.3 6.7 1.0
CG H:HIS92 4.3 6.7 1.0
C3C H:HEM201 4.3 8.2 1.0
C3D H:HEM201 4.3 8.5 1.0
C2B H:HEM201 4.3 8.2 1.0
C2D H:HEM201 4.3 9.9 1.0
C2A H:HEM201 4.3 11.1 1.0
C3A H:HEM201 4.3 9.2 1.0
CG2 H:VAL67 4.7 10.6 1.0
CE1 H:HIS63 4.7 14.9 1.0

Reference:

S.Nagatomo, S.Naoya, M.Ohki, S.Y.Park. High Resolution Crystal Structure of Hemoglobin M Iwate. To Be Published.
Page generated: Thu Aug 8 04:20:49 2024

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