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Iron in PDB 1hmd: The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution

Protein crystallography data

The structure of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution, PDB code: 1hmd was solved by M.A.Holmes, I.Letrong, S.Turley, L.C.Sieker, R.E.Stenkamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 86.840, 86.840, 80.820, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution (pdb code 1hmd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution, PDB code: 1hmd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1hmd

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Iron binding site 1 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe115

b:10.0
occ:1.00
 FE1 A:FEO115 0.0 10.0 1.0
O A:FEO115 2.2 4.5 1.0
OD1 A:ASP106 2.2 10.2 1.0
NE2 A:HIS73 2.2 9.7 1.0
NE2 A:HIS101 2.2 12.5 1.0
NE2 A:HIS77 2.2 8.8 1.0
OE1 A:GLU58 2.3 8.9 1.0
CE1 A:HIS77 3.1 8.2 1.0
CD2 A:HIS101 3.1 11.2 1.0
CE1 A:HIS73 3.2 9.9 1.0
CG A:ASP106 3.2 7.5 1.0
CE1 A:HIS101 3.2 10.2 1.0
CD2 A:HIS73 3.2 9.4 1.0
CD A:GLU58 3.3 7.7 1.0
CD2 A:HIS77 3.3 7.8 1.0
FE2 A:FEO115 3.3 9.5 1.0
OD2 A:ASP106 3.5 11.9 1.0
OE2 A:GLU58 3.6 5.1 1.0
ND1 A:HIS77 4.2 4.8 1.0
ND1 A:HIS73 4.3 10.8 1.0
CG A:HIS101 4.3 10.5 1.0
ND1 A:HIS101 4.3 9.4 1.0
CG A:HIS77 4.4 8.7 1.0
CG A:HIS73 4.4 10.0 1.0
O A:HOH135 4.4 93.2 1.0
CB A:ASP106 4.6 8.6 1.0
CG A:GLU58 4.6 7.1 1.0
NE2 A:HIS54 4.7 7.1 1.0
CE1 A:PHE55 4.9 5.9 1.0
CE2 A:TYR109 4.9 7.3 1.0
CA A:ASP106 4.9 10.2 1.0
CD1 A:PHE55 5.0 8.8 1.0
N A:ASP106 5.0 10.9 1.0

Iron binding site 2 out of 8 in 1hmd

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Iron binding site 2 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe115

b:9.5
occ:1.00
 FE2 A:FEO115 0.0 9.5 1.0
O A:FEO115 1.8 4.5 1.0
NE2 A:HIS25 2.1 7.7 1.0
OD2 A:ASP106 2.1 11.9 1.0
OE2 A:GLU58 2.1 5.1 1.0
NE2 A:HIS54 2.3 7.1 1.0
CD A:GLU58 3.0 7.7 1.0
CG A:ASP106 3.1 7.5 1.0
CE1 A:HIS25 3.1 7.3 1.0
CD2 A:HIS25 3.1 7.0 1.0
CE1 A:HIS54 3.2 5.1 1.0
OE1 A:GLU58 3.3 8.9 1.0
CD2 A:HIS54 3.3 7.1 1.0
FE1 A:FEO115 3.3 10.0 1.0
OD1 A:ASP106 3.4 10.2 1.0
O A:HOH135 3.5 93.2 1.0
OH A:TYR109 4.2 11.0 1.0
ND1 A:HIS25 4.3 8.3 1.0
CG A:HIS25 4.3 8.5 1.0
CG A:GLU58 4.3 7.1 1.0
ND1 A:HIS54 4.3 5.0 1.0
CB A:ASP106 4.4 8.6 1.0
CG A:HIS54 4.4 5.3 1.0
CG2 A:ILE21 4.4 10.0 1.0
CD2 A:HIS101 4.5 11.2 1.0
NE2 A:HIS101 4.6 12.5 1.0
NE2 A:HIS77 4.8 8.8 1.0
CB A:GLU58 4.8 7.2 1.0
CG1 A:ILE102 4.9 5.8 1.0

Iron binding site 3 out of 8 in 1hmd

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Iron binding site 3 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe115

b:15.1
occ:1.00
 FE1 B:FEO115 0.0 15.1 1.0
O B:FEO115 2.1 10.3 1.0
OD1 B:ASP106 2.1 13.8 1.0
NE2 B:HIS77 2.2 15.3 1.0
NE2 B:HIS101 2.2 15.2 1.0
NE2 B:HIS73 2.3 14.4 1.0
OE1 B:GLU58 2.3 12.1 1.0
CD2 B:HIS101 3.1 15.1 1.0
CE1 B:HIS77 3.1 13.9 1.0
CG B:ASP106 3.2 14.1 1.0
CD2 B:HIS73 3.2 11.7 1.0
CD2 B:HIS77 3.2 11.2 1.0
CE1 B:HIS101 3.3 14.8 1.0
CE1 B:HIS73 3.3 13.1 1.0
CD B:GLU58 3.3 11.9 1.0
FE2 B:FEO115 3.3 14.5 1.0
OD2 B:ASP106 3.5 16.0 1.0
OE2 B:GLU58 3.6 11.5 1.0
ND1 B:HIS77 4.2 14.1 1.0
CG B:HIS101 4.3 14.5 1.0
CG B:HIS77 4.3 11.4 1.0
ND1 B:HIS101 4.3 12.5 1.0
ND1 B:HIS73 4.4 15.5 1.0
CG B:HIS73 4.4 15.0 1.0
CB B:ASP106 4.6 12.2 1.0
CG B:GLU58 4.7 11.4 1.0
NE2 B:HIS54 4.7 12.3 1.0
CE1 B:PHE55 4.8 16.1 1.0
CD1 B:PHE55 4.8 12.1 1.0

Iron binding site 4 out of 8 in 1hmd

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Iron binding site 4 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe115

b:14.5
occ:1.00
 FE2 B:FEO115 0.0 14.5 1.0
O B:FEO115 1.8 10.3 1.0
NE2 B:HIS25 2.1 10.7 1.0
OD2 B:ASP106 2.1 16.0 1.0
OE2 B:GLU58 2.1 11.5 1.0
NE2 B:HIS54 2.3 12.3 1.0
CD B:GLU58 3.0 11.9 1.0
CE1 B:HIS25 3.1 12.0 1.0
CG B:ASP106 3.1 14.1 1.0
CE1 B:HIS54 3.1 12.5 1.0
CD2 B:HIS25 3.1 7.5 1.0
OE1 B:GLU58 3.2 12.1 1.0
OD1 B:ASP106 3.3 13.8 1.0
FE1 B:FEO115 3.3 15.1 1.0
CD2 B:HIS54 3.4 10.4 1.0
ND1 B:HIS25 4.2 10.0 1.0
OH B:TYR109 4.3 12.7 1.0
CG B:GLU58 4.3 11.4 1.0
CG B:HIS25 4.3 8.8 1.0
ND1 B:HIS54 4.3 12.4 1.0
CB B:ASP106 4.4 12.2 1.0
CG B:HIS54 4.4 10.1 1.0
CG2 B:ILE21 4.5 9.4 1.0
CD2 B:HIS101 4.6 15.1 1.0
NE2 B:HIS101 4.7 15.2 1.0
NE2 B:HIS77 4.7 15.3 1.0
CB B:GLU58 4.9 12.4 1.0
CG1 B:ILE102 4.9 11.2 1.0

Iron binding site 5 out of 8 in 1hmd

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Iron binding site 5 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe115

b:11.5
occ:1.00
 FE1 C:FEO115 0.0 11.5 1.0
O C:FEO115 2.1 7.2 1.0
OD1 C:ASP106 2.2 10.2 1.0
NE2 C:HIS77 2.2 11.5 1.0
NE2 C:HIS73 2.2 8.2 1.0
NE2 C:HIS101 2.3 12.1 1.0
OE1 C:GLU58 2.4 12.7 1.0
CE1 C:HIS77 3.1 9.8 1.0
CG C:ASP106 3.2 8.6 1.0
CD2 C:HIS101 3.2 9.7 1.0
CD2 C:HIS73 3.2 8.8 1.0
CE1 C:HIS73 3.2 7.5 1.0
CD2 C:HIS77 3.3 7.7 1.0
CE1 C:HIS101 3.3 7.3 1.0
CD C:GLU58 3.3 10.9 1.0
FE2 C:FEO115 3.3 12.6 1.0
OD2 C:ASP106 3.5 10.7 1.0
OE2 C:GLU58 3.6 9.9 1.0
ND1 C:HIS77 4.2 11.3 1.0
O C:HOH147 4.3 0.4 1.0
ND1 C:HIS73 4.3 10.2 1.0
CG C:HIS73 4.4 10.3 1.0
CG C:HIS77 4.4 7.8 1.0
CG C:HIS101 4.4 9.5 1.0
ND1 C:HIS101 4.4 7.8 1.0
CB C:ASP106 4.6 9.7 1.0
CG C:GLU58 4.7 10.7 1.0
NE2 C:HIS54 4.7 8.8 1.0
CE1 C:PHE55 4.8 12.7 1.0
CD1 C:PHE55 4.8 10.6 1.0
CA C:ASP106 4.9 11.5 1.0
N C:ASP106 4.9 12.9 1.0

Iron binding site 6 out of 8 in 1hmd

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Iron binding site 6 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe115

b:12.6
occ:1.00
 FE2 C:FEO115 0.0 12.6 1.0
O C:FEO115 1.8 7.2 1.0
NE2 C:HIS25 2.1 8.2 1.0
OE2 C:GLU58 2.1 9.9 1.0
OD2 C:ASP106 2.2 10.7 1.0
NE2 C:HIS54 2.3 8.8 1.0
CD C:GLU58 3.0 10.9 1.0
CG C:ASP106 3.1 8.6 1.0
CD2 C:HIS25 3.1 9.6 1.0
CE1 C:HIS25 3.1 8.5 1.0
CE1 C:HIS54 3.1 7.5 1.0
OE1 C:GLU58 3.3 12.7 1.0
CD2 C:HIS54 3.3 4.8 1.0
FE1 C:FEO115 3.3 11.5 1.0
OD1 C:ASP106 3.4 10.2 1.0
O C:HOH147 3.7 0.4 1.0
OH C:TYR109 4.2 10.8 1.0
ND1 C:HIS25 4.2 8.8 1.0
CG C:HIS25 4.2 7.7 1.0
CG C:GLU58 4.3 10.7 1.0
ND1 C:HIS54 4.3 9.3 1.0
CB C:ASP106 4.3 9.7 1.0
CG C:HIS54 4.4 7.6 1.0
CG2 C:ILE21 4.5 10.9 1.0
CD2 C:HIS101 4.7 9.7 1.0
NE2 C:HIS101 4.7 12.1 1.0
CB C:GLU58 4.8 10.2 1.0
NE2 C:HIS77 4.8 11.5 1.0
CG1 C:ILE102 4.8 12.4 1.0

Iron binding site 7 out of 8 in 1hmd

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Iron binding site 7 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe115

b:10.0
occ:1.00
 FE1 D:FEO115 0.0 10.0 1.0
O D:FEO115 2.1 5.1 1.0
OD1 D:ASP106 2.2 9.7 1.0
NE2 D:HIS101 2.2 7.1 1.0
NE2 D:HIS77 2.2 8.9 1.0
NE2 D:HIS73 2.2 7.4 1.0
OE1 D:GLU58 2.3 11.8 1.0
CD2 D:HIS101 3.1 7.2 1.0
CE1 D:HIS77 3.1 5.8 1.0
CE1 D:HIS73 3.2 7.3 1.0
CG D:ASP106 3.2 5.8 1.0
CE1 D:HIS101 3.2 10.2 1.0
CD2 D:HIS77 3.3 6.5 1.0
CD2 D:HIS73 3.3 7.4 1.0
CD D:GLU58 3.3 6.8 1.0
FE2 D:FEO115 3.3 10.4 1.0
OD2 D:ASP106 3.5 10.4 1.0
OE2 D:GLU58 3.6 9.8 1.0
ND1 D:HIS77 4.3 7.7 1.0
CG D:HIS101 4.3 9.4 1.0
ND1 D:HIS73 4.3 8.7 1.0
ND1 D:HIS101 4.3 8.1 1.0
CG D:HIS77 4.4 7.9 1.0
CG D:HIS73 4.4 8.3 1.0
CB D:ASP106 4.6 6.9 1.0
CG D:GLU58 4.6 10.2 1.0
NE2 D:HIS54 4.7 5.0 1.0
CE1 D:PHE55 4.9 9.9 1.0
CD1 D:PHE55 4.9 9.8 1.0
CA D:ASP106 4.9 8.2 1.0
CE2 D:TYR109 4.9 6.7 1.0

Iron binding site 8 out of 8 in 1hmd

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Iron binding site 8 out of 8 in the The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of Deoxy and Oxy Hemerythrin at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe115

b:10.4
occ:1.00
 FE2 D:FEO115 0.0 10.4 1.0
O D:FEO115 1.8 5.1 1.0
OD2 D:ASP106 2.1 10.4 1.0
NE2 D:HIS25 2.2 8.7 1.0
OE2 D:GLU58 2.2 9.8 1.0
NE2 D:HIS54 2.2 5.0 1.0
CD D:GLU58 3.0 6.8 1.0
CG D:ASP106 3.1 5.8 1.0
CE1 D:HIS25 3.1 8.2 1.0
CE1 D:HIS54 3.1 6.7 1.0
CD2 D:HIS25 3.2 6.2 1.0
OE1 D:GLU58 3.2 11.8 1.0
OD1 D:ASP106 3.3 9.7 1.0
CD2 D:HIS54 3.3 3.9 1.0
FE1 D:FEO115 3.3 10.0 1.0
OH D:TYR109 4.2 9.2 1.0
ND1 D:HIS25 4.3 8.1 1.0
CG D:GLU58 4.3 10.2 1.0
ND1 D:HIS54 4.3 5.2 1.0
CG D:HIS25 4.3 7.7 1.0
CG2 D:ILE21 4.3 7.2 1.0
CG D:HIS54 4.4 4.4 1.0
CB D:ASP106 4.4 6.9 1.0
CD2 D:HIS101 4.5 7.2 1.0
NE2 D:HIS101 4.6 7.1 1.0
NE2 D:HIS77 4.8 8.9 1.0
CB D:GLU58 4.8 7.6 1.0
CG1 D:ILE102 4.8 7.4 1.0

Reference:

M.A.Holmes, I.Le Trong, S.Turley, L.C.Sieker, R.E.Stenkamp. Structures of Deoxy and Oxy Hemerythrin at 2.0 A Resolution. J.Mol.Biol. V. 218 583 1991.
ISSN: ISSN 0022-2836
PubMed: 2016748
DOI: 10.1016/0022-2836(91)90703-9
Page generated: Sat Aug 3 07:46:34 2024

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