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Iron in PDB 1bcf: The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site

Protein crystallography data

The structure of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site, PDB code: 1bcf was solved by F.Frolow, A.J.Kalb(Gilboa), J.Yariv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 211.100, 211.100, 145.200, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / n/a

Other elements in 1bcf:

The structure of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site also contains other interesting chemical elements:

Manganese (Mn) 24 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site (pdb code 1bcf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site, PDB code: 1bcf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1bcf

Go back to Iron Binding Sites List in 1bcf
Iron binding site 1 out of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


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 A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:16.1
occ:1.00
FE A:HEM200 0.0 16.1 1.0
NC A:HEM200 2.0 8.8 1.0
NA A:HEM200 2.0 7.6 1.0
NB A:HEM200 2.0 8.4 1.0
ND A:HEM200 2.0 7.8 1.0
SD B:MET52 2.6 4.5 1.0
SD A:MET52 2.7 7.0 1.0
C4C A:HEM200 3.0 10.1 1.0
C4A A:HEM200 3.1 7.2 1.0
C1A A:HEM200 3.1 6.2 1.0
C1B A:HEM200 3.1 8.5 1.0
C1D A:HEM200 3.1 7.7 1.0
C4B A:HEM200 3.1 7.3 1.0
C4D A:HEM200 3.1 8.2 1.0
C1C A:HEM200 3.1 7.2 1.0
CG B:MET52 3.5 5.8 1.0
CHD A:HEM200 3.5 9.0 1.0
CHB A:HEM200 3.5 9.0 1.0
CG A:MET52 3.5 7.4 1.0
CHA A:HEM200 3.5 5.0 1.0
CHC A:HEM200 3.5 6.3 1.0
CE B:MET52 3.5 7.7 1.0
CE A:MET52 3.6 8.7 1.0
C2A A:HEM200 4.2 6.7 1.0
C3C A:HEM200 4.3 9.6 1.0
C3A A:HEM200 4.3 7.1 1.0
C3D A:HEM200 4.3 8.3 1.0
C2D A:HEM200 4.3 7.9 1.0
C3B A:HEM200 4.3 8.1 1.0
C2B A:HEM200 4.3 7.0 1.0
C2C A:HEM200 4.4 7.3 1.0
CB B:MET52 4.4 2.6 1.0
CB A:MET52 4.4 3.3 1.0

Iron binding site 2 out of 6 in 1bcf

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Iron binding site 2 out of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


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 A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:16.1
occ:1.00
FE C:HEM201 0.0 16.1 1.0
NC C:HEM201 2.0 8.8 1.0
NA C:HEM201 2.0 7.6 1.0
NB C:HEM201 2.0 8.4 1.0
ND C:HEM201 2.0 7.8 1.0
SD D:MET52 2.6 4.5 1.0
SD C:MET52 2.7 7.0 1.0
C4C C:HEM201 3.0 10.1 1.0
C4A C:HEM201 3.1 7.2 1.0
C1A C:HEM201 3.1 6.2 1.0
C1B C:HEM201 3.1 8.5 1.0
C1D C:HEM201 3.1 7.7 1.0
C4B C:HEM201 3.1 7.3 1.0
C4D C:HEM201 3.1 8.2 1.0
C1C C:HEM201 3.1 7.2 1.0
CG D:MET52 3.5 5.8 1.0
CHD C:HEM201 3.5 9.0 1.0
CHB C:HEM201 3.5 9.0 1.0
CG C:MET52 3.5 7.4 1.0
CHA C:HEM201 3.5 5.0 1.0
CHC C:HEM201 3.5 6.3 1.0
CE D:MET52 3.5 7.7 1.0
CE C:MET52 3.6 8.7 1.0
C2A C:HEM201 4.2 6.7 1.0
C3C C:HEM201 4.3 9.6 1.0
C3A C:HEM201 4.3 7.1 1.0
C3D C:HEM201 4.3 8.3 1.0
C2D C:HEM201 4.3 7.9 1.0
C3B C:HEM201 4.3 8.1 1.0
C2B C:HEM201 4.3 7.0 1.0
C2C C:HEM201 4.4 7.3 1.0
CB D:MET52 4.4 2.6 1.0
CB C:MET52 4.4 3.3 1.0

Iron binding site 3 out of 6 in 1bcf

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Iron binding site 3 out of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


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 A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe202

b:16.1
occ:1.00
FE E:HEM202 0.0 16.1 1.0
NC E:HEM202 2.0 8.8 1.0
NA E:HEM202 2.0 7.6 1.0
NB E:HEM202 2.0 8.4 1.0
ND E:HEM202 2.0 7.8 1.0
SD F:MET52 2.6 4.5 1.0
SD E:MET52 2.7 7.0 1.0
C4C E:HEM202 3.0 10.1 1.0
C4A E:HEM202 3.1 7.2 1.0
C1A E:HEM202 3.1 6.2 1.0
C1B E:HEM202 3.1 8.5 1.0
C1D E:HEM202 3.1 7.7 1.0
C4B E:HEM202 3.1 7.3 1.0
C4D E:HEM202 3.1 8.2 1.0
C1C E:HEM202 3.1 7.2 1.0
CG F:MET52 3.5 5.8 1.0
CHD E:HEM202 3.5 9.0 1.0
CHB E:HEM202 3.5 9.0 1.0
CG E:MET52 3.5 7.4 1.0
CHA E:HEM202 3.5 5.0 1.0
CHC E:HEM202 3.5 6.3 1.0
CE F:MET52 3.5 7.7 1.0
CE E:MET52 3.6 8.7 1.0
C2A E:HEM202 4.2 6.7 1.0
C3C E:HEM202 4.3 9.6 1.0
C3A E:HEM202 4.3 7.1 1.0
C3D E:HEM202 4.3 8.3 1.0
C2D E:HEM202 4.3 7.9 1.0
C3B E:HEM202 4.3 8.1 1.0
C2B E:HEM202 4.3 7.0 1.0
C2C E:HEM202 4.4 7.3 1.0
CB F:MET52 4.4 2.6 1.0
CB E:MET52 4.4 3.3 1.0

Iron binding site 4 out of 6 in 1bcf

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Iron binding site 4 out of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


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 A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe203

b:16.1
occ:1.00
FE G:HEM203 0.0 16.1 1.0
NC G:HEM203 2.0 8.8 1.0
NB G:HEM203 2.0 8.4 1.0
NA G:HEM203 2.0 7.6 1.0
ND G:HEM203 2.0 7.8 1.0
SD H:MET52 2.6 4.5 1.0
SD G:MET52 2.7 7.0 1.0
C4C G:HEM203 3.0 10.1 1.0
C4A G:HEM203 3.1 7.2 1.0
C1A G:HEM203 3.1 6.2 1.0
C1B G:HEM203 3.1 8.5 1.0
C1D G:HEM203 3.1 7.7 1.0
C4B G:HEM203 3.1 7.3 1.0
C4D G:HEM203 3.1 8.2 1.0
C1C G:HEM203 3.1 7.2 1.0
CG H:MET52 3.5 5.8 1.0
CHD G:HEM203 3.5 9.0 1.0
CHB G:HEM203 3.5 9.0 1.0
CG G:MET52 3.5 7.4 1.0
CHA G:HEM203 3.5 5.0 1.0
CHC G:HEM203 3.5 6.3 1.0
CE H:MET52 3.5 7.7 1.0
CE G:MET52 3.6 8.7 1.0
C2A G:HEM203 4.2 6.7 1.0
C3C G:HEM203 4.3 9.6 1.0
C3A G:HEM203 4.3 7.1 1.0
C3D G:HEM203 4.3 8.3 1.0
C2D G:HEM203 4.3 7.9 1.0
C3B G:HEM203 4.3 8.1 1.0
C2B G:HEM203 4.3 7.0 1.0
C2C G:HEM203 4.4 7.3 1.0
CB H:MET52 4.4 2.6 1.0
CB G:MET52 4.4 3.3 1.0

Iron binding site 5 out of 6 in 1bcf

Go back to Iron Binding Sites List in 1bcf
Iron binding site 5 out of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


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 A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe204

b:16.1
occ:1.00
FE I:HEM204 0.0 16.1 1.0
NC I:HEM204 2.0 8.8 1.0
NA I:HEM204 2.0 7.6 1.0
NB I:HEM204 2.0 8.4 1.0
ND I:HEM204 2.0 7.8 1.0
SD J:MET52 2.6 4.5 1.0
SD I:MET52 2.7 7.0 1.0
C4C I:HEM204 3.0 10.1 1.0
C4A I:HEM204 3.1 7.2 1.0
C1A I:HEM204 3.1 6.2 1.0
C1B I:HEM204 3.1 8.5 1.0
C1D I:HEM204 3.1 7.7 1.0
C4B I:HEM204 3.1 7.3 1.0
C4D I:HEM204 3.1 8.2 1.0
C1C I:HEM204 3.1 7.2 1.0
CG J:MET52 3.5 5.8 1.0
CHD I:HEM204 3.5 9.0 1.0
CHB I:HEM204 3.5 9.0 1.0
CG I:MET52 3.5 7.4 1.0
CHA I:HEM204 3.5 5.0 1.0
CHC I:HEM204 3.5 6.3 1.0
CE J:MET52 3.5 7.7 1.0
CE I:MET52 3.6 8.7 1.0
C2A I:HEM204 4.2 6.7 1.0
C3C I:HEM204 4.3 9.6 1.0
C3A I:HEM204 4.3 7.1 1.0
C3D I:HEM204 4.3 8.3 1.0
C2D I:HEM204 4.3 7.9 1.0
C3B I:HEM204 4.3 8.1 1.0
C2B I:HEM204 4.3 7.0 1.0
C2C I:HEM204 4.4 7.3 1.0
CB J:MET52 4.4 2.6 1.0
CB I:MET52 4.4 3.3 1.0

Iron binding site 6 out of 6 in 1bcf

Go back to Iron Binding Sites List in 1bcf
Iron binding site 6 out of 6 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


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 A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe205

b:16.1
occ:1.00
FE K:HEM205 0.0 16.1 1.0
NC K:HEM205 2.0 8.8 1.0
NA K:HEM205 2.0 7.6 1.0
NB K:HEM205 2.0 8.4 1.0
ND K:HEM205 2.0 7.8 1.0
SD L:MET52 2.6 4.5 1.0
SD K:MET52 2.7 7.0 1.0
C4C K:HEM205 3.0 10.1 1.0
C4A K:HEM205 3.1 7.2 1.0
C1A K:HEM205 3.1 6.2 1.0
C1B K:HEM205 3.1 8.5 1.0
C1D K:HEM205 3.1 7.7 1.0
C4B K:HEM205 3.1 7.3 1.0
C4D K:HEM205 3.1 8.2 1.0
C1C K:HEM205 3.1 7.2 1.0
CG L:MET52 3.5 5.8 1.0
CHD K:HEM205 3.5 9.0 1.0
CHB K:HEM205 3.5 9.0 1.0
CG K:MET52 3.5 7.4 1.0
CHA K:HEM205 3.5 5.0 1.0
CHC K:HEM205 3.5 6.3 1.0
CE L:MET52 3.5 7.7 1.0
CE K:MET52 3.6 8.7 1.0
C2A K:HEM205 4.2 6.7 1.0
C3C K:HEM205 4.3 9.6 1.0
C3A K:HEM205 4.3 7.1 1.0
C3D K:HEM205 4.3 8.3 1.0
C2D K:HEM205 4.3 7.9 1.0
C3B K:HEM205 4.3 8.1 1.0
C2B K:HEM205 4.3 7.0 1.0
C2C K:HEM205 4.4 7.3 1.0
CB L:MET52 4.4 2.6 1.0
CB K:MET52 4.4 3.3 1.0

Reference:

F.Frolow, A.J.Kalb, J.Yariv. Structure of A Unique Twofold Symmetric Haem-Binding Site. Nat.Struct.Biol. V. 1 453 1994.
ISSN: ISSN 1072-8368
PubMed: 7664064
DOI: 10.1038/NSB0794-453
Page generated: Wed Jul 16 12:32:19 2025

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