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Iron in PDB 1oj6: Human Brain Neuroglobin Three-Dimensional Structure

Protein crystallography data

The structure of Human Brain Neuroglobin Three-Dimensional Structure, PDB code: 1oj6 was solved by A.Pesce, S.Dewilde, M.Nardini, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.598, 94.927, 67.563, 90.00, 94.38, 90.00
R / Rfree (%) 17.8 / 23.3

Iron Binding Sites:

The binding sites of Iron atom in the Human Brain Neuroglobin Three-Dimensional Structure (pdb code 1oj6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Brain Neuroglobin Three-Dimensional Structure, PDB code: 1oj6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1oj6

Go back to Iron Binding Sites List in 1oj6
Iron binding site 1 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1150

b:3.6
occ:1.00
FE A:HEM1150 0.0 3.6 1.0
NC A:HEM1150 2.0 13.6 1.0
NA A:HEM1150 2.0 26.8 1.0
NB A:HEM1150 2.1 18.8 1.0
NE2 A:HIS96 2.1 17.3 1.0
ND A:HEM1150 2.1 19.7 1.0
NE2 A:HIS64 2.1 12.5 1.0
CD2 A:HIS96 3.0 16.4 1.0
C1C A:HEM1150 3.0 16.4 1.0
C4C A:HEM1150 3.0 15.7 1.0
C1A A:HEM1150 3.0 25.6 1.0
C4A A:HEM1150 3.0 17.9 1.0
C4B A:HEM1150 3.1 13.3 1.0
C1B A:HEM1150 3.1 17.7 1.0
C4D A:HEM1150 3.1 14.9 1.0
C1D A:HEM1150 3.1 11.1 1.0
CE1 A:HIS64 3.1 18.3 1.0
CD2 A:HIS64 3.1 17.5 1.0
CE1 A:HIS96 3.1 19.9 1.0
CHC A:HEM1150 3.4 19.7 1.0
CHD A:HEM1150 3.4 17.6 1.0
CHA A:HEM1150 3.4 18.6 1.0
CHB A:HEM1150 3.4 14.6 1.0
CG A:HIS96 4.2 13.2 1.0
C3C A:HEM1150 4.2 20.1 1.0
C2C A:HEM1150 4.2 21.2 1.0
ND1 A:HIS96 4.2 18.3 1.0
ND1 A:HIS64 4.2 11.4 1.0
C2A A:HEM1150 4.3 26.2 1.0
C3A A:HEM1150 4.3 22.8 1.0
CG A:HIS64 4.3 18.5 1.0
C3B A:HEM1150 4.3 22.7 1.0
C2B A:HEM1150 4.3 26.5 1.0
C3D A:HEM1150 4.3 21.0 1.0
C2D A:HEM1150 4.3 16.9 1.0
CG2 A:VAL68 4.8 13.7 1.0

Iron binding site 2 out of 4 in 1oj6

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Iron binding site 2 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1152

b:2.0
occ:1.00
FE B:HEM1152 0.0 2.0 1.0
NC B:HEM1152 2.0 15.2 1.0
ND B:HEM1152 2.0 12.1 1.0
NE2 B:HIS96 2.0 14.6 1.0
NA B:HEM1152 2.1 23.5 1.0
NB B:HEM1152 2.1 26.8 1.0
NE2 B:HIS64 2.2 15.2 1.0
CD2 B:HIS96 2.9 19.3 1.0
C4C B:HEM1152 2.9 18.1 1.0
C1D B:HEM1152 3.0 18.7 1.0
C1C B:HEM1152 3.0 13.6 1.0
C4D B:HEM1152 3.0 15.9 1.0
C1A B:HEM1152 3.1 17.1 1.0
CE1 B:HIS96 3.1 22.9 1.0
C4B B:HEM1152 3.1 13.0 1.0
C4A B:HEM1152 3.1 19.1 1.0
CE1 B:HIS64 3.1 17.4 1.0
C1B B:HEM1152 3.1 15.9 1.0
CD2 B:HIS64 3.2 15.1 1.0
CHD B:HEM1152 3.3 13.6 1.0
CHA B:HEM1152 3.4 11.1 1.0
CHC B:HEM1152 3.4 12.3 1.0
CHB B:HEM1152 3.5 14.9 1.0
CG B:HIS96 4.1 18.4 1.0
ND1 B:HIS96 4.1 14.7 1.0
C3C B:HEM1152 4.2 15.9 1.0
C2C B:HEM1152 4.2 14.9 1.0
C2D B:HEM1152 4.2 15.3 1.0
C3D B:HEM1152 4.2 14.5 1.0
ND1 B:HIS64 4.3 17.4 1.0
CG B:HIS64 4.3 15.5 1.0
C2A B:HEM1152 4.3 20.1 1.0
C3B B:HEM1152 4.3 18.2 1.0
C3A B:HEM1152 4.3 17.9 1.0
C2B B:HEM1152 4.3 20.2 1.0
CG2 B:VAL68 4.9 11.6 1.0

Iron binding site 3 out of 4 in 1oj6

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Iron binding site 3 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1152

b:2.0
occ:1.00
FE C:HEM1152 0.0 2.0 1.0
ND C:HEM1152 2.0 16.0 1.0
NC C:HEM1152 2.0 15.1 1.0
NE2 C:HIS64 2.1 13.3 1.0
NA C:HEM1152 2.1 17.2 1.0
NB C:HEM1152 2.1 19.4 1.0
NE2 C:HIS96 2.1 16.4 1.0
C4C C:HEM1152 3.0 15.1 1.0
C1D C:HEM1152 3.0 22.4 1.0
CD2 C:HIS96 3.0 18.0 1.0
C4D C:HEM1152 3.0 16.1 1.0
CD2 C:HIS64 3.0 19.0 1.0
C1C C:HEM1152 3.0 13.9 1.0
C1A C:HEM1152 3.1 15.0 1.0
CE1 C:HIS64 3.1 16.8 1.0
C4B C:HEM1152 3.1 17.5 1.0
C1B C:HEM1152 3.1 5.5 1.0
C4A C:HEM1152 3.1 11.2 1.0
CE1 C:HIS96 3.2 19.4 1.0
CHD C:HEM1152 3.3 21.2 1.0
CHA C:HEM1152 3.4 15.3 1.0
CHC C:HEM1152 3.4 17.3 1.0
CHB C:HEM1152 3.5 11.2 1.0
CG C:HIS96 4.2 18.9 1.0
ND1 C:HIS64 4.2 12.7 1.0
CG C:HIS64 4.2 14.3 1.0
C3C C:HEM1152 4.2 11.4 1.0
C2D C:HEM1152 4.2 12.9 1.0
ND1 C:HIS96 4.2 19.0 1.0
C2C C:HEM1152 4.2 18.0 1.0
C3D C:HEM1152 4.2 15.1 1.0
C3B C:HEM1152 4.3 19.7 1.0
C2A C:HEM1152 4.3 16.9 1.0
C2B C:HEM1152 4.3 10.9 1.0
C3A C:HEM1152 4.3 21.0 1.0
CG2 C:VAL68 5.0 14.5 1.0

Iron binding site 4 out of 4 in 1oj6

Go back to Iron Binding Sites List in 1oj6
Iron binding site 4 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1151

b:2.3
occ:1.00
FE D:HEM1151 0.0 2.3 1.0
NA D:HEM1151 1.9 20.0 1.0
NC D:HEM1151 2.0 20.6 1.0
NE2 D:HIS96 2.0 17.8 1.0
ND D:HEM1151 2.1 17.6 1.0
NE2 D:HIS64 2.1 19.4 1.0
NB D:HEM1151 2.1 26.4 1.0
C1A D:HEM1151 3.0 16.3 1.0
CD2 D:HIS96 3.0 19.9 1.0
C4A D:HEM1151 3.0 21.1 1.0
C4C D:HEM1151 3.0 22.7 1.0
CE1 D:HIS96 3.0 21.4 1.0
CE1 D:HIS64 3.0 17.6 1.0
C4D D:HEM1151 3.0 17.9 1.0
C1C D:HEM1151 3.1 17.2 1.0
C1D D:HEM1151 3.1 19.5 1.0
CD2 D:HIS64 3.1 23.1 1.0
C4B D:HEM1151 3.1 12.6 1.0
C1B D:HEM1151 3.1 19.3 1.0
CHA D:HEM1151 3.4 18.7 1.0
CHD D:HEM1151 3.4 17.7 1.0
CHB D:HEM1151 3.4 14.4 1.0
CHC D:HEM1151 3.5 11.9 1.0
ND1 D:HIS96 4.1 21.7 1.0
CG D:HIS96 4.1 19.9 1.0
ND1 D:HIS64 4.2 18.3 1.0
C2A D:HEM1151 4.2 23.2 1.0
C3A D:HEM1151 4.2 23.9 1.0
CG D:HIS64 4.2 20.3 1.0
C3C D:HEM1151 4.2 19.2 1.0
C2C D:HEM1151 4.3 18.3 1.0
C3D D:HEM1151 4.3 17.1 1.0
C2D D:HEM1151 4.3 24.6 1.0
C3B D:HEM1151 4.3 26.6 1.0
C2B D:HEM1151 4.3 21.3 1.0
CG2 D:VAL68 5.0 19.2 1.0

Reference:

A.Pesce, S.Dewilde, M.Nardini, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Human Brain Neuroglobin Structure Reveals A Distinct Mode of Controlling Oxygen Affinity Structure V. 11 1087 2003.
ISSN: ISSN 0969-2126
PubMed: 12962627
DOI: 10.1016/S0969-2126(03)00166-7
Page generated: Sat Aug 3 12:31:43 2024

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