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Iron in PDB 4mpm: Wild-Type Human Neuroglobin

Protein crystallography data

The structure of Wild-Type Human Neuroglobin, PDB code: 4mpm was solved by B.G.Guimaraes, B.Golinelli-Pimpaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.24 / 1.74
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 139.150, 48.490, 39.280, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.9

Iron Binding Sites:

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

Iron binding site 1 out of 2 in 4mpm

Go back to Iron Binding Sites List in 4mpm
Iron binding site 1 out of 2 in the Wild-Type Human Neuroglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Wild-Type Human Neuroglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:12.6
occ:1.00
FE A:HEM201 0.0 12.6 1.0
NA A:HEM201 2.0 13.4 1.0
NC A:HEM201 2.0 12.2 1.0
NB A:HEM201 2.0 12.7 1.0
ND A:HEM201 2.0 12.8 1.0
NE2 A:HIS64 2.0 13.2 1.0
NE2 A:HIS96 2.1 16.2 1.0
C4B A:HEM201 3.0 12.9 1.0
C1B A:HEM201 3.0 13.4 1.0
C4D A:HEM201 3.0 13.5 1.0
C4A A:HEM201 3.0 13.8 1.0
C1C A:HEM201 3.0 12.2 1.0
C1D A:HEM201 3.0 13.0 1.0
C4C A:HEM201 3.0 12.5 1.0
C1A A:HEM201 3.0 13.9 1.0
CD2 A:HIS64 3.0 13.7 1.0
CD2 A:HIS96 3.0 16.9 1.0
CE1 A:HIS64 3.0 12.4 1.0
CE1 A:HIS96 3.1 16.0 1.0
CHB A:HEM201 3.3 14.1 1.0
CHC A:HEM201 3.4 13.1 1.0
CHA A:HEM201 3.4 14.2 1.0
CHD A:HEM201 3.4 13.3 1.0
CG A:HIS64 4.2 11.3 1.0
ND1 A:HIS64 4.2 12.1 1.0
CG A:HIS96 4.2 15.3 1.0
ND1 A:HIS96 4.2 16.7 1.0
C2B A:HEM201 4.2 13.7 1.0
C3A A:HEM201 4.2 14.8 1.0
C3B A:HEM201 4.3 13.6 1.0
C2C A:HEM201 4.3 12.8 1.0
C2A A:HEM201 4.3 14.9 1.0
C3D A:HEM201 4.3 14.2 1.0
C3C A:HEM201 4.3 12.7 1.0
C2D A:HEM201 4.3 13.6 1.0
CG2 A:VAL68 4.9 10.3 1.0

Iron binding site 2 out of 2 in 4mpm

Go back to Iron Binding Sites List in 4mpm
Iron binding site 2 out of 2 in the Wild-Type Human Neuroglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Wild-Type Human Neuroglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:10.3
occ:1.00
FE B:HEM201 0.0 10.3 1.0
NA B:HEM201 1.9 10.7 1.0
ND B:HEM201 2.0 10.3 1.0
NC B:HEM201 2.0 10.2 1.0
NB B:HEM201 2.0 10.1 1.0
NE2 B:HIS96 2.1 13.9 1.0
NE2 B:HIS64 2.1 12.6 1.0
C4D B:HEM201 3.0 10.8 1.0
C1B B:HEM201 3.0 10.6 1.0
C1A B:HEM201 3.0 11.0 1.0
C4C B:HEM201 3.0 10.4 1.0
C1D B:HEM201 3.0 10.6 1.0
C4B B:HEM201 3.0 10.4 1.0
C4A B:HEM201 3.0 10.8 1.0
C1C B:HEM201 3.0 10.2 1.0
CD2 B:HIS96 3.1 13.2 1.0
CE1 B:HIS96 3.1 13.8 1.0
CD2 B:HIS64 3.1 13.2 1.0
CE1 B:HIS64 3.1 12.1 1.0
CHA B:HEM201 3.3 11.3 1.0
CHB B:HEM201 3.4 11.1 1.0
CHD B:HEM201 3.4 11.1 1.0
CHC B:HEM201 3.4 10.8 1.0
CG B:HIS96 4.2 12.8 1.0
ND1 B:HIS96 4.2 13.9 1.0
CG B:HIS64 4.2 11.8 1.0
C2A B:HEM201 4.2 11.7 1.0
C3A B:HEM201 4.2 11.6 1.0
C3D B:HEM201 4.2 11.4 1.0
ND1 B:HIS64 4.3 13.0 1.0
C2B B:HEM201 4.3 10.8 1.0
C2D B:HEM201 4.3 11.1 1.0
C3C B:HEM201 4.3 10.8 1.0
C2C B:HEM201 4.3 10.8 1.0
C3B B:HEM201 4.3 10.9 1.0
CG2 B:VAL68 4.9 9.3 1.0

Reference:

B.G.Guimaraes, D.Hamdane, C.Lechauve, M.C.Marden, B.Golinelli-Pimpaneau. The Crystal Structure of Wild-Type Human Brain Neuroglobin Reveals Flexibility of the Disulfide Bond That Regulates Oxygen Affinity. Acta Crystallogr.,Sect.D V. 70 1005 2014.
ISSN: ISSN 0907-4449
PubMed: 24699645
DOI: 10.1107/S1399004714000078
Page generated: Sun Dec 13 15:41:55 2020

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