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Iron in PDB 1umo: The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man

Protein crystallography data

The structure of The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man, PDB code: 1umo was solved by D.De Sanctis, S.Dewilde, A.Pesce, 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) 29.88 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.617, 72.001, 98.334, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 28.4

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man (pdb code 1umo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man, PDB code: 1umo:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1umo

Go back to Iron Binding Sites List in 1umo
Iron binding site 1 out of 2 in the The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1172

b:35.3
occ:1.00
FE A:HEM1172 0.0 35.3 1.0
NB A:HEM1172 2.0 30.9 1.0
NA A:HEM1172 2.0 32.8 1.0
ND A:HEM1172 2.1 32.8 1.0
NC A:HEM1172 2.2 31.9 1.0
NE2 A:HIS113 2.2 31.5 1.0
NE2 A:HIS81 2.7 41.4 0.5
C4A A:HEM1172 3.0 32.3 1.0
C1B A:HEM1172 3.0 29.0 1.0
C1A A:HEM1172 3.1 33.7 1.0
C4B A:HEM1172 3.1 30.8 1.0
C4D A:HEM1172 3.1 33.8 1.0
C1C A:HEM1172 3.2 30.6 1.0
CE1 A:HIS113 3.2 32.7 1.0
C1D A:HEM1172 3.2 32.1 1.0
CD2 A:HIS113 3.2 33.3 1.0
C4C A:HEM1172 3.2 31.8 1.0
CHB A:HEM1172 3.3 31.4 1.0
CD2 A:HIS81 3.4 41.7 0.5
CHA A:HEM1172 3.4 33.4 1.0
CHC A:HEM1172 3.5 30.0 1.0
CHD A:HEM1172 3.6 31.6 1.0
NE2 A:HIS81 3.8 45.1 0.5
CE1 A:HIS81 3.9 41.8 0.5
C3A A:HEM1172 4.2 34.1 1.0
C2B A:HEM1172 4.2 27.3 1.0
C2A A:HEM1172 4.2 35.9 1.0
C3B A:HEM1172 4.2 29.2 1.0
ND1 A:HIS113 4.3 32.5 1.0
CE1 A:HIS81 4.3 45.2 0.5
CG A:HIS113 4.3 33.0 1.0
C3D A:HEM1172 4.4 33.3 1.0
C2C A:HEM1172 4.4 31.0 1.0
C2D A:HEM1172 4.4 32.3 1.0
C3C A:HEM1172 4.4 30.9 1.0
CG2 A:VAL85 4.5 39.5 0.5
CG2 A:VAL85 4.6 39.3 0.5
CD2 A:HIS117 4.6 43.0 1.0
CG A:HIS81 4.6 42.5 0.5
ND1 A:HIS81 4.8 43.2 0.5
NE2 A:HIS117 4.9 42.4 1.0

Iron binding site 2 out of 2 in 1umo

Go back to Iron Binding Sites List in 1umo
Iron binding site 2 out of 2 in the The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1172

b:37.9
occ:1.00
FE B:HEM1172 0.0 37.9 1.0
NE2 B:HIS113 2.0 30.3 1.0
NB B:HEM1172 2.1 36.5 1.0
NC B:HEM1172 2.1 35.2 1.0
NA B:HEM1172 2.1 37.0 1.0
ND B:HEM1172 2.2 37.2 1.0
NE2 B:HIS81 2.6 34.3 1.0
CE1 B:HIS113 2.9 31.0 1.0
CD2 B:HIS113 3.0 30.7 1.0
C4B B:HEM1172 3.1 36.1 1.0
C4A B:HEM1172 3.1 37.0 1.0
C1C B:HEM1172 3.1 36.1 1.0
C1B B:HEM1172 3.1 36.9 1.0
C1A B:HEM1172 3.1 37.6 1.0
C4C B:HEM1172 3.1 36.3 1.0
C1D B:HEM1172 3.1 36.0 1.0
C4D B:HEM1172 3.1 38.3 1.0
CD2 B:HIS81 3.4 37.1 1.0
CHC B:HEM1172 3.4 35.8 1.0
CHB B:HEM1172 3.4 37.8 1.0
CHD B:HEM1172 3.5 35.9 1.0
CHA B:HEM1172 3.5 38.0 1.0
CE1 B:HIS81 3.7 34.6 1.0
ND1 B:HIS113 4.1 32.0 1.0
CG B:HIS113 4.1 34.3 1.0
C3A B:HEM1172 4.3 37.0 1.0
C3B B:HEM1172 4.3 37.9 1.0
C2B B:HEM1172 4.3 37.9 1.0
C2A B:HEM1172 4.3 36.2 1.0
C2C B:HEM1172 4.3 35.8 1.0
C3C B:HEM1172 4.3 35.3 1.0
C2D B:HEM1172 4.4 37.4 1.0
C3D B:HEM1172 4.4 38.5 1.0
CG B:HIS81 4.6 36.0 1.0
ND1 B:HIS81 4.7 37.9 1.0

Reference:

D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination. J.Mol.Biol. V. 336 917 2004.
ISSN: ISSN 0022-2836
PubMed: 15095869
DOI: 10.1016/J.JMB.2003.12.063
Page generated: Sun Dec 13 14:33:36 2020

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