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Iron in PDB 1ury: Cytoglobin Cavities

Protein crystallography data

The structure of Cytoglobin Cavities, PDB code: 1ury 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 / 2.4
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.848, 70.524, 98.728, 90.00, 90.00, 90.00
R / Rfree (%) 19.702 / 25.442

Other elements in 1ury:

The structure of Cytoglobin Cavities also contains other interesting chemical elements:

Xenon (Xe) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cytoglobin Cavities (pdb code 1ury). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cytoglobin Cavities, PDB code: 1ury:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1ury

Go back to Iron Binding Sites List in 1ury
Iron binding site 1 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytoglobin Cavities within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:17.9
occ:1.00
FE A:HEM700 0.0 17.9 1.0
NB A:HEM700 2.0 15.0 1.0
NA A:HEM700 2.0 17.4 1.0
NC A:HEM700 2.1 18.3 1.0
NE2 A:HIS81 2.1 31.8 1.0
NE2 A:HIS113 2.1 23.1 1.0
ND A:HEM700 2.2 19.2 1.0
CE1 A:HIS81 2.7 32.3 1.0
CE1 A:HIS113 2.9 22.5 1.0
C1B A:HEM700 3.0 15.7 1.0
C4A A:HEM700 3.0 16.8 1.0
C4B A:HEM700 3.0 19.1 1.0
C1A A:HEM700 3.1 18.9 1.0
C4C A:HEM700 3.1 19.3 1.0
C1C A:HEM700 3.1 19.4 1.0
C1D A:HEM700 3.1 19.1 1.0
C4D A:HEM700 3.2 19.1 1.0
CD2 A:HIS113 3.2 26.2 1.0
CD2 A:HIS81 3.3 31.7 1.0
CHB A:HEM700 3.4 16.3 1.0
CHC A:HEM700 3.5 20.2 1.0
CHD A:HEM700 3.5 20.4 1.0
CHA A:HEM700 3.5 18.5 1.0
ND1 A:HIS81 3.8 32.9 1.0
ND1 A:HIS113 4.0 23.7 1.0
CG A:HIS81 4.2 26.2 1.0
C2B A:HEM700 4.2 16.8 1.0
C3A A:HEM700 4.2 19.6 1.0
CG A:HIS113 4.2 21.9 1.0
C3B A:HEM700 4.2 18.6 1.0
C2A A:HEM700 4.3 21.3 1.0
C3C A:HEM700 4.3 18.7 1.0
C2C A:HEM700 4.3 19.5 1.0
C3D A:HEM700 4.4 21.0 1.0
C2D A:HEM700 4.4 21.1 1.0
CG2 A:VAL85 4.7 21.0 1.0

Iron binding site 2 out of 4 in 1ury

Go back to Iron Binding Sites List in 1ury
Iron binding site 2 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytoglobin Cavities within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1175

b:26.2
occ:0.50
FE2 A:FC61175 0.0 26.2 0.5
C11 A:FC61175 1.8 25.2 0.5
C23 A:FC61175 1.8 25.3 0.5
C21 A:FC61175 1.8 26.8 0.5
C22 A:FC61175 1.8 23.5 0.5
C24 A:FC61175 1.8 25.1 0.5
C26 A:FC61175 1.8 27.9 0.5
N11 A:FC61175 3.0 24.8 0.5
N23 A:FC61175 3.0 25.1 0.5
N22 A:FC61175 3.0 14.2 1.0
N25 A:FC61175 3.0 28.2 0.5
N24 A:FC61175 3.0 21.4 0.5
N21 A:FC61175 3.0 30.0 0.5
CD A:LYS125 4.3 23.5 1.0
CB B:SER55 4.5 20.4 1.0
NE A:ARG155 4.5 25.4 1.0
CD A:ARG155 4.6 25.8 1.0
CD2 A:TYR159 4.7 26.6 1.0
OG B:SER55 4.7 21.8 1.0
N B:SER55 4.8 19.9 1.0
NZ A:LYS125 4.9 28.7 1.0
CZ A:ARG155 5.0 21.8 1.0

Iron binding site 3 out of 4 in 1ury

Go back to Iron Binding Sites List in 1ury
Iron binding site 3 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytoglobin Cavities within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe700

b:18.0
occ:1.00
FE B:HEM700 0.0 18.0 1.0
NC B:HEM700 1.9 17.7 1.0
NE2 B:HIS113 2.0 20.9 1.0
NA B:HEM700 2.0 15.9 1.0
ND B:HEM700 2.0 18.5 1.0
NB B:HEM700 2.0 17.1 1.0
NE2 B:HIS81 2.1 24.2 1.0
CE1 B:HIS81 2.9 26.0 1.0
C4C B:HEM700 2.9 16.9 1.0
CE1 B:HIS113 2.9 20.2 1.0
C1D B:HEM700 3.0 18.1 1.0
C1C B:HEM700 3.0 18.8 1.0
CD2 B:HIS113 3.0 22.9 1.0
C4A B:HEM700 3.0 15.5 1.0
C1A B:HEM700 3.1 16.0 1.0
C1B B:HEM700 3.1 17.9 1.0
C4B B:HEM700 3.1 20.1 1.0
C4D B:HEM700 3.1 16.0 1.0
CD2 B:HIS81 3.2 24.9 1.0
CHD B:HEM700 3.3 18.5 1.0
CHC B:HEM700 3.4 20.8 1.0
CHB B:HEM700 3.4 16.5 1.0
CHA B:HEM700 3.5 14.0 1.0
ND1 B:HIS81 4.0 27.4 1.0
ND1 B:HIS113 4.1 20.9 1.0
CG B:HIS113 4.1 22.5 1.0
C3C B:HEM700 4.2 17.1 1.0
C2C B:HEM700 4.2 18.1 1.0
C2D B:HEM700 4.2 18.9 1.0
CG B:HIS81 4.3 23.0 1.0
C3A B:HEM700 4.3 16.4 1.0
C2A B:HEM700 4.3 17.2 1.0
C3D B:HEM700 4.3 18.6 1.0
C3B B:HEM700 4.3 19.2 1.0
C2B B:HEM700 4.3 17.2 1.0
CG2 B:VAL85 4.7 24.5 1.0
CD2 B:HIS117 4.9 22.3 1.0

Iron binding site 4 out of 4 in 1ury

Go back to Iron Binding Sites List in 1ury
Iron binding site 4 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytoglobin Cavities within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1175

b:48.8
occ:1.00
FE2 B:FC61175 0.0 48.8 1.0
C21 B:FC61175 1.8 46.0 1.0
C23 B:FC61175 1.8 47.2 1.0
C22 B:FC61175 1.8 48.6 1.0
C26 B:FC61175 1.8 44.8 1.0
C11 B:FC61175 1.8 48.0 1.0
C24 B:FC61175 1.8 49.0 1.0
N25 B:FC61175 3.0 44.9 1.0
N23 B:FC61175 3.0 47.8 1.0
N21 B:FC61175 3.0 34.8 1.0
N22 B:FC61175 3.0 49.3 1.0
N11 B:FC61175 3.0 43.6 1.0
N24 B:FC61175 3.0 48.3 1.0
CE B:LYS125 4.3 25.4 1.0
NE B:ARG155 4.3 26.9 1.0
CB A:SER55 4.4 20.1 1.0
CD1 B:TYR159 4.5 25.1 1.0
CD B:ARG155 4.6 26.1 1.0
OG A:SER55 4.6 20.8 1.0
N A:SER55 4.8 19.9 1.0
CZ B:ARG155 4.8 26.5 1.0
CG A:PRO54 4.9 19.1 1.0

Reference:

D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Cytoglobin Cavities Biochem.Biophys.Res.Commun. V. 316 1217 2004.
ISSN: ISSN 0006-291X
PubMed: 15044115
DOI: 10.1016/J.BBRC.2004.03.007
Page generated: Sun Dec 13 14:33:44 2020

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