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Iron in PDB 1ux9: Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation

Protein crystallography data

The structure of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation, PDB code: 1ux9 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) 29.8 / 2.4
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.840, 70.520, 98.730, 90.00, 90.00, 90.00
R / Rfree (%) 19.163 / 23.804

Other elements in 1ux9:

The structure of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation also contains other interesting chemical elements:

Xenon (Xe) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation (pdb code 1ux9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation, PDB code: 1ux9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1ux9

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Iron binding site 1 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1172

b:20.1
occ:1.00
FE A:HEM1172 0.0 20.1 1.0
NA A:HEM1172 2.0 19.0 1.0
NB A:HEM1172 2.0 18.0 1.0
NC A:HEM1172 2.0 19.8 1.0
NE2 A:HIS81 2.1 34.8 1.0
NE2 A:HIS113 2.1 22.5 1.0
ND A:HEM1172 2.2 21.0 1.0
CE1 A:HIS81 2.6 35.4 1.0
CE1 A:HIS113 2.9 21.3 1.0
C4A A:HEM1172 3.0 18.7 1.0
C1B A:HEM1172 3.0 17.7 1.0
C4B A:HEM1172 3.1 21.5 1.0
C4C A:HEM1172 3.1 21.5 1.0
C1A A:HEM1172 3.1 20.2 1.0
C1C A:HEM1172 3.1 22.0 1.0
C1D A:HEM1172 3.2 20.5 1.0
C4D A:HEM1172 3.2 19.7 1.0
CD2 A:HIS113 3.2 25.2 1.0
CD2 A:HIS81 3.3 34.6 1.0
CHB A:HEM1172 3.4 18.0 1.0
CHC A:HEM1172 3.4 23.0 1.0
CHD A:HEM1172 3.5 21.9 1.0
CHA A:HEM1172 3.5 19.2 1.0
ND1 A:HIS81 3.8 36.3 1.0
ND1 A:HIS113 4.0 23.0 1.0
CG A:HIS81 4.2 28.8 1.0
CG A:HIS113 4.2 21.2 1.0
C3A A:HEM1172 4.2 20.4 1.0
C2A A:HEM1172 4.2 21.5 1.0
C2B A:HEM1172 4.3 19.3 1.0
C3B A:HEM1172 4.3 21.8 1.0
C3C A:HEM1172 4.3 20.8 1.0
C2C A:HEM1172 4.3 21.4 1.0
C3D A:HEM1172 4.4 22.0 1.0
C2D A:HEM1172 4.4 22.4 1.0
CG2 A:VAL85 4.8 22.9 1.0

Iron binding site 2 out of 4 in 1ux9

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Iron binding site 2 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1176

b:31.2
occ:0.50
FE2 A:FC61176 0.0 31.2 0.5
C24 A:FC61176 1.8 30.2 0.5
C11 A:FC61176 1.8 30.0 0.5
C22 A:FC61176 1.8 31.5 0.5
C26 A:FC61176 1.8 28.4 0.5
C23 A:FC61176 1.8 33.0 0.5
C21 A:FC61176 1.8 30.3 0.5
N24 A:FC61176 3.0 29.9 0.5
N11 A:FC61176 3.0 29.8 0.5
N21 A:FC61176 3.0 19.3 1.0
N22 A:FC61176 3.0 32.3 0.5
N23 A:FC61176 3.0 35.5 0.5
N25 A:FC61176 3.0 26.6 0.5
CD A:LYS125 4.3 23.4 1.0
CB B:SER55 4.4 21.6 1.0
NE A:ARG155 4.5 28.9 1.0
CD A:ARG155 4.6 28.8 1.0
CD2 A:TYR159 4.7 26.8 1.0
OG B:SER55 4.8 22.9 1.0
NZ A:LYS125 4.8 28.0 1.0
N B:SER55 4.8 21.1 1.0
CZ A:ARG155 5.0 25.9 1.0

Iron binding site 3 out of 4 in 1ux9

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Iron binding site 3 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1172

b:20.0
occ:1.00
FE B:HEM1172 0.0 20.0 1.0
NC B:HEM1172 1.9 19.8 1.0
NE2 B:HIS113 2.0 21.8 1.0
NA B:HEM1172 2.0 17.4 1.0
NB B:HEM1172 2.0 19.0 1.0
ND B:HEM1172 2.0 19.9 1.0
NE2 B:HIS81 2.1 28.4 1.0
CE1 B:HIS81 2.8 30.1 1.0
CE1 B:HIS113 2.9 21.3 1.0
C4C B:HEM1172 2.9 18.6 1.0
C1D B:HEM1172 3.0 19.5 1.0
C1C B:HEM1172 3.0 20.9 1.0
CD2 B:HIS113 3.0 22.9 1.0
C4A B:HEM1172 3.0 17.0 1.0
C1B B:HEM1172 3.0 20.1 1.0
C1A B:HEM1172 3.1 17.6 1.0
C4B B:HEM1172 3.1 21.9 1.0
C4D B:HEM1172 3.1 17.5 1.0
CD2 B:HIS81 3.3 29.0 1.0
CHD B:HEM1172 3.3 19.9 1.0
CHB B:HEM1172 3.4 18.4 1.0
CHC B:HEM1172 3.4 23.3 1.0
CHA B:HEM1172 3.5 14.8 1.0
ND1 B:HIS81 4.0 31.7 1.0
ND1 B:HIS113 4.0 22.2 1.0
CG B:HIS113 4.1 22.5 1.0
C3C B:HEM1172 4.2 19.2 1.0
C2C B:HEM1172 4.2 19.7 1.0
C3A B:HEM1172 4.2 18.0 1.0
C2D B:HEM1172 4.2 19.9 1.0
CG B:HIS81 4.3 26.9 1.0
C2A B:HEM1172 4.3 18.5 1.0
C2B B:HEM1172 4.3 19.8 1.0
C3B B:HEM1172 4.3 21.2 1.0
C3D B:HEM1172 4.3 19.4 1.0
CG2 B:VAL85 4.7 26.8 1.0
CD2 B:HIS117 4.9 22.4 1.0

Iron binding site 4 out of 4 in 1ux9

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Iron binding site 4 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1176

b:54.4
occ:1.00
FE2 B:FC61176 0.0 54.4 1.0
C22 B:FC61176 1.8 51.5 1.0
C11 B:FC61176 1.8 52.5 1.0
C26 B:FC61176 1.8 54.0 1.0
C21 B:FC61176 1.9 54.5 1.0
C23 B:FC61176 1.9 50.2 1.0
C24 B:FC61176 1.9 53.2 1.0
N22 B:FC61176 3.0 50.2 1.0
N11 B:FC61176 3.0 53.0 1.0
N21 B:FC61176 3.0 54.8 1.0
N23 B:FC61176 3.0 40.0 1.0
N25 B:FC61176 3.0 53.6 1.0
N24 B:FC61176 3.0 48.3 1.0
CE B:LYS125 4.3 25.7 1.0
CB A:SER55 4.3 20.8 1.0
NE B:ARG155 4.4 28.7 1.0
CD1 B:TYR159 4.5 25.6 1.0
CD B:ARG155 4.6 27.7 1.0
OG A:SER55 4.6 21.0 1.0
N A:SER55 4.8 20.5 1.0
CZ B:ARG155 4.8 27.9 1.0
CG A:PRO54 5.0 19.5 1.0

Reference:

D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding 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 14:33:54 2020

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