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Iron in PDB 1o9r: The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding

Protein crystallography data

The structure of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding, PDB code: 1o9r was solved by A.Ilari, P.Ceci, E.Chiancone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 1.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.046, 90.349, 105.656, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20

Iron Binding Sites:

The binding sites of Iron atom in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding (pdb code 1o9r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding, PDB code: 1o9r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1o9r

Go back to Iron Binding Sites List in 1o9r
Iron binding site 1 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1163

b:25.7
occ:0.30
OE2 A:GLU71 2.0 28.9 1.0
O B:HOH2045 2.1 25.7 1.0
O B:HOH2036 2.2 22.8 1.0
OD2 A:ASP67 2.3 11.0 0.3
OD1 A:ASP67 2.7 12.5 0.3
CG A:ASP67 2.9 13.8 0.3
CD A:GLU71 3.3 20.8 1.0
NE2 B:HIS40 3.4 16.8 1.0
CE1 B:HIS40 3.9 15.7 1.0
CG A:GLU71 4.0 19.3 1.0
OD1 B:ASP56 4.1 19.8 1.0
OE1 A:GLU71 4.2 25.3 1.0
NE2 B:HIS52 4.2 16.3 1.0
NZ C:LYS149 4.3 24.0 1.0
NZ B:LYS37 4.3 21.8 1.0
CB A:ASP67 4.4 13.9 0.3
CB A:ASP67 4.5 18.1 0.7
CD2 B:HIS40 4.6 16.2 1.0
CE1 B:HIS52 4.6 14.6 1.0
OD2 A:ASP67 4.6 24.4 0.7
CG A:ASP67 4.7 20.4 0.7
CG B:ASP56 5.0 20.3 1.0
OD2 B:ASP56 5.0 19.5 1.0

Iron binding site 2 out of 6 in 1o9r

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Iron binding site 2 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1163

b:27.3
occ:0.30
OE2 B:GLU71 1.9 27.3 1.0
O A:HOH2046 2.1 24.4 1.0
O A:HOH2041 2.1 22.3 1.0
OD1 B:ASP67 2.2 13.9 0.3
OD2 B:ASP67 2.7 10.9 0.3
CG B:ASP67 2.9 15.2 0.3
CD B:GLU71 3.1 22.7 1.0
NE2 A:HIS40 3.6 16.9 1.0
CG B:GLU71 3.9 19.8 1.0
OE1 B:GLU71 4.0 24.9 1.0
CE1 A:HIS40 4.1 15.2 1.0
NZ D:LYS149 4.1 21.3 1.0
OD1 A:ASP56 4.2 19.9 1.0
NE2 A:HIS52 4.3 15.9 1.0
CB B:ASP67 4.3 13.8 0.3
CB B:ASP67 4.5 15.0 0.7
NZ A:LYS37 4.5 22.6 1.0
OD1 B:ASP67 4.7 23.5 0.7
CD2 A:HIS40 4.8 16.4 1.0
CE1 A:HIS52 4.8 15.3 1.0
CG B:ASP67 4.8 17.7 0.7

Iron binding site 3 out of 6 in 1o9r

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Iron binding site 3 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1163

b:31.7
occ:0.50
OE2 C:GLU71 2.3 29.4 1.0
OD1 C:ASP67 2.4 16.8 0.5
OD2 C:ASP67 2.4 15.8 0.5
CG C:ASP67 2.8 17.5 0.5
CD C:GLU71 3.4 23.1 1.0
CG C:GLU71 4.0 22.1 1.0
O C:HOH2054 4.3 39.8 1.0
CB C:ASP67 4.3 14.0 0.5
CG C:ASP67 4.4 22.3 0.5
OD1 C:ASP67 4.4 23.5 0.5
OE1 C:GLU71 4.4 28.1 1.0
CB C:ASP67 4.4 17.9 0.5
NZ E:LYS149 4.8 25.3 1.0
OD2 C:ASP67 4.8 24.1 0.5

Iron binding site 4 out of 6 in 1o9r

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Iron binding site 4 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1163

b:29.4
occ:0.50
OE2 D:GLU71 2.2 27.8 1.0
O D:HOH2048 2.2 23.0 1.0
OD1 D:ASP67 2.3 16.0 0.5
OD2 D:ASP67 2.6 16.9 0.5
CG D:ASP67 2.9 16.7 0.5
CD D:GLU71 3.3 21.5 1.0
CG D:GLU71 4.0 22.4 1.0
OE1 D:GLU71 4.3 27.1 1.0
OD1 D:ASP67 4.3 22.1 0.5
CB D:ASP67 4.3 14.8 0.5
CB D:ASP67 4.4 15.9 0.5
CG D:ASP67 4.6 18.4 0.5

Iron binding site 5 out of 6 in 1o9r

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Iron binding site 5 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1163

b:27.2
occ:0.50
O F:HOH2043 2.1 23.6 1.0
OE2 E:GLU71 2.2 30.2 1.0
O F:HOH2034 2.3 24.9 1.0
OD2 E:ASP67 2.4 14.2 0.5
OD1 E:ASP67 2.5 14.4 0.5
O E:HOH2050 2.7 52.7 1.0
NE2 F:HIS40 2.8 18.0 1.0
CG E:ASP67 2.9 15.0 0.5
CD E:GLU71 3.4 24.1 1.0
CE1 F:HIS40 3.5 16.8 1.0
CD2 F:HIS40 3.9 15.3 1.0
CG E:GLU71 4.0 22.0 1.0
OD1 F:ASP56 4.0 21.4 1.0
NE2 F:HIS52 4.1 15.1 1.0
NZ F:LYS37 4.2 18.2 1.0
OE1 E:GLU71 4.3 29.7 1.0
CB E:ASP67 4.4 11.9 0.5
CG E:ASP67 4.4 21.8 0.5
CE1 F:HIS52 4.4 15.3 1.0
CB E:ASP67 4.4 18.1 0.5
OD1 E:ASP67 4.6 24.4 0.5
NZ A:LYS149 4.7 25.1 1.0
OD2 E:ASP67 4.7 24.2 0.5
NE1 F:TRP41 4.8 14.5 1.0
OD2 F:ASP56 4.8 17.2 1.0
ND1 F:HIS40 4.8 14.6 1.0
CG F:ASP56 4.8 19.8 1.0
CD1 F:TRP41 5.0 14.4 1.0
CG F:HIS40 5.0 15.1 1.0

Iron binding site 6 out of 6 in 1o9r

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Iron binding site 6 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1163

b:28.8
occ:0.50
O E:HOH2035 2.1 21.3 1.0
OE2 F:GLU71 2.2 29.9 1.0
O E:HOH2028 2.3 24.4 1.0
OD1 F:ASP67 2.4 14.4 0.5
OD2 F:ASP67 2.5 15.8 0.5
O F:HOH2057 2.7 45.3 1.0
CG F:ASP67 2.9 16.3 0.5
NE2 E:HIS40 2.9 16.8 1.0
CD F:GLU71 3.3 22.4 1.0
CE1 E:HIS40 3.6 15.9 1.0
CG F:GLU71 4.0 21.7 1.0
CD2 E:HIS40 4.0 15.6 1.0
NE2 E:HIS52 4.1 15.7 1.0
OD1 E:ASP56 4.1 21.0 1.0
NZ E:LYS37 4.3 19.8 1.0
OE1 F:GLU71 4.3 28.9 1.0
CB F:ASP67 4.3 14.4 0.5
CE1 E:HIS52 4.4 15.5 1.0
CG F:ASP67 4.5 21.7 0.5
CB F:ASP67 4.5 17.1 0.5
OD1 F:ASP67 4.6 23.9 0.5
OD2 E:ASP56 4.8 18.4 1.0
NE1 E:TRP41 4.8 14.9 1.0
ND1 E:HIS40 4.8 15.1 1.0
CG E:ASP56 4.9 18.2 1.0
OD2 F:ASP67 4.9 24.6 0.5
CD1 E:TRP41 5.0 14.8 1.0

Reference:

P.Ceci, A.Ilari, E.Falvo, E.Chiancone. The Dps Protein of Agrobacterium Tumefaciens Does Not Bind to Dna But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, and Hydroxyl-Radical Scavenging Properties J.Biol.Chem. V. 278 20319 2003.
ISSN: ISSN 0021-9258
PubMed: 12660233
DOI: 10.1074/JBC.M302114200
Page generated: Sun Dec 13 14:26:34 2020

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