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Iron in PDB 1sum: Crystal Structure of A Hypothetical Protein at 2.0 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution, PDB code: 1sum was solved by J.Liu, Y.Lou, H.Yokota, P.D.Adams, R.Kim, S.H.Kim, Berkeley Structuralgenomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.677, 90.677, 45.255, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.5

Other elements in 1sum:

The structure of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution (pdb code 1sum). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution, PDB code: 1sum:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 1sum

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Iron binding site 1 out of 7 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe236

b:75.7
occ:1.00
OE2 B:GLU11 2.3 23.0 1.0
OE1 B:GLU7 2.4 15.5 1.0
CD B:GLU11 3.1 19.6 1.0
OE1 B:GLU11 3.3 22.8 1.0
CD B:GLU7 3.5 16.2 1.0
CG B:GLU7 4.0 14.7 1.0
CG B:GLU11 4.5 17.4 1.0
OE2 B:GLU7 4.6 17.8 1.0
NZ B:LYS8 4.9 18.3 1.0

Iron binding site 2 out of 7 in 1sum

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Iron binding site 2 out of 7 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe237

b:40.3
occ:1.00
O B:HOH615 2.2 33.2 1.0
OE1 B:GLU91 2.3 11.4 1.0
OD1 B:ASP53 2.3 18.5 1.0
OE2 B:GLU49 2.3 15.3 1.0
OD1 B:ASP95 2.4 13.4 1.0
O3 B:PO3569 2.4 69.2 1.0
O2 B:PO3569 2.6 71.8 1.0
P B:PO3569 2.9 72.1 1.0
CG B:ASP53 3.2 16.4 1.0
OD2 B:ASP53 3.2 22.8 1.0
CG B:ASP95 3.4 16.1 1.0
CD B:GLU91 3.4 14.9 1.0
CD B:GLU49 3.4 14.7 1.0
O1 B:PO3569 3.5 69.8 1.0
OD2 B:ASP95 3.7 14.6 1.0
NI B:NI301 4.0 71.6 1.0
CG B:GLU91 4.0 14.8 1.0
CG B:GLU49 4.0 15.3 1.0
O B:HOH575 4.0 38.9 1.0
FE B:FE238 4.3 45.0 1.0
OE2 B:GLU91 4.4 18.6 1.0
OE1 B:GLU49 4.4 15.1 1.0
O B:GLU91 4.5 12.3 1.0
O B:GLU49 4.6 15.2 1.0
CB B:ASP53 4.6 15.1 1.0
CB B:ASP95 4.7 13.6 1.0
O B:HOH611 4.8 72.5 1.0
CA B:ASP95 4.9 14.0 1.0
N B:ASP95 4.9 13.3 1.0

Iron binding site 3 out of 7 in 1sum

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Iron binding site 3 out of 7 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe238

b:45.0
occ:1.00
OD2 B:ASP95 2.3 14.6 1.0
OE2 B:GLU91 2.4 18.6 1.0
OD1 B:ASN92 2.5 17.7 1.0
O B:HOH628 2.6 36.7 1.0
O B:HOH589 2.6 29.5 1.0
OE1 B:GLU91 2.7 11.4 1.0
O1 B:PO3569 2.7 69.8 1.0
CD B:GLU91 2.9 14.9 1.0
CG B:ASP95 3.5 16.1 1.0
O2 B:PO3569 3.6 71.8 1.0
CG B:ASN92 3.7 16.5 1.0
P B:PO3569 3.7 72.1 1.0
FE B:FE239 4.0 49.0 1.0
OD1 B:ASP95 4.0 13.4 1.0
FE B:FE237 4.3 40.3 1.0
CA B:ASN92 4.4 13.4 1.0
CG B:GLU91 4.4 14.8 1.0
ND2 B:ASN92 4.5 19.9 1.0
N B:ASN92 4.5 13.7 1.0
OE2 B:GLU88 4.6 23.9 1.0
CB B:ASN92 4.6 13.7 1.0
CB B:ASP95 4.7 13.6 1.0
O3 B:PO3569 4.7 69.2 1.0
C B:GLU91 4.7 13.6 1.0
OE1 B:GLU88 4.7 28.5 1.0
O B:GLU91 4.8 12.3 1.0
CD B:GLU88 5.0 23.5 1.0

Iron binding site 4 out of 7 in 1sum

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Iron binding site 4 out of 7 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe239

b:49.0
occ:1.00
OE1 B:GLU88 2.3 28.5 1.0
OE2 B:GLU56 2.4 29.0 1.0
OE2 B:GLU91 2.5 18.6 1.0
O B:HOH589 2.7 29.5 1.0
O B:HOH579 2.7 35.5 1.0
OE1 B:GLU56 3.1 33.3 1.0
CD B:GLU56 3.1 26.9 1.0
CD B:GLU88 3.3 23.5 1.0
CD B:GLU91 3.3 14.9 1.0
OE2 B:GLU88 3.6 23.9 1.0
O B:HOH577 3.9 46.9 1.0
FE B:FE238 4.0 45.0 1.0
CG B:GLU91 4.0 14.8 1.0
OE1 B:GLU91 4.2 11.4 1.0
CB B:GLU91 4.3 13.6 1.0
O1 B:PO3569 4.4 69.8 1.0
CG B:GLU56 4.5 21.0 1.0
OD1 B:ASN92 4.6 17.7 1.0
CG B:GLU88 4.6 17.9 1.0
O B:HOH576 4.6 41.9 1.0
CB B:GLU88 4.9 16.6 1.0
CA B:GLU88 5.0 16.4 1.0

Iron binding site 5 out of 7 in 1sum

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Iron binding site 5 out of 7 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe240

b:36.9
occ:1.00
O B:HOH603 2.3 26.1 1.0
OD1 B:ASP195 2.3 14.6 1.0
OD1 B:ASP156 2.3 12.5 1.0
OE2 B:GLU191 2.4 13.6 1.0
OD1 B:ASP152 2.5 16.3 1.0
O1 B:PO3568 2.6 42.6 1.0
O3 B:PO3568 2.6 38.6 1.0
P B:PO3568 2.9 50.2 1.0
CG B:ASP152 3.3 15.9 1.0
OD2 B:ASP152 3.3 15.6 1.0
CG B:ASP195 3.4 17.2 1.0
CG B:ASP156 3.4 13.3 1.0
CD B:GLU191 3.4 14.0 1.0
OD2 B:ASP195 3.7 16.4 1.0
OD2 B:ASP156 3.7 14.7 1.0
FE B:FE242 3.7 46.1 1.0
FE B:FE241 3.8 37.0 1.0
CG B:GLU191 4.1 15.2 1.0
O B:GLU191 4.1 14.0 1.0
OE1 B:GLU191 4.4 14.6 1.0
O2 B:PO3568 4.4 51.3 1.0
O B:ASP152 4.5 14.7 1.0
O B:HOH573 4.6 35.2 1.0
CB B:ASP195 4.7 14.9 1.0
CB B:ASP156 4.7 13.5 1.0
O B:HOH627 4.7 33.2 1.0
CB B:ASP152 4.7 14.6 1.0
N B:ASP195 4.8 14.1 1.0
CA B:ASP195 4.9 14.6 1.0
CA B:ASP156 5.0 13.6 1.0
N B:ASP156 5.0 13.2 1.0

Iron binding site 6 out of 7 in 1sum

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Iron binding site 6 out of 7 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe241

b:37.0
occ:1.00
O B:HOH627 2.2 33.2 1.0
O3 B:PO3568 2.2 38.6 1.0
OD2 B:ASP195 2.3 16.4 1.0
O B:HOH624 2.3 35.9 1.0
OE2 B:GLU191 2.4 13.6 1.0
O B:HOH634 2.4 31.5 1.0
OE1 B:GLU191 2.5 14.6 1.0
CD B:GLU191 2.8 14.0 1.0
CG B:ASP195 3.3 17.2 1.0
OD1 B:ASP195 3.6 14.6 1.0
P B:PO3568 3.7 50.2 1.0
FE B:FE240 3.8 36.9 1.0
O B:HOH610 4.2 36.0 1.0
CG B:GLU191 4.3 15.2 1.0
O2 B:PO3568 4.4 51.3 1.0
CB B:ASP195 4.7 14.9 1.0
O B:GLU191 4.7 14.0 1.0
O1 B:PO3568 4.7 42.6 1.0

Iron binding site 7 out of 7 in 1sum

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Iron binding site 7 out of 7 in the Crystal Structure of A Hypothetical Protein at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of A Hypothetical Protein at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe242

b:46.1
occ:1.00
O1 B:PO3568 2.1 42.6 1.0
O B:HOH573 2.3 35.2 1.0
OD1 B:ASP152 2.4 16.3 1.0
O B:HOH590 2.4 42.9 1.0
OD2 B:ASP156 2.4 14.7 1.0
CG B:ASP152 3.4 15.9 1.0
CG B:ASP156 3.5 13.3 1.0
P B:PO3568 3.5 50.2 1.0
OD1 B:ASP156 3.7 12.5 1.0
FE B:FE240 3.7 36.9 1.0
CB B:ASP152 3.8 14.6 1.0
O2 B:PO3568 4.2 51.3 1.0
O B:ASP152 4.3 14.7 1.0
C B:ASP152 4.3 15.0 1.0
N B:SER153 4.5 15.5 1.0
OD2 B:ASP152 4.5 15.6 1.0
O3 B:PO3568 4.6 38.6 1.0
OG B:SER153 4.7 15.8 1.0
CA B:ASP152 4.7 14.7 1.0
CA B:SER153 4.7 15.1 1.0
CA B:HIS217 4.8 48.0 1.0
CB B:ASP156 4.8 13.5 1.0
O B:CYS149 4.9 15.7 1.0
OD1 B:ASP195 5.0 14.6 1.0

Reference:

J.Liu, Y.Lou, H.Yokota, P.D.Adams, R.Kim, S.H.Kim. Crystal Structure of A Phou Protein Homologue: A New Class of Metalloprotein Containing Multinuclear Iron Clusters. J.Biol.Chem. V. 280 15960 2005.
ISSN: ISSN 0021-9258
PubMed: 15716271
DOI: 10.1074/JBC.M414117200
Page generated: Sun Dec 13 14:32:07 2020

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