Iron in PDB 5d8s: 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa

Enzymatic activity of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa

All present enzymatic activity of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa:
1.16.3.1;

Protein crystallography data

The structure of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa, PDB code: 5d8s was solved by S.Lovell, K.P.Battaile, Y.Wang, H.Yao, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.72 / 2.55
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 205.556, 205.556, 115.769, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 26.1

Other elements in 5d8s:

The structure of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Potassium (K) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa (pdb code 5d8s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa, PDB code: 5d8s:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 5d8s

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Iron binding site 1 out of 7 in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:31.7
occ:1.00
 FE A:HEM202 0.0 31.7 1.0
NC A:HEM202 2.0 41.5 1.0
NB A:HEM202 2.0 42.7 1.0
ND A:HEM202 2.0 45.4 1.0
NA A:HEM202 2.1 35.1 1.0
SD A:MET52 2.4 29.7 1.0
SD B:MET52 2.4 34.2 1.0
C4B A:HEM202 3.0 36.7 1.0
C4C A:HEM202 3.0 33.9 1.0
C1C A:HEM202 3.0 37.9 1.0
C1D A:HEM202 3.0 36.5 1.0
C4D A:HEM202 3.1 34.0 1.0
C1B A:HEM202 3.1 34.7 1.0
C4A A:HEM202 3.1 29.6 1.0
C1A A:HEM202 3.1 33.8 1.0
CE A:MET52 3.2 26.4 1.0
CE B:MET52 3.3 36.8 1.0
CHC A:HEM202 3.4 30.8 1.0
CHD A:HEM202 3.4 37.6 1.0
CG A:MET52 3.4 24.2 1.0
CHA A:HEM202 3.5 31.7 1.0
CHB A:HEM202 3.5 39.0 1.0
CG B:MET52 3.7 29.1 1.0
CB A:MET52 4.2 28.2 1.0
CB B:MET52 4.2 25.7 1.0
C3B A:HEM202 4.2 35.6 1.0
C3C A:HEM202 4.3 33.9 1.0
C2D A:HEM202 4.3 31.3 1.0
C2C A:HEM202 4.3 39.0 1.0
C3D A:HEM202 4.3 35.8 1.0
C3A A:HEM202 4.3 29.9 1.0
C2B A:HEM202 4.3 33.7 1.0
C2A A:HEM202 4.3 31.0 1.0

Iron binding site 2 out of 7 in 5d8s

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Iron binding site 2 out of 7 in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:35.9
occ:1.00
 FE C:HEM202 0.0 35.9 1.0
NC C:HEM202 2.0 40.9 1.0
NB C:HEM202 2.0 43.5 1.0
ND C:HEM202 2.1 44.5 1.0
NA C:HEM202 2.1 46.6 1.0
SD C:MET52 2.4 29.5 1.0
SD H:MET52 2.4 29.3 1.0
C1C C:HEM202 3.0 46.0 1.0
C4C C:HEM202 3.0 43.4 1.0
C4B C:HEM202 3.0 42.3 1.0
C1D C:HEM202 3.1 40.9 1.0
C1B C:HEM202 3.1 41.2 1.0
C4D C:HEM202 3.1 37.5 1.0
C4A C:HEM202 3.1 46.0 1.0
C1A C:HEM202 3.1 40.6 1.0
CE C:MET52 3.3 39.3 1.0
CHC C:HEM202 3.4 39.2 1.0
CHD C:HEM202 3.4 44.3 1.0
CG H:MET52 3.4 34.7 1.0
CE H:MET52 3.4 37.7 1.0
CHB C:HEM202 3.4 42.3 1.0
CHA C:HEM202 3.5 34.4 1.0
CG C:MET52 3.5 36.2 1.0
CB H:MET52 4.1 48.5 1.0
CB C:MET52 4.1 34.6 1.0
C3C C:HEM202 4.3 40.6 1.0
C2C C:HEM202 4.3 49.7 1.0
C3B C:HEM202 4.3 42.5 1.0
C3D C:HEM202 4.3 42.1 1.0
C2D C:HEM202 4.3 42.0 1.0
C2B C:HEM202 4.3 43.7 1.0
C3A C:HEM202 4.3 45.3 1.0
C2A C:HEM202 4.3 37.8 1.0
CD1 C:ILE49 4.9 38.1 1.0

Iron binding site 3 out of 7 in 5d8s

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Iron binding site 3 out of 7 in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:38.6
occ:1.00
 FE D:HEM201 0.0 38.6 1.0
ND D:HEM201 2.0 38.0 1.0
NB D:HEM201 2.0 30.9 1.0
NC D:HEM201 2.0 29.0 1.0
NA D:HEM201 2.0 35.7 1.0
SD J:MET52 2.5 33.1 1.0
SD D:MET52 2.5 37.9 1.0
C4D D:HEM201 3.0 34.8 1.0
C4B D:HEM201 3.0 35.1 1.0
C1C D:HEM201 3.0 35.0 1.0
C1A D:HEM201 3.0 34.9 1.0
C1B D:HEM201 3.1 36.2 1.0
C4A D:HEM201 3.1 35.7 1.0
C1D D:HEM201 3.1 31.1 1.0
C4C D:HEM201 3.1 39.8 1.0
CE D:MET52 3.2 35.7 1.0
CE J:MET52 3.3 36.6 1.0
CHA D:HEM201 3.3 29.1 1.0
CHC D:HEM201 3.3 37.4 1.0
CG D:MET52 3.4 35.2 1.0
CHB D:HEM201 3.5 38.4 1.0
CHD D:HEM201 3.5 32.9 1.0
CG J:MET52 3.8 31.2 1.0
CB D:MET52 4.1 35.0 1.0
C3D D:HEM201 4.2 39.3 1.0
C3B D:HEM201 4.2 41.0 1.0
C2A D:HEM201 4.2 34.3 1.0
C2D D:HEM201 4.3 32.4 1.0
C3A D:HEM201 4.3 34.7 1.0
C2C D:HEM201 4.3 38.3 1.0
C2B D:HEM201 4.3 30.4 1.0
C3C D:HEM201 4.3 42.1 1.0
CB J:MET52 4.3 33.0 1.0
CD1 J:ILE49 4.8 30.9 1.0

Iron binding site 4 out of 7 in 5d8s

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Iron binding site 4 out of 7 in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:32.7
occ:1.00
 FE E:HEM201 0.0 32.7 1.0
ND E:HEM201 2.0 31.9 1.0
NC E:HEM201 2.0 34.1 1.0
NA E:HEM201 2.0 33.4 1.0
NB E:HEM201 2.1 27.4 1.0
SD G:MET52 2.4 31.2 1.0
SD E:MET52 2.5 31.5 1.0
C4D E:HEM201 2.9 33.5 1.0
C1A E:HEM201 3.0 28.3 1.0
C1C E:HEM201 3.0 34.4 1.0
C4B E:HEM201 3.0 31.2 1.0
C1D E:HEM201 3.1 32.3 1.0
C4C E:HEM201 3.1 40.6 1.0
C4A E:HEM201 3.1 27.7 1.0
C1B E:HEM201 3.2 34.2 1.0
CE E:MET52 3.3 31.5 1.0
CHA E:HEM201 3.3 34.5 1.0
CE G:MET52 3.3 22.5 1.0
CHC E:HEM201 3.3 33.6 1.0
CHD E:HEM201 3.5 43.0 1.0
CG G:MET52 3.5 34.3 1.0
CHB E:HEM201 3.5 33.5 1.0
CG E:MET52 3.6 31.6 1.0
C3D E:HEM201 4.2 37.1 1.0
CB G:MET52 4.2 36.7 1.0
C2A E:HEM201 4.2 35.0 1.0
C2C E:HEM201 4.2 37.2 1.0
C2D E:HEM201 4.2 34.6 1.0
CB E:MET52 4.2 35.5 1.0
C3B E:HEM201 4.3 29.0 1.0
C3C E:HEM201 4.3 38.9 1.0
C3A E:HEM201 4.3 30.5 1.0
C2B E:HEM201 4.3 34.0 1.0

Iron binding site 5 out of 7 in 5d8s

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Iron binding site 5 out of 7 in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:34.2
occ:1.00
 FE F:HEM201 0.0 34.2 1.0
NC F:HEM201 2.0 40.4 1.0
NB F:HEM201 2.0 40.9 1.0
ND F:HEM201 2.0 45.6 1.0
NA F:HEM201 2.1 44.4 1.0
SD K:MET52 2.4 29.6 1.0
SD F:MET52 2.4 29.1 1.0
C4B F:HEM201 3.0 40.3 1.0
C4C F:HEM201 3.0 42.2 1.0
C1D F:HEM201 3.1 43.5 1.0
C1C F:HEM201 3.1 33.7 1.0
C1B F:HEM201 3.1 36.5 1.0
C4D F:HEM201 3.1 45.2 1.0
C4A F:HEM201 3.1 47.5 1.0
C1A F:HEM201 3.1 38.4 1.0
CE K:MET52 3.2 34.1 1.0
CE F:MET52 3.3 40.9 1.0
CHC F:HEM201 3.4 34.8 1.0
CHD F:HEM201 3.4 39.2 1.0
CHB F:HEM201 3.5 43.5 1.0
CHA F:HEM201 3.5 43.3 1.0
CG F:MET52 3.6 34.0 1.0
CG K:MET52 3.7 38.9 1.0
CB K:MET52 4.2 35.8 1.0
C3B F:HEM201 4.3 38.8 1.0
C3C F:HEM201 4.3 41.1 1.0
C2D F:HEM201 4.3 40.7 1.0
C3D F:HEM201 4.3 40.8 1.0
C2C F:HEM201 4.3 37.8 1.0
C2B F:HEM201 4.3 45.4 1.0
C3A F:HEM201 4.3 39.5 1.0
C2A F:HEM201 4.3 42.1 1.0
CB F:MET52 4.3 34.5 1.0

Iron binding site 6 out of 7 in 5d8s

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Iron binding site 6 out of 7 in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:43.9
occ:0.50
 FE I:HEM201 0.0 43.9 0.5
NC I:HEM201 2.1 55.2 0.5
NB I:HEM201 2.1 54.6 0.5
ND I:HEM201 2.1 52.2 0.5
NA I:HEM201 2.1 52.0 0.5
SD I:MET52 2.4 37.3 1.0
C1B I:HEM201 3.0 51.2 0.5
C1D I:HEM201 3.1 52.3 0.5
C4B I:HEM201 3.1 51.2 0.5
C4A I:HEM201 3.1 52.4 0.5
C1C I:HEM201 3.1 50.0 0.5
C4C I:HEM201 3.1 51.9 0.5
C4D I:HEM201 3.1 47.7 0.5
C1A I:HEM201 3.2 47.7 0.5
CHD I:HEM201 3.4 50.6 0.5
CHB I:HEM201 3.4 50.6 0.5
CHC I:HEM201 3.4 46.9 0.5
CE I:MET52 3.5 51.2 1.0
CHA I:HEM201 3.5 49.8 0.5
CG I:MET52 3.7 49.0 1.0
CB I:MET52 4.2 49.2 1.0
C2B I:HEM201 4.2 50.8 0.5
C3B I:HEM201 4.3 50.9 0.5
C2D I:HEM201 4.3 52.6 0.5
C2C I:HEM201 4.3 50.7 0.5
C3C I:HEM201 4.3 50.6 0.5
C3A I:HEM201 4.3 52.5 0.5
C3D I:HEM201 4.3 47.9 0.5
C2A I:HEM201 4.3 47.8 0.5

Iron binding site 7 out of 7 in 5d8s

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Iron binding site 7 out of 7 in the 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 2.55A Resolution Structure of Bfrb (E85A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe201

b:29.9
occ:0.50
 FE L:HEM201 0.0 29.9 0.5
NA L:HEM201 2.0 28.5 0.5
NB L:HEM201 2.0 31.8 0.5
ND L:HEM201 2.1 28.8 0.5
NC L:HEM201 2.1 30.9 0.5
SD L:MET52 2.4 30.3 1.0
C1A L:HEM201 3.0 29.2 0.5
C4A L:HEM201 3.0 28.5 0.5
C4D L:HEM201 3.0 29.4 0.5
C1C L:HEM201 3.1 30.8 0.5
C4B L:HEM201 3.1 31.1 0.5
C1B L:HEM201 3.1 31.6 0.5
C1D L:HEM201 3.1 28.2 0.5
C4C L:HEM201 3.1 31.8 0.5
CE L:MET52 3.3 28.6 1.0
CHA L:HEM201 3.4 29.6 0.5
CHC L:HEM201 3.4 31.2 0.5
CHB L:HEM201 3.4 27.6 0.5
CHD L:HEM201 3.5 28.6 0.5
CG L:MET52 3.7 29.4 1.0
C2A L:HEM201 4.2 28.1 0.5
C3A L:HEM201 4.2 27.7 0.5
C3D L:HEM201 4.3 28.2 0.5
C3B L:HEM201 4.3 27.4 0.5
C2D L:HEM201 4.3 28.0 0.5
C2B L:HEM201 4.3 30.5 0.5
C2C L:HEM201 4.3 28.8 0.5
C3C L:HEM201 4.3 28.9 0.5
CB L:MET52 4.4 26.2 1.0

Reference:

Y.Wang, H.Yao, Y.Cheng, S.Lovell, K.P.Battaile, C.R.Midaugh, M.Rivera. Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots. Biochemistry V. 54 6162 2015.
ISSN: ISSN 0006-2960
PubMed: 26368531
DOI: 10.1021/ACS.BIOCHEM.5B00937
Page generated: Sun Dec 13 15:59:14 2020

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