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Iron in PDB 5d8y: 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa

Enzymatic activity of 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa

All present enzymatic activity of 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa:
1.16.3.1;

Protein crystallography data

The structure of 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa, PDB code: 5d8y 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) 48.75 / 2.05
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 125.845, 125.845, 272.518, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 19.6

Other elements in 5d8y:

The structure of 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Potassium (K) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 156;

Binding sites:

The binding sites of Iron atom in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa (pdb code 5d8y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 156 binding sites of Iron where determined in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa, PDB code: 5d8y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 156 in 5d8y

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Iron binding site 1 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) 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 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:37.4
occ:1.00
O A:HOH421 2.2 33.8 1.0
NE2 F:HIS155 2.3 30.9 1.0
NE2 A:HIS153 2.3 24.2 1.0
O A:HOH332 2.4 21.9 1.0
O A:HOH368 2.4 30.5 1.0
O F:HOH391 2.4 29.7 1.0
CD2 F:HIS155 3.2 29.1 1.0
CE1 F:HIS155 3.3 26.1 1.0
CD2 A:HIS153 3.3 23.8 1.0
CE1 A:HIS153 3.3 20.7 1.0
O A:HOH436 4.0 46.8 1.0
NE2 A:GLN137 4.1 17.4 1.0
O A:HOH306 4.1 33.4 1.0
O F:HOH326 4.2 18.1 1.0
CG F:HIS155 4.3 32.2 1.0
ND1 F:HIS155 4.3 26.2 1.0
NE A:ARG39 4.4 55.1 1.0
ND1 A:HIS153 4.4 20.2 1.0
CG A:HIS153 4.4 22.9 1.0
O F:HOH394 4.7 34.8 1.0
NH2 A:ARG39 4.8 46.0 1.0
O A:HOH410 4.8 28.4 1.0
CZ A:ARG39 5.0 54.8 1.0

Iron binding site 2 out of 156 in 5d8y

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Iron binding site 2 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) 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 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:36.4
occ:1.00
O Q:HOH365 2.3 25.2 1.0
O Q:HOH400 2.3 35.5 1.0
O Q:HOH332 2.3 28.1 1.0
NE2 Q:HIS153 2.3 22.1 1.0
NE2 A:HIS155 2.4 28.9 1.0
O A:HOH432 2.5 33.9 1.0
CD2 A:HIS155 3.2 29.1 1.0
CD2 Q:HIS153 3.3 23.4 1.0
CE1 Q:HIS153 3.3 28.2 1.0
CE1 A:HIS155 3.3 31.6 1.0
NE2 Q:GLN137 4.1 19.5 1.0
O A:HOH347 4.1 24.0 1.0
CE A:MET154 4.3 37.0 1.0
CG A:HIS155 4.4 29.9 1.0
ND1 Q:HIS153 4.4 24.3 1.0
ND1 A:HIS155 4.4 32.8 1.0
CG Q:HIS153 4.4 27.1 1.0
NE Q:ARG39 4.5 58.4 1.0
O A:HOH425 4.7 33.1 1.0
O Q:HOH385 4.9 22.0 1.0

Iron binding site 3 out of 156 in 5d8y

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Iron binding site 3 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) 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 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:33.1
occ:1.00
OE1 A:GLU51 2.2 26.7 1.0
OE1 A:GLU18 2.2 32.3 1.0
OE1 A:GLU127 2.2 37.7 1.0
ND1 A:HIS54 2.3 21.0 1.0
O A:ACT209 2.4 32.6 1.0
OE2 A:GLU18 2.4 22.1 1.0
CD A:GLU18 2.6 23.3 1.0
CD A:GLU127 3.0 33.5 1.0
OE2 A:GLU127 3.1 28.9 1.0
CE1 A:HIS54 3.2 21.7 1.0
CD A:GLU51 3.2 27.1 1.0
CG A:HIS54 3.4 19.5 1.0
C A:ACT209 3.4 36.7 1.0
OXT A:ACT209 3.6 30.5 1.0
O A:HOH318 3.7 29.6 1.0
CB A:HIS54 3.7 16.9 1.0
OE2 A:GLU51 3.8 34.4 1.0
FE A:FE2205 3.8 39.1 1.0
CG A:GLU18 4.1 20.1 1.0
CA A:GLU51 4.2 22.9 1.0
CG2 A:ILE123 4.2 26.9 1.0
CG A:GLU51 4.3 19.1 1.0
CB A:GLU51 4.3 18.9 1.0
NE2 A:HIS54 4.3 23.0 1.0
CD2 A:HIS54 4.5 18.4 1.0
CG A:GLU127 4.5 28.1 1.0
CH3 A:ACT209 4.7 35.4 1.0
CB A:GLU18 4.8 16.6 1.0
CA A:GLU18 4.9 15.9 1.0
CE1 A:HIS130 5.0 31.5 1.0

Iron binding site 4 out of 156 in 5d8y

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Iron binding site 4 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) 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 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:45.2
occ:1.00
NE2 A:HIS10 2.3 33.7 1.0
O A:HOH412 2.4 39.0 1.0
O A:HOH340 2.4 31.9 1.0
O A:HOH426 2.4 34.0 1.0
ND1 A:HIS107 2.5 33.4 1.0
O A:HOH422 2.5 32.5 1.0
CE1 A:HIS10 3.2 26.7 1.0
CG A:HIS107 3.4 29.9 1.0
CD2 A:HIS10 3.4 27.2 1.0
CE1 A:HIS107 3.5 49.0 1.0
CB A:HIS107 3.6 24.6 1.0
O A:HOH411 4.3 34.2 1.0
ND1 A:HIS10 4.3 27.2 1.0
O A:GLU103 4.5 20.3 1.0
CG A:HIS10 4.5 24.3 1.0
CD2 A:HIS107 4.6 36.6 1.0
NE2 A:HIS107 4.6 41.4 1.0
CA A:HIS107 4.8 19.6 1.0

Iron binding site 5 out of 156 in 5d8y

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Iron binding site 5 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) 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 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:39.1
occ:1.00
OE2 A:GLU127 2.2 28.9 1.0
OE1 A:GLU94 2.2 26.8 1.0
OE2 A:GLU51 2.3 34.4 1.0
ND1 A:HIS130 2.3 28.2 1.0
OXT A:ACT209 2.4 30.5 1.0
OE2 A:GLU94 2.5 22.5 1.0
CD A:GLU94 2.7 26.9 1.0
CE1 A:HIS130 3.0 31.5 1.0
CD A:GLU51 3.1 27.1 1.0
CD A:GLU127 3.2 33.5 1.0
OE1 A:GLU51 3.2 26.7 1.0
C A:ACT209 3.5 36.7 1.0
CG A:HIS130 3.5 33.9 1.0
OE1 A:GLU127 3.7 37.7 1.0
O A:ACT209 3.7 32.6 1.0
FE A:FE2203 3.8 33.1 1.0
CB A:HIS130 3.9 17.8 1.0
CG A:GLU94 4.2 23.9 1.0
NE2 A:HIS130 4.2 30.6 1.0
CA A:GLU127 4.3 17.6 1.0
CE2 A:TYR25 4.3 19.3 1.0
CG A:GLU127 4.3 28.1 1.0
OH A:TYR25 4.3 26.4 1.0
CB A:GLU127 4.4 20.8 1.0
O A:HOH419 4.4 33.6 1.0
CD2 A:HIS130 4.5 29.0 1.0
CG A:GLU51 4.5 19.1 1.0
CH3 A:ACT209 4.8 35.4 1.0
CZ A:TYR25 4.9 24.3 1.0

Iron binding site 6 out of 156 in 5d8y

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Iron binding site 6 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) 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 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:60.0
occ:1.00
O B:HOH352 2.4 35.0 1.0
O J:HOH310 2.4 34.8 1.0
O B:HOH337 2.4 36.7 1.0
O A:HOH312 2.4 41.8 1.0
OD1 B:ASP34 3.7 33.8 1.0
OD2 B:ASP34 3.9 33.2 1.0
OD1 J:ASP132 4.0 26.1 1.0
CG B:ASP34 4.1 19.8 1.0
OE1 J:GLU135 4.1 29.5 1.0
O J:HOH409 4.2 31.5 1.0
O B:ASP34 4.3 20.9 1.0
O A:LEU63 4.6 20.9 1.0
O A:PHE64 4.7 20.3 1.0
OG1 J:THR136 4.7 21.8 1.0
CA A:PHE64 4.8 23.0 1.0
CB J:GLU135 4.8 23.7 1.0
CD1 A:PHE64 4.8 21.3 1.0
O A:HOH362 4.9 41.4 1.0
N A:MET1 5.0 33.0 1.0

Iron binding site 7 out of 156 in 5d8y

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Iron binding site 7 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) 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 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:62.1
occ:1.00
O A:HOH336 2.3 31.1 1.0
O A:HOH321 2.4 32.9 1.0
O F:HOH303 2.4 53.5 1.0
O E:HOH304 2.4 33.5 1.0
OD1 F:ASP34 3.7 32.3 1.0
OD2 F:ASP34 3.7 34.4 1.0
CG F:ASP34 4.0 24.2 1.0
O A:HOH435 4.0 42.6 1.0
OD1 A:ASP132 4.1 25.3 1.0
OE1 A:GLU135 4.2 28.4 1.0
O F:ASP34 4.3 24.5 1.0
OG1 A:THR136 4.5 23.1 1.0
O E:PHE64 4.6 20.4 1.0
O E:LEU63 4.7 21.3 1.0
CB A:GLU135 4.8 19.1 1.0
CA E:PHE64 4.8 21.0 1.0
O E:HOH359 4.8 45.0 1.0
CD1 E:PHE64 5.0 19.8 1.0

Iron binding site 8 out of 156 in 5d8y

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Iron binding site 8 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:95.2
occ:1.00
OD2 A:ASP118 2.4 44.3 1.0
OE2 J:GLU125 3.2 58.8 1.0
OD2 A:ASP122 3.3 42.6 1.0
CG A:ASP118 3.5 36.2 1.0
OE1 J:GLU125 3.8 47.6 1.0
CD J:GLU125 3.9 52.9 1.0
OD1 A:ASP118 4.1 42.1 1.0
NZ J:LYS121 4.2 56.9 1.0
CG A:ASP122 4.3 31.7 1.0
OD1 A:ASP122 4.4 36.1 1.0
O A:HOH369 4.5 29.8 1.0
CB A:ASP118 4.7 25.0 1.0

Iron binding site 9 out of 156 in 5d8y

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Iron binding site 9 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:41.6
occ:1.00
O B:HOH405 2.2 32.0 1.0
O B:HOH330 2.2 25.4 1.0
NE2 C:HIS155 2.3 33.1 1.0
O B:HOH367 2.3 27.1 1.0
NE2 B:HIS153 2.4 23.2 1.0
O C:HOH391 2.5 29.5 1.0
CD2 C:HIS155 3.2 31.9 1.0
CD2 B:HIS153 3.3 23.6 1.0
CE1 C:HIS155 3.4 32.1 1.0
CE1 B:HIS153 3.4 23.0 1.0
NE2 B:GLN137 4.0 20.7 1.0
O B:HOH306 4.1 33.3 1.0
O B:HOH422 4.2 41.8 1.0
O C:HOH319 4.2 19.1 1.0
CG C:HIS155 4.4 29.9 1.0
ND1 C:HIS155 4.4 32.4 1.0
ND1 B:HIS153 4.4 27.2 1.0
CG B:HIS153 4.5 24.3 1.0
NE B:ARG39 4.5 47.4 1.0
O C:HOH392 4.6 30.6 1.0
O B:HOH399 4.9 28.0 1.0
OH B:TYR149 5.0 26.4 1.0
CD B:GLN137 5.0 21.5 1.0

Iron binding site 10 out of 156 in 5d8y

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Iron binding site 10 out of 156 in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:40.0
occ:1.00
NE2 B:HIS155 2.3 32.4 1.0
O J:HOH367 2.3 24.4 1.0
O J:HOH394 2.4 32.1 1.0
O B:HOH408 2.4 31.9 1.0
NE2 J:HIS153 2.4 30.6 1.0
O J:HOH393 2.5 36.7 1.0
CD2 B:HIS155 3.2 36.2 1.0
CE1 B:HIS155 3.3 27.8 1.0
CE1 J:HIS153 3.3 28.3 1.0
CD2 J:HIS153 3.3 26.0 1.0
O J:HOH313 4.0 42.0 1.0
O B:HOH361 4.1 31.6 1.0
NE2 J:GLN137 4.1 23.0 1.0
O J:HOH411 4.1 45.7 1.0
NE J:ARG39 4.4 55.2 1.0
ND1 B:HIS155 4.4 40.3 1.0
CG B:HIS155 4.4 41.7 1.0
ND1 J:HIS153 4.4 25.3 1.0
CG J:HIS153 4.5 26.0 1.0
O B:HOH407 4.8 36.2 1.0
O J:HOH368 4.9 30.0 1.0
CD J:ARG39 5.0 44.0 1.0
NH2 J:ARG39 5.0 41.1 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 15:59:18 2020

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