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Magnesium in PDB 5d8q: 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa

Enzymatic activity of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa

All present enzymatic activity of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa:
1.16.3.1;

Protein crystallography data

The structure of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa, PDB code: 5d8q 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) 48.43 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.864, 169.989, 125.662, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26.3

Other elements in 5d8q:

The structure of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Arsenic (As) 3 atoms
Iron (Fe) 7 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa (pdb code 5d8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa, PDB code: 5d8q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5d8q

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Magnesium binding site 1 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:39.5
occ:1.00
O L:HOH354 2.0 34.1 1.0
O A:HOH349 2.0 36.6 1.0
O B:HOH305 2.1 43.1 1.0
O B:HOH301 2.1 37.0 1.0
O L:HOH317 2.1 40.9 1.0
O L:HOH333 2.1 39.5 1.0
OD1 B:ASP34 3.9 39.9 1.0
OD2 B:ASP34 3.9 39.3 1.0
OD1 L:ASP132 4.0 34.6 1.0
O B:ASP34 4.2 30.3 1.0
OE1 L:GLU135 4.2 36.7 1.0
CG B:ASP34 4.2 36.4 1.0
OG1 L:THR136 4.4 37.4 1.0
O A:PHE64 4.6 32.1 1.0
O A:LEU63 4.7 33.1 1.0
CA A:PHE64 4.8 32.0 1.0
CB L:GLU135 4.8 33.5 1.0
CD1 A:PHE64 4.9 30.6 1.0

Magnesium binding site 2 out of 12 in 5d8q

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Magnesium binding site 2 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:35.2
occ:1.00
O A:HOH375 2.0 30.0 1.0
O K:HOH325 2.0 37.9 1.0
O F:HOH237 2.0 37.7 1.0
O A:HOH314 2.0 35.6 1.0
O A:HOH308 2.1 35.5 1.0
O K:HOH311 2.1 32.0 1.0
OD1 A:ASP132 3.9 30.1 1.0
OE1 A:GLU135 4.1 29.8 1.0
O K:ASP34 4.1 32.2 1.0
OG1 A:THR136 4.1 27.5 1.0
OD2 K:ASP34 4.2 27.6 1.0
OD1 K:ASP34 4.2 34.6 1.0
O F:HOH202 4.4 38.2 1.0
CG K:ASP34 4.5 35.0 1.0
CB A:GLU135 4.6 29.5 1.0
O F:PHE64 4.7 32.7 1.0
N A:THR136 5.0 32.9 1.0

Magnesium binding site 3 out of 12 in 5d8q

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Magnesium binding site 3 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:35.7
occ:1.00
O B:HOH323 2.0 37.6 1.0
O G:HOH226 2.0 29.0 1.0
O G:HOH241 2.1 37.1 1.0
O G:HOH281 2.1 35.6 1.0
O A:HOH306 2.1 28.5 1.0
O A:HOH303 2.2 34.7 1.0
OD1 G:ASP132 3.7 30.5 1.0
OD2 A:ASP34 4.1 32.9 1.0
OE1 G:GLU135 4.1 28.8 1.0
OD1 A:ASP34 4.1 28.1 1.0
OG1 G:THR136 4.2 26.0 1.0
CG A:ASP34 4.4 31.1 1.0
O A:ASP34 4.5 30.4 1.0
O B:PHE64 4.5 25.4 1.0
CB G:GLU135 4.7 25.4 1.0
CD1 B:PHE64 4.7 25.4 1.0
O B:LEU63 4.7 26.7 1.0
CA B:PHE64 4.8 28.4 1.0
N B:MET1 4.8 36.3 1.0
CG G:ASP132 4.9 32.4 1.0

Magnesium binding site 4 out of 12 in 5d8q

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Magnesium binding site 4 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:44.9
occ:1.00
O C:HOH315 2.0 39.1 1.0
O C:HOH309 2.1 46.0 1.0
O E:HOH312 2.1 51.6 1.0
O E:HOH303 2.1 48.3 1.0
O G:HOH269 2.1 40.6 1.0
OD1 E:ASP34 3.9 33.9 1.0
OD1 C:ASP132 4.0 42.0 1.0
OE1 C:GLU135 4.0 45.1 1.0
O E:ASP34 4.1 37.4 1.0
OG1 C:THR136 4.1 36.1 1.0
CB C:GLU135 4.4 40.4 1.0
CG E:ASP34 4.6 35.4 1.0
OD2 E:ASP34 4.7 49.0 1.0
N C:THR136 4.9 40.0 1.0
CD C:GLU135 4.9 47.4 1.0
C C:GLU135 4.9 41.0 1.0
N G:MET1 5.0 45.1 1.0
CD1 G:PHE64 5.0 25.0 1.0

Magnesium binding site 5 out of 12 in 5d8q

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Magnesium binding site 5 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg204

b:38.7
occ:1.00
O B:HOH321 2.0 30.0 1.0
O C:HOH340 2.0 35.9 1.0
O H:HOH302 2.0 33.3 1.0
O B:HOH362 2.0 32.9 1.0
O H:HOH305 2.0 33.3 1.0
O B:HOH330 2.1 34.5 1.0
OD2 H:ASP34 3.7 33.2 1.0
OD1 B:ASP132 3.7 36.1 1.0
OD1 H:ASP34 3.9 32.7 1.0
CG H:ASP34 4.1 34.5 1.0
O H:ASP34 4.2 32.4 1.0
OE1 B:GLU135 4.3 32.9 1.0
O C:PHE64 4.4 31.1 1.0
OG1 B:THR136 4.4 27.5 1.0
O C:LEU63 4.5 28.5 1.0
CD1 C:PHE64 4.6 28.2 1.0
CA C:PHE64 4.6 31.8 1.0
CB B:GLU135 4.8 30.4 1.0
N C:MET1 4.9 40.7 1.0
OE2 C:GLU66 4.9 55.4 1.0
CG B:ASP132 4.9 33.3 1.0
C C:PHE64 5.0 29.8 1.0

Magnesium binding site 6 out of 12 in 5d8q

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Magnesium binding site 6 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:45.7
occ:1.00
O G:HOH207 2.0 37.0 1.0
O G:HOH203 2.0 38.4 1.0
O E:HOH326 2.1 36.5 1.0
O D:HOH334 2.1 35.2 1.0
O G:HOH217 2.1 43.5 1.0
O D:HOH302 2.1 37.1 1.0
OD1 D:ASP132 3.5 43.3 1.0
OE1 D:GLU135 3.7 40.0 1.0
OG1 D:THR136 3.9 31.1 1.0
CB D:GLU135 4.1 32.2 1.0
OD1 G:ASP34 4.2 45.5 1.0
O G:ASP34 4.2 33.2 1.0
OD2 G:ASP34 4.3 45.6 1.0
CG G:ASP34 4.6 41.4 1.0
CD D:GLU135 4.6 37.2 1.0
CG D:ASP132 4.6 42.4 1.0
N D:THR136 4.7 39.0 1.0
O D:ASP132 4.8 35.9 1.0
CD1 E:PHE64 4.9 38.9 1.0
O E:PHE64 4.9 38.5 1.0
N E:MET1 4.9 45.4 1.0
CA D:THR136 5.0 34.2 1.0
C D:GLU135 5.0 43.6 1.0

Magnesium binding site 7 out of 12 in 5d8q

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Magnesium binding site 7 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg201

b:38.8
occ:1.00
O H:HOH303 2.0 41.4 1.0
O C:HOH314 2.1 42.5 1.0
OD2 C:ASP34 4.1 47.8 1.0
O H:PHE64 4.1 34.1 1.0
OE2 H:GLU66 4.4 47.7 1.0
O H:LEU63 4.4 42.3 1.0
O C:ASP34 4.6 37.1 1.0
N H:MET1 4.6 48.1 1.0
CA H:PHE64 4.6 39.9 1.0
OD1 C:ASP34 4.6 48.5 1.0
CG C:ASP34 4.6 45.4 1.0
CD1 H:PHE64 4.8 33.6 1.0
C H:PHE64 4.8 40.5 1.0
CG H:GLU66 4.8 52.8 1.0

Magnesium binding site 8 out of 12 in 5d8q

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Magnesium binding site 8 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg202

b:44.5
occ:1.00
O I:HOH309 2.0 45.4 1.0
O I:HOH313 2.1 42.1 1.0
OD2 I:ASP34 4.2 56.7 1.0
OD1 I:ASP34 4.7 51.1 1.0
O I:ASP34 4.8 51.2 1.0
CG I:ASP34 4.8 48.9 1.0

Magnesium binding site 9 out of 12 in 5d8q

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Magnesium binding site 9 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg203

b:54.5
occ:1.00
O I:HOH314 2.0 40.5 1.0
O J:HOH306 2.0 51.1 1.0
O I:HOH312 2.0 45.1 1.0
O D:HOH329 2.1 58.9 1.0
O J:HOH309 2.2 40.2 1.0
OD1 J:ASP34 3.8 33.4 1.0
OD1 I:ASP132 4.3 36.0 1.0
OD2 J:ASP34 4.3 46.3 1.0
O J:ASP34 4.3 42.7 1.0
OE1 I:GLU135 4.4 54.0 1.0
CG J:ASP34 4.4 45.0 1.0
O D:LEU63 4.6 52.9 1.0
OG1 I:THR136 4.7 53.4 1.0
CB I:GLU135 4.7 45.8 1.0
O D:PHE64 4.7 48.5 1.0
CA D:PHE64 4.9 42.8 1.0

Magnesium binding site 10 out of 12 in 5d8q

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Magnesium binding site 10 out of 12 in the 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 2.20A Resolution Structure of Bfrb (L68A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg202

b:49.5
occ:1.00
O K:HOH302 2.0 34.1 1.0
O D:HOH310 2.0 38.7 1.0
O D:HOH304 2.0 31.0 1.0
O J:HOH326 2.0 37.3 1.0
O D:HOH305 2.1 31.5 1.0
O J:HOH339 2.1 53.0 1.0
OD1 K:ASP132 3.5 29.3 1.0
OD1 D:ASP34 3.8 39.6 1.0
O D:ASP34 3.9 34.0 1.0
OG1 K:THR136 4.0 33.7 1.0
OE1 K:GLU135 4.0 47.3 1.0
OD2 D:ASP34 4.4 36.8 1.0
CG D:ASP34 4.4 39.3 1.0
CB K:GLU135 4.5 37.4 1.0
CG K:ASP132 4.6 32.2 1.0
O J:PHE64 4.8 36.3 1.0
CA J:PHE64 4.9 33.9 1.0
O K:ASP132 5.0 33.3 1.0
O J:LEU63 5.0 37.1 1.0
CD1 J:PHE64 5.0 28.8 1.0
CD K:GLU135 5.0 56.4 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: Mon Dec 14 20:10:34 2020

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