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Potassium 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:

Iron (Fe) 156 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 6 binding sites of Potassium where determined in the 2.05A Resolution Structure of Iron Bound Bfrb (L68A E81A) From Pseudomonas Aeruginosa, PDB code: 5d8y:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5d8y

Go back to Potassium Binding Sites List in 5d8y
Potassium binding site 1 out of 6 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 Potassium with other atoms in the K 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:K210

b:26.9
occ:1.00
 OE1 A:GLN151 2.7 17.4 1.0
OE1 Q:GLN151 2.8 21.0 1.0
OE1 H:GLN151 2.8 19.8 1.0
OE1 F:GLN151 2.8 22.0 1.0
OD1 Q:ASN148 3.0 21.1 1.0
OD1 H:ASN148 3.1 22.1 1.0
OD1 A:ASN148 3.1 21.0 1.0
OD1 F:ASN148 3.2 19.6 1.0
CD A:GLN151 3.7 20.4 1.0
CD Q:GLN151 3.7 21.5 1.0
CD F:GLN151 3.7 17.8 1.0
CD H:GLN151 3.8 18.2 1.0
CG Q:ASN148 3.8 26.0 1.0
CG A:ASN148 3.8 20.5 1.0
CG H:ASN148 3.8 21.1 1.0
O F:HOH374 3.9 41.4 1.0
NE2 F:GLN151 3.9 22.7 1.0
CG F:ASN148 3.9 25.3 1.0
NE2 A:GLN151 3.9 17.1 1.0
NE2 Q:GLN151 3.9 23.2 1.0
NE2 H:GLN151 4.0 26.1 1.0
ND2 A:ASN148 4.2 25.3 1.0
ND2 Q:ASN148 4.2 26.4 1.0
ND2 F:ASN148 4.2 22.0 1.0
ND2 H:ASN148 4.2 19.1 1.0
CB Q:ASN148 4.8 17.9 1.0
CB H:ASN148 4.9 23.4 1.0
CB A:ASN148 4.9 17.8 1.0

Potassium binding site 2 out of 6 in 5d8y

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Potassium binding site 2 out of 6 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 Potassium with other atoms in the K 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
B:K210

b:35.9
occ:1.00
 OE1 B:GLN151 2.8 24.2 1.0
OE1 C:GLN151 2.9 23.9 1.0
OE1 J:GLN151 2.9 25.1 1.0
OE1 W:GLN151 2.9 21.0 1.0
OD1 B:ASN148 3.0 24.1 1.0
OD1 W:ASN148 3.0 22.4 1.0
OD1 C:ASN148 3.1 23.8 1.0
OD1 J:ASN148 3.1 29.8 1.0
CD B:GLN151 3.8 18.4 1.0
CG C:ASN148 3.8 26.3 1.0
CG W:ASN148 3.8 25.4 1.0
CG B:ASN148 3.8 21.2 1.0
CD C:GLN151 3.8 23.7 1.0
CG J:ASN148 3.8 26.8 1.0
CD J:GLN151 3.8 23.3 1.0
CD W:GLN151 3.9 26.0 1.0
NE2 B:GLN151 3.9 23.8 1.0
NE2 C:GLN151 4.0 23.0 1.0
NE2 J:GLN151 4.0 21.0 1.0
ND2 C:ASN148 4.1 31.6 1.0
NE2 W:GLN151 4.1 23.4 1.0
ND2 J:ASN148 4.2 30.3 1.0
ND2 B:ASN148 4.2 25.8 1.0
ND2 W:ASN148 4.2 25.2 1.0
CB W:ASN148 4.9 20.9 1.0
CB J:ASN148 4.9 21.1 1.0
CB B:ASN148 4.9 19.9 1.0
CB C:ASN148 4.9 24.1 1.0

Potassium binding site 3 out of 6 in 5d8y

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Potassium binding site 3 out of 6 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 Potassium with other atoms in the K 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
D:K210

b:32.9
occ:1.00
 OE1 D:GLN151 2.8 20.2 1.0
OE1 T:GLN151 2.8 24.2 1.0
OE1 R:GLN151 2.9 18.7 1.0
OE1 U:GLN151 2.9 23.6 1.0
OD1 U:ASN148 3.0 26.0 1.0
OD1 D:ASN148 3.0 23.7 1.0
OD1 T:ASN148 3.1 23.4 1.0
OD1 R:ASN148 3.1 23.1 1.0
O T:HOH395 3.8 39.8 1.0
CD T:GLN151 3.8 17.5 1.0
CD D:GLN151 3.8 22.8 1.0
CD R:GLN151 3.8 20.7 1.0
CG D:ASN148 3.8 23.1 1.0
CD U:GLN151 3.8 22.3 1.0
CG T:ASN148 3.8 28.5 1.0
CG U:ASN148 3.8 26.5 1.0
CG R:ASN148 3.9 23.9 1.0
NE2 T:GLN151 3.9 25.9 1.0
NE2 R:GLN151 4.0 20.4 1.0
NE2 D:GLN151 4.0 25.9 1.0
NE2 U:GLN151 4.0 25.2 1.0
ND2 D:ASN148 4.2 23.4 1.0
ND2 U:ASN148 4.2 20.2 1.0
ND2 T:ASN148 4.3 26.7 1.0
ND2 R:ASN148 4.3 26.8 1.0
CB T:ASN148 4.9 23.6 1.0
CB D:ASN148 4.9 20.3 1.0
CB U:ASN148 5.0 24.3 1.0

Potassium binding site 4 out of 6 in 5d8y

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Potassium binding site 4 out of 6 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 Potassium with other atoms in the K 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
E:K210

b:39.0
occ:1.00
 OE1 O:GLN151 2.8 27.6 1.0
OE1 I:GLN151 2.9 30.3 1.0
OE1 E:GLN151 2.9 23.5 1.0
OE1 K:GLN151 2.9 24.9 1.0
OD1 E:ASN148 3.0 25.3 1.0
OD1 O:ASN148 3.0 25.9 1.0
OD1 I:ASN148 3.1 28.4 1.0
OD1 K:ASN148 3.1 23.9 1.0
CG O:ASN148 3.7 27.7 1.0
CG E:ASN148 3.8 24.9 1.0
CD I:GLN151 3.8 23.8 1.0
CG K:ASN148 3.8 28.6 1.0
CD O:GLN151 3.8 26.7 1.0
CD E:GLN151 3.8 24.6 1.0
CG I:ASN148 3.8 32.5 1.0
CD K:GLN151 3.9 26.4 1.0
NE2 I:GLN151 3.9 22.3 1.0
NE2 E:GLN151 4.0 27.9 1.0
ND2 O:ASN148 4.1 35.1 1.0
NE2 K:GLN151 4.1 30.9 1.0
NE2 O:GLN151 4.1 21.4 1.0
ND2 E:ASN148 4.2 26.8 1.0
ND2 K:ASN148 4.2 28.2 1.0
ND2 I:ASN148 4.2 33.3 1.0
CB O:ASN148 4.9 23.4 1.0
CB E:ASN148 4.9 24.2 1.0
CB K:ASN148 4.9 22.7 1.0
CB I:ASN148 5.0 24.4 1.0

Potassium binding site 5 out of 6 in 5d8y

Go back to Potassium Binding Sites List in 5d8y
Potassium binding site 5 out of 6 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 Potassium with other atoms in the K 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
G:K210

b:31.5
occ:1.00
 OE1 V:GLN151 2.8 20.0 1.0
OE1 M:GLN151 2.9 22.2 1.0
OE1 P:GLN151 2.9 25.3 1.0
OE1 G:GLN151 2.9 20.5 1.0
OD1 P:ASN148 2.9 24.6 1.0
OD1 G:ASN148 3.0 23.8 1.0
OD1 M:ASN148 3.0 20.6 1.0
OD1 V:ASN148 3.1 23.3 1.0
CG P:ASN148 3.7 32.0 1.0
CG G:ASN148 3.7 26.4 1.0
CD V:GLN151 3.7 19.7 1.0
CG M:ASN148 3.8 26.4 1.0
CD M:GLN151 3.8 21.3 1.0
CG V:ASN148 3.8 29.7 1.0
CD P:GLN151 3.9 23.0 1.0
CD G:GLN151 3.9 26.1 1.0
NE2 V:GLN151 4.0 20.2 1.0
NE2 M:GLN151 4.0 22.9 1.0
ND2 P:ASN148 4.0 25.6 1.0
ND2 G:ASN148 4.1 23.2 1.0
NE2 P:GLN151 4.1 25.9 1.0
ND2 M:ASN148 4.2 20.1 1.0
NE2 G:GLN151 4.2 21.8 1.0
ND2 V:ASN148 4.2 23.9 1.0
CB M:ASN148 4.8 21.9 1.0
CB P:ASN148 4.9 24.5 1.0
CB G:ASN148 4.9 28.7 1.0
CB V:ASN148 5.0 23.9 1.0

Potassium binding site 6 out of 6 in 5d8y

Go back to Potassium Binding Sites List in 5d8y
Potassium binding site 6 out of 6 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 Potassium with other atoms in the K 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
L:K210

b:30.6
occ:1.00
 OE1 X:GLN151 2.8 18.1 1.0
OE1 L:GLN151 2.9 20.1 1.0
OE1 N:GLN151 2.9 19.1 1.0
OE1 S:GLN151 2.9 21.2 1.0
OD1 X:ASN148 3.0 23.0 1.0
OD1 L:ASN148 3.1 20.6 1.0
OD1 S:ASN148 3.1 19.2 1.0
OD1 N:ASN148 3.1 22.9 1.0
CD X:GLN151 3.7 19.3 1.0
CG N:ASN148 3.7 27.1 1.0
CG L:ASN148 3.8 25.6 1.0
CD N:GLN151 3.8 19.6 1.0
CG X:ASN148 3.8 21.1 1.0
CD L:GLN151 3.8 20.0 1.0
CD S:GLN151 3.8 20.4 1.0
NE2 X:GLN151 3.9 21.7 1.0
CG S:ASN148 3.9 24.2 1.0
NE2 N:GLN151 4.0 20.5 1.0
NE2 S:GLN151 4.0 21.2 1.0
O L:HOH375 4.0 39.6 1.0
ND2 N:ASN148 4.0 27.5 1.0
NE2 L:GLN151 4.1 20.4 1.0
ND2 L:ASN148 4.2 21.7 1.0
ND2 S:ASN148 4.2 21.7 1.0
ND2 X:ASN148 4.2 22.5 1.0
CB N:ASN148 4.9 18.9 1.0
CB L:ASN148 4.9 18.2 1.0
CB X:ASN148 4.9 19.6 1.0
CB S:ASN148 5.0 20.1 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: Mon Aug 12 13:11:52 2024

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