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Barium in PDB 6l7u: Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data

Protein crystallography data

The structure of Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data, PDB code: 6l7u was solved by N.Kuwabara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.24 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.147, 119.241, 255.839, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.4

Other elements in 6l7u:

The structure of Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data (pdb code 6l7u). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 4 binding sites of Barium where determined in the Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data, PDB code: 6l7u:
Jump to Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in 6l7u

Go back to Barium Binding Sites List in 6l7u
Barium binding site 1 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba503

b:0.6
occ:1.00
O A:HOH696 3.0 70.0 1.0
O A:HOH680 3.5 56.5 1.0
OD2 A:ASP364 4.0 70.1 1.0
OD1 A:ASP362 4.0 63.9 1.0
OD2 A:ASP360 4.9 62.7 1.0
CG A:ASP362 4.9 58.2 1.0
OD2 A:ASP362 4.9 63.3 1.0

Barium binding site 2 out of 4 in 6l7u

Go back to Barium Binding Sites List in 6l7u
Barium binding site 2 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba503

b:0.8
occ:1.00
O B:HOH616 3.1 62.6 1.0
O B:HOH677 3.3 57.6 1.0
OD1 B:ASP362 3.6 67.8 1.0
O B:HOH607 3.6 52.2 1.0
OD2 B:ASP364 3.7 62.5 1.0
OD2 B:ASP360 4.0 74.6 1.0
CG B:ASP362 4.4 58.5 1.0
OD2 B:ASP362 4.4 66.3 1.0
CG B:ASP360 4.6 66.6 1.0
OD1 B:ASP360 4.6 69.0 1.0
N B:GLY345 4.9 45.5 1.0
CG B:ASP364 4.9 55.9 1.0
CA B:GLY345 4.9 36.5 1.0

Barium binding site 3 out of 4 in 6l7u

Go back to Barium Binding Sites List in 6l7u
Barium binding site 3 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba503

b:0.4
occ:1.00
O C:HOH698 3.4 60.5 1.0
OD2 C:ASP364 4.0 62.4 1.0
O C:HOH673 4.0 51.1 1.0
OD1 C:ASP362 4.4 61.1 1.0
O C:HOH681 4.5 59.3 1.0
OD2 C:ASP360 4.8 60.9 1.0

Barium binding site 4 out of 4 in 6l7u

Go back to Barium Binding Sites List in 6l7u
Barium binding site 4 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba504

b:0.3
occ:1.00
O D:HOH610 3.0 61.5 1.0
O D:HOH675 3.7 56.2 1.0
OD2 D:ASP364 4.1 69.0 1.0
OD1 D:ASP362 4.2 61.5 1.0
OD2 D:ASP360 4.4 65.3 1.0
OD1 D:ASP360 4.6 63.7 1.0
N D:GLY345 4.6 53.1 1.0
CG D:ASP360 4.6 61.0 1.0
CA D:GLY345 4.7 44.6 1.0

Reference:

K.Kobayashi, M.Kanagawa, H.Tsumoto, R.Kato, H.Manya, T.Endo, T.Senda, T.Toda, N.Kuwabara, R.Imae, T.Tanaka, M.Mizuno. Crystal Structures of Fukutin-Related Protein (Fkrp), A Ribitol-Phosphate Transferase Related to Muscular Dystrophy Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-019-14220-Z
Page generated: Sat Dec 12 01:58:10 2020

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