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Barium in PDB 6kam: Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor

Protein crystallography data

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

Resolution Low / High (Å) 45.69 / 2.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.571, 119.240, 254.646, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.9

Other elements in 6kam:

The structure of Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor 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, Cdp-Ribtol, and Sugar Acceptor (pdb code 6kam). 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, Cdp-Ribtol, and Sugar Acceptor, PDB code: 6kam:
Jump to Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in 6kam

Go back to Barium Binding Sites List in 6kam
Barium binding site 1 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba506

b:0.2
occ:1.00
O2A A:CDP504 2.6 91.4 1.0
OD1 A:ASP362 2.6 69.0 1.0
O3B A:CDP504 2.7 95.1 1.0
OD1 A:ASP360 2.9 69.7 1.0
PA A:CDP504 3.2 91.5 1.0
OD2 A:ASP364 3.3 76.7 1.0
OD2 A:ASP360 3.3 71.2 1.0
O5' A:CDP504 3.4 87.6 1.0
O3A A:CDP504 3.4 94.5 1.0
CG A:ASP360 3.5 68.0 1.0
PB A:CDP504 3.6 95.9 1.0
CG A:ASP362 3.8 66.0 1.0
O A:ASP362 4.1 60.5 1.0
C5' A:CDP504 4.3 84.4 1.0
OD2 A:ASP362 4.4 67.4 1.0
C4' A:CDP504 4.4 82.0 1.0
CG A:ASP364 4.5 74.5 1.0
O1B A:CDP504 4.5 96.9 1.0
N A:ASP362 4.6 63.5 1.0
C A:ASP362 4.6 59.4 1.0
CA A:GLY345 4.6 60.0 1.0
N A:GLY345 4.6 63.5 1.0
O1A A:CDP504 4.7 97.2 1.0
O3' A:CDP504 4.7 80.3 1.0
CZ A:TYR361 4.8 82.2 1.0
O2B A:CDP504 4.8 98.8 1.0
CB A:ASP362 4.8 63.1 1.0
CE2 A:TYR361 4.9 79.5 1.0
C3' A:CDP504 4.9 81.1 1.0
CA A:ASP362 4.9 61.4 1.0
CB A:ASP360 4.9 63.5 1.0

Barium binding site 2 out of 4 in 6kam

Go back to Barium Binding Sites List in 6kam
Barium binding site 2 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba505

b:0.8
occ:1.00
O2A B:CDP503 2.5 56.6 1.0
OD1 B:ASP362 2.5 53.1 1.0
OD2 B:ASP364 2.6 65.6 1.0
O1B B:CDP503 2.8 64.6 1.0
OD2 B:ASP360 3.3 65.8 1.0
OD1 B:ASP360 3.4 64.9 1.0
O B:ASP362 3.4 51.5 1.0
CG B:ASP360 3.7 63.5 1.0
CG B:ASP362 3.7 54.6 1.0
PA B:CDP503 3.8 59.3 1.0
CG B:ASP364 3.8 63.8 1.0
C B:ASP362 4.0 52.5 1.0
PB B:CDP503 4.0 68.1 1.0
O3A B:CDP503 4.2 64.0 1.0
N B:GLY345 4.2 46.0 1.0
O5' B:CDP503 4.3 59.4 1.0
CA B:GLY345 4.4 42.0 1.0
OD1 B:ASP364 4.4 66.5 1.0
OD2 B:ASP362 4.4 57.5 1.0
N B:ASP362 4.5 57.2 1.0
CA B:ASP362 4.6 55.9 1.0
N B:VAL363 4.7 52.2 1.0
CB B:ASP362 4.8 55.5 1.0
N B:SER346 4.8 44.1 1.0
CB B:ASP364 4.8 60.3 1.0
N B:ASP364 4.8 54.2 1.0
C B:GLY345 4.9 42.2 1.0
CA B:VAL363 4.9 52.4 1.0
OG B:SER346 4.9 53.1 1.0
C4' B:CDP503 4.9 55.7 1.0
O3B B:CDP503 4.9 66.7 1.0
O2B B:CDP503 5.0 77.2 1.0
O1A B:CDP503 5.0 59.7 1.0
C B:VAL363 5.0 54.1 1.0

Barium binding site 3 out of 4 in 6kam

Go back to Barium Binding Sites List in 6kam
Barium binding site 3 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba506

b:0.7
occ:1.00
OD1 C:ASP362 2.6 73.8 1.0
OD2 C:ASP364 2.6 72.0 1.0
O3B C:CDP504 2.7 97.4 1.0
O2A C:CDP504 2.7 98.7 1.0
OD2 C:ASP360 3.2 61.5 1.0
PA C:CDP504 3.4 94.2 1.0
O5' C:CDP504 3.4 88.3 1.0
OD1 C:ASP360 3.5 58.7 1.0
O3A C:CDP504 3.7 98.3 1.0
PB C:CDP504 3.7 99.3 1.0
CG C:ASP360 3.8 58.7 1.0
O C:ASP362 3.8 62.0 1.0
CG C:ASP362 3.8 71.9 1.0
CG C:ASP364 3.9 71.1 1.0
N C:GLY345 4.3 65.2 1.0
C C:ASP362 4.3 61.9 1.0
OD2 C:ASP362 4.4 75.9 1.0
C5' C:CDP504 4.6 81.9 1.0
CA C:GLY345 4.6 63.5 1.0
O2B C:CDP504 4.7 100.0 1.0
OD1 C:ASP364 4.7 73.5 1.0
CB C:ASP364 4.7 69.6 1.0
N C:ASP362 4.8 61.3 1.0
C5 C:RB0505 4.8 99.4 1.0
O1A C:CDP504 4.8 95.6 1.0
O1B C:CDP504 4.8 99.8 1.0
C4' C:CDP504 4.9 78.0 1.0
CA C:ASP362 4.9 62.8 1.0
CB C:ASP362 5.0 67.2 1.0
N C:ASP364 5.0 66.2 1.0
N C:VAL363 5.0 61.4 1.0

Barium binding site 4 out of 4 in 6kam

Go back to Barium Binding Sites List in 6kam
Barium binding site 4 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba506

b:0.5
occ:1.00
OD1 D:ASP362 2.6 82.2 1.0
OD2 D:ASP364 2.6 69.5 1.0
O1B D:CDP504 2.7 77.5 1.0
O2A D:CDP504 2.7 64.4 1.0
OD2 D:ASP360 3.0 67.0 1.0
OD1 D:ASP360 3.5 68.6 1.0
CG D:ASP360 3.6 66.4 1.0
O D:ASP362 3.6 66.7 1.0
CG D:ASP362 3.8 79.5 1.0
PA D:CDP504 3.8 68.2 1.0
CG D:ASP364 3.9 69.7 1.0
O5' D:CDP504 3.9 67.1 1.0
PB D:CDP504 4.0 77.4 1.0
N D:GLY345 4.1 57.1 1.0
CA D:GLY345 4.1 53.3 1.0
C D:ASP362 4.2 67.4 1.0
O3A D:CDP504 4.2 76.3 1.0
OD2 D:ASP362 4.4 83.2 1.0
N D:SER346 4.5 52.1 1.0
C D:GLY345 4.6 52.2 1.0
OD1 D:ASP364 4.7 72.8 1.0
O2B D:CDP504 4.7 82.3 1.0
N D:ASP362 4.7 68.7 1.0
O D:HOH644 4.7 53.3 1.0
CB D:ASP364 4.8 65.9 1.0
C5' D:CDP504 4.8 63.4 1.0
CA D:ASP362 4.8 70.2 1.0
N D:VAL363 4.8 64.7 1.0
C4' D:CDP504 4.8 60.4 1.0
CB D:ASP362 4.9 74.5 1.0
OG D:SER346 4.9 51.0 1.0
N D:ASP364 4.9 62.3 1.0
O D:HOH627 5.0 65.4 1.0
CA D:VAL363 5.0 60.9 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: Wed Jul 10 15:55:24 2024

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