Atomistry » Barium » PDB 5wky-7awm » 6kam
Atomistry »
  Barium »
    PDB 5wky-7awm »
      6kam »

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: Sat Dec 12 01:58:06 2020

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy