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Zinc 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:

Barium (Ba) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Fkrp in Complex with Ba Ion, Ba-Sad Data, PDB code: 6l7u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6l7u

Go back to Zinc Binding Sites List in 6l7u
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:43.3
occ:1.00
SG A:CYS317 2.3 38.6 1.0
SG A:CYS318 2.4 39.2 1.0
SG A:CYS289 2.5 37.9 1.0
SG A:CYS296 2.5 43.5 1.0
N A:CYS318 3.1 32.7 1.0
CB A:CYS289 3.4 35.4 1.0
CB A:CYS296 3.4 35.0 1.0
CB A:CYS317 3.4 40.5 1.0
CB A:CYS318 3.5 36.7 1.0
CA A:CYS318 3.6 36.7 1.0
C A:CYS317 3.6 38.2 1.0
N A:CYS289 3.7 43.2 1.0
N A:CYS296 3.9 40.4 1.0
CB A:PRO315 4.0 37.2 1.0
CA A:CYS317 4.0 41.7 1.0
CA A:CYS289 4.1 43.8 1.0
CA A:CYS296 4.2 43.5 1.0
O A:CYS317 4.3 35.7 1.0
N A:CYS317 4.5 39.1 1.0
CG A:PRO315 4.6 33.8 1.0
C A:GLY288 4.8 44.8 1.0
C A:CYS289 4.8 44.7 1.0
C A:ARG295 4.9 43.4 1.0
O A:CYS289 4.9 44.5 1.0
O A:PRO315 4.9 37.5 1.0
CA A:GLY288 5.0 38.6 1.0

Zinc binding site 2 out of 4 in 6l7u

Go back to Zinc Binding Sites List in 6l7u
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:46.5
occ:1.00
SG B:CYS318 2.3 47.5 1.0
SG B:CYS317 2.4 41.2 1.0
SG B:CYS289 2.5 58.0 1.0
SG B:CYS296 2.5 43.6 1.0
CB B:CYS289 2.8 50.3 1.0
N B:CYS318 3.1 37.6 1.0
CB B:CYS318 3.5 40.6 1.0
CB B:CYS296 3.5 40.4 1.0
CA B:CYS318 3.6 38.3 1.0
N B:CYS289 3.6 50.9 1.0
CB B:CYS317 3.6 42.3 1.0
CA B:CYS289 3.7 50.8 1.0
C B:CYS317 3.7 40.0 1.0
N B:CYS296 4.0 54.0 1.0
CB B:PRO315 4.1 37.9 1.0
CA B:CYS317 4.2 36.9 1.0
CA B:CYS296 4.3 46.5 1.0
O B:CYS317 4.5 44.2 1.0
N B:CYS317 4.6 37.5 1.0
C B:GLY288 4.7 50.9 1.0
CG B:PRO315 4.7 38.5 1.0
O B:PRO315 4.9 40.6 1.0
C B:ARG295 5.0 58.2 1.0
NE B:ARG275 5.0 48.5 1.0

Zinc binding site 3 out of 4 in 6l7u

Go back to Zinc Binding Sites List in 6l7u
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:43.9
occ:1.00
SG C:CYS317 2.2 65.4 1.0
SG C:CYS318 2.3 35.3 1.0
SG C:CYS289 2.5 37.4 1.0
SG C:CYS296 2.7 41.9 1.0
N C:CYS318 3.1 39.9 1.0
CB C:CYS296 3.3 44.0 1.0
CB C:CYS317 3.3 52.9 1.0
CB C:CYS289 3.4 37.3 1.0
CB C:CYS318 3.4 39.8 1.0
CA C:CYS318 3.5 37.7 1.0
C C:CYS317 3.5 44.7 1.0
N C:CYS296 3.8 47.8 1.0
N C:CYS289 3.8 37.4 1.0
CB C:PRO315 4.0 39.9 1.0
CA C:CYS317 4.0 52.0 1.0
O C:CYS317 4.1 40.9 1.0
CA C:CYS296 4.1 47.5 1.0
CA C:CYS289 4.2 45.0 1.0
CG C:PRO315 4.6 37.8 1.0
C C:ARG295 4.8 47.4 1.0
O C:PRO315 4.9 39.1 1.0
C C:GLY288 4.9 45.6 1.0
C C:CYS289 5.0 49.8 1.0
C C:CYS318 5.0 38.9 1.0
N C:CYS317 5.0 49.3 1.0
CA C:ARG295 5.0 44.8 1.0

Zinc binding site 4 out of 4 in 6l7u

Go back to Zinc Binding Sites List in 6l7u
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:46.6
occ:1.00
SG D:CYS318 2.3 44.5 1.0
SG D:CYS289 2.4 43.5 1.0
SG D:CYS317 2.4 40.1 1.0
SG D:CYS296 2.5 39.4 1.0
N D:CYS318 3.0 27.7 1.0
CB D:CYS289 3.3 39.6 1.0
CB D:CYS318 3.4 35.6 1.0
CB D:CYS296 3.4 40.1 1.0
CA D:CYS318 3.5 33.6 1.0
CB D:CYS317 3.5 39.6 1.0
C D:CYS317 3.6 35.2 1.0
N D:CYS289 3.7 40.5 1.0
N D:CYS296 3.9 47.7 1.0
CB D:PRO315 4.1 36.2 1.0
CA D:CYS317 4.1 34.3 1.0
CA D:CYS289 4.1 38.9 1.0
CA D:CYS296 4.2 47.3 1.0
O D:CYS317 4.3 34.8 1.0
N D:CYS317 4.5 39.1 1.0
CG D:PRO315 4.7 37.9 1.0
O D:PRO315 4.8 45.0 1.0
C D:ARG295 4.8 48.1 1.0
C D:GLY288 4.9 37.7 1.0
C D:CYS289 4.9 42.3 1.0
CA D:ARG295 4.9 47.9 1.0
C D:CYS318 5.0 35.7 1.0
O D:CYS289 5.0 39.9 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 Dec 16 12:13:51 2020

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