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Zinc in PDB 6l7t: Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote Data

Protein crystallography data

The structure of Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote Data, PDB code: 6l7t was solved by N.Kuwabara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.05 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.999, 119.480, 257.789, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21

Other elements in 6l7t:

The structure of Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote Data also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote Data (pdb code 6l7t). 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 Mg Ion, Zinc Low Remote Data, PDB code: 6l7t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6l7t

Go back to Zinc Binding Sites List in 6l7t
Zinc binding site 1 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote 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 Mg Ion, Zinc Low Remote Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:35.6
occ:1.00
SG A:CYS317 2.3 31.9 1.0
SG A:CYS289 2.3 49.0 1.0
SG A:CYS318 2.4 29.6 1.0
SG A:CYS296 2.4 31.9 1.0
N A:CYS318 3.1 28.9 1.0
CB A:CYS289 3.4 51.6 1.0
CB A:CYS317 3.4 29.6 1.0
CB A:CYS296 3.4 29.8 1.0
CB A:CYS318 3.5 28.6 1.0
CA A:CYS318 3.5 29.5 1.0
C A:CYS317 3.6 31.0 1.0
N A:CYS289 3.7 31.2 1.0
N A:CYS296 3.9 30.2 1.0
CB A:PRO315 4.0 27.4 1.0
CA A:CYS317 4.0 30.0 1.0
CA A:CYS289 4.1 33.6 1.0
CA A:CYS296 4.3 29.6 1.0
O A:CYS317 4.4 31.2 1.0
N A:CYS317 4.5 28.4 1.0
CG A:PRO315 4.7 29.0 1.0
C A:GLY288 4.8 33.2 1.0
C A:CYS289 4.8 33.2 1.0
O A:CYS289 4.9 32.2 1.0
CA A:GLY288 4.9 28.4 1.0
O A:HOH822 5.0 40.8 1.0
O A:PRO315 5.0 30.4 1.0
C A:ARG295 5.0 34.0 1.0

Zinc binding site 2 out of 4 in 6l7t

Go back to Zinc Binding Sites List in 6l7t
Zinc binding site 2 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote 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 Mg Ion, Zinc Low Remote Data within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:47.9
occ:1.00
SG B:CYS318 2.3 40.5 1.0
SG B:CYS289 2.3 52.8 1.0
SG B:CYS317 2.4 41.7 1.0
SG B:CYS296 2.4 42.8 1.0
CB B:CYS289 3.0 52.1 1.0
CB B:CYS296 3.3 41.8 1.0
N B:CYS318 3.3 33.9 1.0
CB B:CYS318 3.4 34.5 1.0
N B:CYS296 3.4 44.2 1.0
CB B:CYS317 3.5 43.1 1.0
CA B:CYS318 3.6 32.0 1.0
C B:CYS317 3.8 39.9 1.0
N B:CYS289 3.8 51.0 1.0
CA B:CYS289 3.9 50.0 1.0
CA B:CYS296 3.9 43.1 1.0
CA B:CYS317 4.2 44.0 1.0
O B:CYS317 4.4 41.7 1.0
C B:ARG295 4.4 47.5 1.0
CA B:ARG295 4.6 47.4 1.0
CB B:PRO315 4.6 30.7 1.0
CD1 B:LEU413 4.7 46.7 1.0
C B:GLY288 4.9 49.8 1.0
N B:CYS317 5.0 48.3 1.0

Zinc binding site 3 out of 4 in 6l7t

Go back to Zinc Binding Sites List in 6l7t
Zinc binding site 3 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote 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 Mg Ion, Zinc Low Remote Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:36.2
occ:1.00
SG C:CYS317 2.3 34.9 1.0
SG C:CYS296 2.4 32.3 1.0
SG C:CYS318 2.4 25.4 1.0
SG C:CYS289 2.4 35.5 1.0
N C:CYS318 3.1 24.5 1.0
CB C:CYS289 3.4 38.3 1.0
CB C:CYS296 3.4 33.5 1.0
CB C:CYS317 3.4 25.9 1.0
CB C:CYS318 3.5 31.4 1.0
CA C:CYS318 3.6 27.6 1.0
C C:CYS317 3.7 28.3 1.0
N C:CYS289 3.7 33.1 1.0
N C:CYS296 3.8 34.2 1.0
CB C:PRO315 3.9 23.4 1.0
CA C:CYS317 4.1 28.3 1.0
CA C:CYS289 4.1 36.0 1.0
CA C:CYS296 4.2 35.5 1.0
O C:CYS317 4.4 28.5 1.0
N C:CYS317 4.5 25.6 1.0
CG C:PRO315 4.6 24.1 1.0
C C:GLY288 4.8 32.9 1.0
C C:CYS289 4.9 37.5 1.0
C C:ARG295 4.9 35.8 1.0
O C:CYS289 4.9 39.5 1.0
CA C:GLY288 4.9 28.1 1.0
O C:PRO315 5.0 30.6 1.0

Zinc binding site 4 out of 4 in 6l7t

Go back to Zinc Binding Sites List in 6l7t
Zinc binding site 4 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion, Zinc Low Remote 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 Mg Ion, Zinc Low Remote Data within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:40.9
occ:1.00
SG D:CYS318 2.3 35.6 1.0
SG D:CYS289 2.3 33.4 1.0
SG D:CYS317 2.3 31.2 1.0
SG D:CYS296 2.4 42.7 1.0
N D:CYS318 3.1 29.4 1.0
CB D:CYS289 3.3 41.3 1.0
CB D:CYS296 3.4 41.7 1.0
CB D:CYS317 3.4 29.3 1.0
CB D:CYS318 3.5 35.3 1.0
CA D:CYS318 3.6 30.4 1.0
C D:CYS317 3.6 32.6 1.0
N D:CYS289 3.7 34.6 1.0
N D:CYS296 3.8 45.1 1.0
CA D:CYS317 4.1 28.2 1.0
CA D:CYS289 4.1 39.8 1.0
CB D:PRO315 4.2 33.6 1.0
CA D:CYS296 4.2 44.2 1.0
O D:CYS317 4.3 30.6 1.0
N D:CYS317 4.5 32.4 1.0
C D:GLY288 4.8 34.1 1.0
C D:ARG295 4.8 46.2 1.0
CG D:PRO315 4.8 35.4 1.0
C D:CYS289 4.9 42.3 1.0
O D:PRO315 4.9 38.6 1.0
CA D:ARG295 4.9 42.8 1.0
CA D:GLY288 4.9 29.1 1.0
O D:CYS289 4.9 45.1 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 12:13:50 2020

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