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Zinc in PDB 6kak: Crystal Structure of Fkrp in Complex with Mg Ion

Protein crystallography data

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

Resolution Low / High (Å) 49.41 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.822, 119.419, 258.075, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.7

Other elements in 6kak:

The structure of Crystal Structure of Fkrp in Complex with Mg Ion also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6kak

Go back to Zinc Binding Sites List in 6kak
Zinc binding site 1 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:29.8
occ:1.00
 SG A:CYS318 2.4 28.9 1.0
SG A:CYS317 2.4 25.7 1.0
SG A:CYS296 2.4 30.4 1.0
SG A:CYS289 2.4 29.4 1.0
N A:CYS318 3.1 29.2 1.0
CB A:CYS296 3.4 30.9 1.0
CB A:CYS289 3.4 28.4 1.0
CB A:CYS317 3.4 30.2 1.0
CB A:CYS318 3.5 25.2 1.0
CA A:CYS318 3.6 25.6 1.0
C A:CYS317 3.6 31.4 1.0
N A:CYS289 3.7 30.5 1.0
N A:CYS296 3.9 30.9 1.0
CB A:PRO315 3.9 32.5 1.0
CA A:CYS317 4.0 30.4 1.0
CA A:CYS289 4.1 29.0 1.0
CA A:CYS296 4.2 33.3 1.0
O A:CYS317 4.4 28.8 1.0
N A:CYS317 4.5 28.9 1.0
CG A:PRO315 4.6 31.2 1.0
C A:GLY288 4.8 32.3 1.0
C A:CYS289 4.8 30.8 1.0
O A:CYS289 4.9 27.5 1.0
CA A:GLY288 4.9 29.6 1.0
O A:PRO315 4.9 27.4 1.0
C A:ARG295 5.0 30.4 1.0

Zinc binding site 2 out of 4 in 6kak

Go back to Zinc Binding Sites List in 6kak
Zinc binding site 2 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:38.2
occ:1.00
 SG B:CYS318 2.3 35.9 1.0
SG B:CYS289 2.3 48.5 1.0
SG B:CYS317 2.4 36.9 1.0
SG B:CYS296 2.5 34.7 1.0
CB B:CYS289 2.9 36.8 1.0
N B:CYS318 3.0 31.0 1.0
CB B:CYS296 3.4 36.9 1.0
CB B:CYS317 3.5 37.2 1.0
CB B:CYS318 3.5 32.6 1.0
N B:CYS289 3.5 40.0 1.0
CA B:CYS318 3.6 30.7 1.0
C B:CYS317 3.7 32.7 1.0
CA B:CYS289 3.7 41.4 1.0
N B:CYS296 4.0 40.1 1.0
CB B:PRO315 4.0 31.0 1.0
CA B:CYS317 4.1 32.5 1.0
CA B:CYS296 4.3 39.6 1.0
O B:CYS317 4.4 35.4 1.0
N B:CYS317 4.5 32.6 1.0
C B:GLY288 4.6 45.3 1.0
CG B:PRO315 4.7 31.7 1.0
NE B:ARG275 5.0 34.9 1.0
CA B:GLY288 5.0 40.2 1.0
O B:PRO315 5.0 35.2 1.0

Zinc binding site 3 out of 4 in 6kak

Go back to Zinc Binding Sites List in 6kak
Zinc binding site 3 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:30.9
occ:1.00
 SG C:CYS318 2.3 27.9 1.0
SG C:CYS289 2.4 29.8 1.0
SG C:CYS317 2.4 26.4 1.0
SG C:CYS296 2.4 30.3 1.0
N C:CYS318 3.1 28.6 1.0
CB C:CYS289 3.4 29.9 1.0
CB C:CYS296 3.4 32.7 1.0
CB C:CYS317 3.5 26.1 1.0
CB C:CYS318 3.5 20.9 1.0
CA C:CYS318 3.6 23.8 1.0
C C:CYS317 3.7 34.3 1.0
N C:CYS289 3.7 28.2 1.0
N C:CYS296 3.9 30.1 1.0
CB C:PRO315 3.9 31.8 1.0
CA C:CYS317 4.1 30.4 1.0
CA C:CYS289 4.1 28.3 1.0
CA C:CYS296 4.2 33.6 1.0
O C:CYS317 4.4 31.0 1.0
N C:CYS317 4.5 26.0 1.0
CG C:PRO315 4.6 27.5 1.0
C C:GLY288 4.8 32.9 1.0
C C:CYS289 4.9 31.8 1.0
O C:PRO315 4.9 25.8 1.0
CA C:GLY288 4.9 30.3 1.0
C C:ARG295 5.0 30.6 1.0
O C:CYS289 5.0 31.6 1.0

Zinc binding site 4 out of 4 in 6kak

Go back to Zinc Binding Sites List in 6kak
Zinc binding site 4 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:33.2
occ:1.00
 SG D:CYS289 2.3 34.9 1.0
SG D:CYS318 2.3 38.0 1.0
SG D:CYS317 2.4 31.4 1.0
SG D:CYS296 2.4 33.7 1.0
N D:CYS318 3.0 29.4 1.0
CB D:CYS289 3.3 33.8 1.0
CB D:CYS296 3.4 35.8 1.0
CB D:CYS317 3.5 28.9 1.0
CB D:CYS318 3.5 33.5 1.0
CA D:CYS318 3.5 31.7 1.0
C D:CYS317 3.6 31.1 1.0
N D:CYS289 3.7 34.4 1.0
N D:CYS296 3.9 37.3 1.0
CA D:CYS317 4.0 26.7 1.0
CB D:PRO315 4.1 34.2 1.0
CA D:CYS289 4.1 35.3 1.0
CA D:CYS296 4.2 39.8 1.0
O D:CYS317 4.3 33.5 1.0
N D:CYS317 4.5 31.1 1.0
O D:PRO315 4.8 35.4 1.0
CG D:PRO315 4.8 34.1 1.0
C D:GLY288 4.8 38.3 1.0
C D:CYS289 4.9 37.3 1.0
C D:ARG295 4.9 42.4 1.0
O D:CYS289 5.0 35.6 1.0
CA D:ARG295 5.0 41.3 1.0
CA D:GLY288 5.0 34.8 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: Tue Oct 29 01:35:17 2024

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