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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Fkrp in Complex with Mg Ion, PDB code: 6kak:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6kak

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Magnesium binding site 1 out of 7 in the Crystal Structure of Fkrp in Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg504

b:70.6
occ:1.00
 O A:HOH617 2.0 71.7 1.0
O A:HOH687 2.1 70.8 1.0
O A:HOH853 2.2 65.3 1.0
OD2 A:ASP362 2.2 36.4 1.0
O A:HOH800 2.3 44.1 1.0
O A:HOH609 2.3 37.3 1.0
CG A:ASP362 3.2 34.9 1.0
OD1 A:ASP362 3.6 37.9 1.0
OD2 A:ASP416 4.0 46.4 1.0
OD2 A:ASP364 4.1 41.8 1.0
OD1 A:ASP364 4.1 40.1 1.0
NE2 A:HIS414 4.4 44.9 1.0
CG A:ASP364 4.5 41.1 1.0
CB A:ASP362 4.5 27.9 1.0

Magnesium binding site 2 out of 7 in 6kak

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Magnesium binding site 2 out of 7 in the Crystal Structure of Fkrp in Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg505

b:0.8
occ:1.00
 OD2 A:ASP364 3.0 41.8 1.0
N A:SER346 3.3 31.2 1.0
CA A:GLY345 3.5 33.0 1.0
N A:GLY345 3.5 35.9 1.0
OG A:SER346 3.6 32.8 1.0
C A:GLY345 3.6 34.5 1.0
O A:HOH609 3.8 37.3 1.0
OD1 A:ASP362 3.8 37.9 1.0
O A:HOH689 3.8 35.1 1.0
O A:ASP362 3.8 35.1 1.0
CG A:ASP364 4.0 41.1 1.0
OD2 A:ASP360 4.1 58.9 1.0
N A:ASP364 4.2 38.2 1.0
CB A:ASP364 4.2 40.6 1.0
CA A:SER346 4.3 30.3 1.0
O A:HOH697 4.3 28.7 1.0
CB A:SER346 4.5 28.8 1.0
C A:ASP362 4.5 32.1 1.0
O A:GLY345 4.5 34.2 1.0
CA A:VAL363 4.5 32.5 1.0
C A:VAL363 4.6 34.5 1.0
O A:HOH764 4.6 52.0 1.0
O A:GLU343 4.7 43.6 1.0
C A:GLY344 4.7 35.3 1.0
N A:VAL363 4.8 34.6 1.0
CA A:ASP364 4.9 38.5 1.0
CG A:ASP362 4.9 34.9 1.0
CG A:ASP360 5.0 52.5 1.0

Magnesium binding site 3 out of 7 in 6kak

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Magnesium binding site 3 out of 7 in the Crystal Structure of Fkrp in Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg504

b:56.2
occ:1.00
 OD2 B:ASP362 2.1 58.2 1.0
O B:HOH708 2.1 56.6 1.0
O B:HOH602 2.1 53.2 1.0
O B:HOH622 2.3 36.2 1.0
O B:HOH668 2.5 50.3 1.0
CG B:ASP362 3.1 45.1 1.0
OD1 B:ASP362 3.5 49.2 1.0
OD2 B:ASP416 3.9 48.7 1.0
OD1 B:ASP364 3.9 44.1 1.0
OD2 B:ASP364 4.2 44.5 1.0
CB B:ASP362 4.4 34.9 1.0
CG B:ASP364 4.5 42.8 1.0
CE1 B:HIS414 4.6 41.2 1.0
O B:HOH717 4.6 56.8 1.0
CG B:ASP416 5.0 47.1 1.0

Magnesium binding site 4 out of 7 in 6kak

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Magnesium binding site 4 out of 7 in the Crystal Structure of Fkrp in Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg505

b:61.4
occ:1.00
 O B:HOH610 2.3 62.7 1.0
O B:HOH717 2.4 56.8 1.0
OD2 B:ASP364 3.0 44.5 1.0
OD1 B:ASP362 3.0 49.2 1.0
OD2 B:ASP360 3.1 57.6 1.0
O B:HOH622 3.4 36.2 1.0
O B:ASP362 3.4 36.6 1.0
N B:SER346 3.8 28.2 1.0
CA B:GLY345 3.8 32.5 1.0
N B:GLY345 3.8 33.2 1.0
O B:HOH660 3.9 28.8 1.0
OG B:SER346 3.9 33.2 1.0
C B:GLY345 4.0 32.4 1.0
CG B:ASP364 4.0 42.8 1.0
C B:ASP362 4.1 35.5 1.0
CG B:ASP362 4.2 45.1 1.0
CG B:ASP360 4.3 56.0 1.0
N B:ASP364 4.3 30.9 1.0
CA B:VAL363 4.4 29.7 1.0
O B:HOH716 4.5 31.5 1.0
N B:VAL363 4.5 33.0 1.0
CB B:ASP364 4.6 36.2 1.0
C B:VAL363 4.6 34.3 1.0
CA B:SER346 4.7 32.8 1.0
CB B:SER346 4.9 35.0 1.0
O B:GLY345 4.9 31.9 1.0
OD1 B:ASP364 5.0 44.1 1.0
CA B:ASP362 5.0 30.4 1.0
C B:GLY344 5.0 33.5 1.0
OD2 B:ASP362 5.0 58.2 1.0

Magnesium binding site 5 out of 7 in 6kak

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Magnesium binding site 5 out of 7 in the Crystal Structure of Fkrp in Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Fkrp in Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:60.6
occ:1.00
 O C:HOH801 2.1 61.3 1.0
O C:HOH762 2.2 45.1 1.0
O C:HOH620 2.2 41.1 1.0
OD2 C:ASP362 2.3 42.9 1.0
O C:HOH613 2.3 42.0 1.0
CG C:ASP362 3.3 39.9 1.0
OD1 C:ASP362 3.7 39.7 1.0
OD2 C:ASP416 4.2 45.4 1.0
OD1 C:ASP364 4.3 40.5 1.0
OD2 C:ASP364 4.3 42.8 1.0
NE2 C:HIS414 4.5 41.2 1.0
CB C:ASP362 4.6 32.2 1.0
CG C:ASP364 4.8 40.3 1.0

Magnesium binding site 6 out of 7 in 6kak

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Magnesium binding site 6 out of 7 in the Crystal Structure of Fkrp in Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Fkrp in Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:87.3
occ:1.00
 O D:HOH607 2.0 90.6 1.0
O D:HOH606 2.3 44.7 1.0
OD2 D:ASP362 2.3 48.8 1.0
CG D:ASP362 3.4 44.8 1.0
OD1 D:ASP362 3.8 42.4 1.0
OD2 D:ASP416 3.8 59.4 1.0
OD1 D:ASP364 4.1 49.9 1.0
OD2 D:ASP364 4.3 50.1 1.0
NE2 D:HIS414 4.6 50.6 1.0
CG D:ASP364 4.7 51.7 1.0
CB D:ASP362 4.7 40.7 1.0
CG D:ASP416 4.9 54.5 1.0

Magnesium binding site 7 out of 7 in 6kak

Go back to Magnesium Binding Sites List in 6kak
Magnesium binding site 7 out of 7 in the Crystal Structure of Fkrp in Complex with Mg Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Fkrp in Complex with Mg Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg505

b:0.8
occ:1.00
 O D:HOH704 2.0 0.6 1.0
O D:HOH672 2.5 59.2 1.0
O D:ASN61 4.3 35.8 1.0
O D:PRO246 4.4 53.6 1.0
OD1 D:ASP60 4.5 49.8 1.0
O D:HOH785 4.8 38.9 1.0
O D:GLN245 4.8 51.9 1.0
O D:HOH711 4.9 42.7 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 Aug 13 10:26:59 2025

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