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Magnesium in PDB 6kal: Crystal Structure of Fkrp in Complex with Mg Ion and Cmp

Protein crystallography data

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

Resolution Low / High (Å) 48.99 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.583, 118.674, 252.695, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.1

Other elements in 6kal:

The structure of Crystal Structure of Fkrp in Complex with Mg Ion and Cmp 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 and Cmp (pdb code 6kal). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp, PDB code: 6kal:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6kal

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Magnesium binding site 1 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:0.1
occ:1.00
 O2P A:C5P503 2.2 0.9 1.0
OD2 A:ASP364 2.2 76.7 1.0
OD1 A:ASP362 2.2 0.7 1.0
O A:HOH604 3.0 78.4 1.0
P A:C5P503 3.4 0.0 1.0
O A:ASP362 3.4 61.8 1.0
O3P A:C5P503 3.4 0.8 1.0
CG A:ASP364 3.4 70.7 1.0
CG A:ASP362 3.4 95.9 1.0
OD2 A:ASP360 3.5 83.0 1.0
C A:ASP362 3.9 59.8 1.0
OD1 A:ASP360 3.9 82.0 1.0
OD2 A:ASP362 4.0 0.5 1.0
CG A:ASP360 4.0 78.6 1.0
N A:GLY345 4.1 56.5 1.0
N A:ASP364 4.2 51.9 1.0
OD1 A:ASP364 4.2 71.8 1.0
CA A:GLY345 4.3 56.5 1.0
CB A:ASP364 4.3 61.7 1.0
N A:SER346 4.4 55.4 1.0
OG A:SER346 4.4 54.9 1.0
O5' A:C5P503 4.4 0.6 1.0
N A:VAL363 4.4 52.8 1.0
CA A:VAL363 4.5 45.9 1.0
C A:VAL363 4.5 49.2 1.0
O1P A:C5P503 4.5 0.7 1.0
CB A:ASP362 4.6 82.5 1.0
C A:GLY345 4.6 54.5 1.0
CA A:ASP362 4.6 66.8 1.0
N A:ASP362 4.8 63.5 1.0
CA A:ASP364 4.9 55.7 1.0

Magnesium binding site 2 out of 8 in 6kal

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Magnesium binding site 2 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:79.0
occ:1.00
 OD2 A:ASP362 2.1 0.5 1.0
OD2 A:ASP416 2.3 77.5 1.0
O A:HOH604 2.4 78.4 1.0
OD1 A:ASP364 3.1 71.8 1.0
CG A:ASP362 3.3 95.9 1.0
CG A:ASP416 3.5 77.1 1.0
OD1 A:ASP362 3.9 0.7 1.0
CG A:ASP364 4.0 70.7 1.0
CZ2 A:TRP418 4.1 70.1 1.0
OD2 A:ASP364 4.1 76.7 1.0
CB A:ASP416 4.2 73.5 1.0
NH2 A:ARG404 4.4 89.1 1.0
NE2 A:HIS414 4.4 70.7 1.0
OD1 A:ASP416 4.4 79.3 1.0
CB A:ASP362 4.4 82.5 1.0
CH2 A:TRP418 4.8 73.7 1.0
CD2 A:HIS414 5.0 69.8 1.0

Magnesium binding site 3 out of 8 in 6kal

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Magnesium binding site 3 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:58.4
occ:1.00
 OD2 B:ASP364 2.0 80.7 1.0
O2P B:C5P504 2.0 63.5 1.0
OD1 B:ASP362 2.0 82.6 1.0
CG B:ASP364 3.2 73.7 1.0
CG B:ASP362 3.2 77.7 1.0
OD2 B:ASP360 3.4 60.5 1.0
P B:C5P504 3.4 60.7 1.0
O B:ASP362 3.6 45.5 1.0
OD1 B:ASP360 3.7 59.0 1.0
OD2 B:ASP362 3.7 85.8 1.0
OD1 B:ASP364 3.8 79.1 1.0
O5' B:C5P504 3.9 57.9 1.0
CG B:ASP360 3.9 58.4 1.0
C B:ASP362 4.0 49.5 1.0
O1P B:C5P504 4.0 53.3 1.0
N B:GLY345 4.0 44.8 1.0
CA B:GLY345 4.2 40.5 1.0
CB B:ASP364 4.3 62.0 1.0
N B:ASP364 4.4 46.3 1.0
CB B:ASP362 4.4 68.7 1.0
MG B:MG506 4.4 71.2 1.0
O3P B:C5P504 4.6 62.7 1.0
CA B:ASP362 4.6 57.6 1.0
OG B:SER346 4.6 45.7 1.0
N B:SER346 4.6 41.1 1.0
N B:VAL363 4.6 49.1 1.0
N B:ASP362 4.7 54.2 1.0
C B:VAL363 4.7 45.6 1.0
C B:GLY345 4.7 40.7 1.0
CA B:VAL363 4.7 46.5 1.0
C5' B:C5P504 4.8 50.6 1.0
CA B:ASP364 5.0 52.7 1.0

Magnesium binding site 4 out of 8 in 6kal

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Magnesium binding site 4 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:71.2
occ:1.00
 OD2 B:ASP362 2.2 85.8 1.0
OD1 B:ASP364 2.3 79.1 1.0
OD2 B:ASP416 2.4 73.2 1.0
CG B:ASP362 3.2 77.7 1.0
CG B:ASP364 3.4 73.7 1.0
O B:HOH646 3.5 62.5 1.0
CG B:ASP416 3.5 68.3 1.0
OD1 B:ASP362 3.7 82.6 1.0
OD2 B:ASP364 3.7 80.7 1.0
CB B:ASP416 4.0 58.6 1.0
CZ2 B:TRP418 4.1 58.8 1.0
NE1 B:TRP418 4.2 56.1 1.0
O2P B:C5P504 4.3 63.5 1.0
CB B:ASP362 4.4 68.7 1.0
MG B:MG505 4.4 58.4 1.0
CE2 B:TRP418 4.5 58.4 1.0
OD1 B:ASP416 4.6 72.4 1.0
CB B:ASP364 4.7 62.0 1.0
CE1 B:HIS414 4.7 66.5 1.0

Magnesium binding site 5 out of 8 in 6kal

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Magnesium binding site 5 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:60.8
occ:1.00
 OD2 C:ASP364 2.1 83.7 1.0
OD1 C:ASP362 2.4 68.7 1.0
O3P C:C5P504 2.5 0.2 1.0
O C:HOH623 2.6 82.9 1.0
OD2 C:ASP360 3.3 73.9 1.0
CG C:ASP364 3.3 75.6 1.0
CG C:ASP362 3.6 68.4 1.0
O C:ASP362 3.7 58.4 1.0
OD1 C:ASP360 3.9 73.3 1.0
OD1 C:ASP364 4.0 76.4 1.0
P C:C5P504 4.0 0.2 1.0
CG C:ASP360 4.0 69.2 1.0
OD2 C:ASP362 4.1 71.9 1.0
O2P C:C5P504 4.4 0.4 1.0
C C:ASP362 4.4 55.9 1.0
N C:GLY345 4.4 52.3 1.0
CB C:ASP364 4.5 68.5 1.0
CA C:GLY345 4.6 49.5 1.0
O1P C:C5P504 4.8 0.9 1.0
CB C:ASP362 4.8 64.0 1.0
N C:ASP364 4.9 50.7 1.0
O5' C:C5P504 4.9 0.1 1.0
N C:ASP362 4.9 55.5 1.0
MG C:MG506 4.9 0.9 1.0
CA C:ASP362 4.9 59.1 1.0

Magnesium binding site 6 out of 8 in 6kal

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Magnesium binding site 6 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg506

b:0.9
occ:1.00
 OD2 C:ASP362 2.2 71.9 1.0
OD2 C:ASP416 2.4 76.0 1.0
O C:HOH623 2.6 82.9 1.0
CG C:ASP362 3.4 68.4 1.0
CG C:ASP416 3.6 74.4 1.0
OD1 C:ASP364 3.7 76.4 1.0
CE1 C:HIS414 3.9 65.0 1.0
OD1 C:ASP362 3.9 68.7 1.0
NH2 C:ARG404 4.1 68.3 1.0
CB C:ASP416 4.4 68.3 1.0
CB C:ASP362 4.5 64.0 1.0
OD1 C:ASP416 4.5 77.2 1.0
CG C:ASP364 4.6 75.6 1.0
CZ2 C:TRP418 4.6 56.5 1.0
OD2 C:ASP364 4.7 83.7 1.0
NE2 C:HIS414 4.7 64.5 1.0
ND1 C:HIS414 4.9 65.2 1.0
MG C:MG505 4.9 60.8 1.0

Magnesium binding site 7 out of 8 in 6kal

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Magnesium binding site 7 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg505

b:57.8
occ:1.00
 OD2 D:ASP364 2.0 80.3 1.0
O2P D:C5P504 2.1 61.6 1.0
OD1 D:ASP362 2.2 82.6 1.0
O D:HOH606 2.4 70.0 1.0
CG D:ASP362 3.1 76.2 1.0
P D:C5P504 3.2 65.0 1.0
CG D:ASP364 3.2 75.5 1.0
OD2 D:ASP362 3.3 81.4 1.0
OD2 D:ASP360 3.4 60.4 1.0
O3P D:C5P504 3.4 68.8 1.0
O5' D:C5P504 3.8 65.0 1.0
OD1 D:ASP360 3.9 64.2 1.0
O D:ASP362 3.9 56.3 1.0
OD1 D:ASP364 4.0 81.2 1.0
CG D:ASP360 4.0 59.9 1.0
N D:GLY345 4.2 48.8 1.0
C D:ASP362 4.3 56.1 1.0
CB D:ASP364 4.3 65.7 1.0
MG D:MG506 4.3 71.1 1.0
CB D:ASP362 4.4 67.8 1.0
CA D:GLY345 4.5 46.1 1.0
O1P D:C5P504 4.5 63.7 1.0
N D:ASP364 4.7 52.6 1.0
C5' D:C5P504 4.7 61.5 1.0
CA D:ASP362 4.8 59.4 1.0
N D:VAL363 4.8 54.0 1.0
N D:SER346 4.9 43.4 1.0
N D:ASP362 4.9 55.1 1.0
C D:VAL363 4.9 53.4 1.0
OG D:SER346 5.0 43.2 1.0
CA D:VAL363 5.0 48.7 1.0

Magnesium binding site 8 out of 8 in 6kal

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Magnesium binding site 8 out of 8 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Fkrp in Complex with Mg Ion and Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg506

b:71.1
occ:1.00
 OD2 D:ASP416 2.2 72.4 1.0
OD2 D:ASP362 2.3 81.4 1.0
OD1 D:ASP364 2.4 81.2 1.0
O D:HOH606 2.6 70.0 1.0
CG D:ASP364 3.3 75.5 1.0
CG D:ASP416 3.3 70.0 1.0
OD2 D:ASP364 3.5 80.3 1.0
CG D:ASP362 3.5 76.2 1.0
CZ2 D:TRP418 3.8 62.0 1.0
CB D:ASP416 3.8 63.0 1.0
OD1 D:ASP362 4.2 82.6 1.0
NE1 D:TRP418 4.3 55.5 1.0
MG D:MG505 4.3 57.8 1.0
NE2 D:HIS414 4.3 71.9 1.0
CE2 D:TRP418 4.4 59.6 1.0
OD1 D:ASP416 4.4 72.7 1.0
O3P D:C5P504 4.6 68.8 1.0
CB D:ASP362 4.6 67.8 1.0
CB D:ASP364 4.7 65.7 1.0
NH2 D:ARG404 4.8 73.1 1.0
CH2 D:TRP418 4.8 65.1 1.0
CD2 D:HIS414 5.0 70.9 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: Tue Oct 1 06:49:13 2024

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