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Magnesium in PDB 5d92: Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum

Protein crystallography data

The structure of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum, PDB code: 5d92 was solved by O.B.Clarke, D.T.Tomasek, C.D.Jorge, M.Belcher Dufrisne, M.Kim, S.Banerjee, K.R.Rajashankar, W.A.Hendrickson, H.Santos, F.Mancia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 166.97 / 3.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.002, 62.489, 169.759, 90.00, 99.77, 90.00
R / Rfree (%) 28 / 30

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum (pdb code 5d92). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum, PDB code: 5d92:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5d92

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Magnesium binding site 1 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg313

b:64.3
occ:1.00
OD1 D:ASP87 1.9 60.0 1.0
OD2 D:ASP66 2.0 66.0 1.0
OD1 D:ASP66 2.2 67.8 1.0
OAX D:58A315 2.2 74.8 1.0
OAW D:58A315 2.3 72.8 1.0
OD2 D:ASP87 2.3 63.5 1.0
OD2 D:ASP91 2.3 62.0 1.0
CG D:ASP87 2.3 60.8 1.0
CG D:ASP66 2.4 66.0 1.0
PAV D:58A315 2.7 80.2 1.0
CG D:ASP91 3.4 61.1 1.0
MG D:MG314 3.5 63.7 1.0
OAY D:58A315 3.7 74.9 1.0
CB D:ASP87 3.8 59.2 1.0
OD1 D:ASP91 3.8 76.6 1.0
CB D:ASP66 3.9 63.5 1.0
OAU D:58A315 4.1 70.0 1.0
CAZ D:58A315 4.3 71.2 1.0
O D:ASP87 4.3 54.7 1.0
C D:ASP87 4.4 54.6 1.0
CA D:ASP87 4.6 55.9 1.0
O5' D:58A315 4.6 63.0 1.0
OAT D:58A315 4.6 65.7 1.0
CB D:ASP91 4.7 56.2 1.0
PAR D:58A315 4.7 63.3 1.0
CA D:ASP66 4.8 62.1 1.0
O D:ASP66 5.0 62.6 1.0

Magnesium binding site 2 out of 8 in 5d92

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Magnesium binding site 2 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg314

b:63.7
occ:1.00
OD1 D:ASP66 2.0 67.8 1.0
OAT D:58A315 2.1 65.7 1.0
OD1 D:ASP69 2.1 63.8 1.0
O D:ASP66 2.1 62.6 1.0
OD2 D:ASP87 2.1 63.5 1.0
OAW D:58A315 2.3 72.8 1.0
O5' D:58A315 2.7 63.0 1.0
PAR D:58A315 2.8 63.3 1.0
C D:ASP66 3.0 62.8 1.0
CG D:ASP66 3.2 66.0 1.0
CG D:ASP87 3.2 60.8 1.0
CG D:ASP69 3.2 60.4 1.0
PAV D:58A315 3.5 80.2 1.0
MG D:MG313 3.5 64.3 1.0
CA D:ASP66 3.6 62.1 1.0
N D:GLY70 3.6 61.5 1.0
OAU D:58A315 3.6 70.0 1.0
OD2 D:ASP69 3.7 74.0 1.0
OD1 D:ASP87 3.9 60.0 1.0
CA D:GLY70 3.9 63.2 1.0
CB D:ASP66 3.9 63.5 1.0
O4' D:58A315 4.0 64.3 1.0
C5' D:58A315 4.1 62.7 1.0
N D:ILE67 4.1 71.2 1.0
CAG D:58A315 4.1 63.9 1.0
OAS D:58A315 4.1 66.3 1.0
OAX D:58A315 4.2 74.8 1.0
OD2 D:ASP66 4.2 66.0 1.0
CB D:ASP87 4.3 59.2 1.0
C D:ASP69 4.4 61.3 1.0
CB D:ASP69 4.5 58.3 1.0
CA D:ILE67 4.6 61.3 1.0
CAF D:58A315 4.7 60.5 1.0
C4' D:58A315 4.7 65.6 1.0
OAY D:58A315 4.8 74.9 1.0
CA D:ASP69 4.8 59.4 1.0
CAZ D:58A315 4.9 71.2 1.0
N D:ASP69 4.9 59.0 1.0
N D:ASP66 4.9 62.1 1.0
O D:SER65 5.0 57.8 1.0

Magnesium binding site 3 out of 8 in 5d92

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Magnesium binding site 3 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:59.6
occ:1.00
OD1 A:ASP87 1.9 59.1 1.0
OAW A:58A311 2.0 65.6 1.0
OD1 A:ASP66 2.0 66.2 1.0
OD2 A:ASP66 2.1 60.8 1.0
CG A:ASP87 2.3 58.9 1.0
OD2 A:ASP91 2.3 59.2 1.0
CG A:ASP66 2.4 61.7 1.0
OD2 A:ASP87 2.5 64.8 1.0
OAX A:58A311 2.5 63.8 1.0
PAV A:58A311 2.7 60.9 1.0
MG A:MG310 3.4 61.6 1.0
CG A:ASP91 3.4 59.0 1.0
CB A:ASP87 3.5 57.7 1.0
CB A:ASP66 3.9 60.9 1.0
OAU A:58A311 3.9 63.6 1.0
OAY A:58A311 3.9 63.3 1.0
OD1 A:ASP91 4.0 78.8 1.0
O A:ASP87 4.0 54.9 1.0
C A:ASP87 4.0 53.6 1.0
OAT A:58A311 4.1 61.4 1.0
CA A:ASP87 4.3 53.5 1.0
PAR A:58A311 4.4 60.1 1.0
N A:SER88 4.5 52.9 1.0
O5' A:58A311 4.6 61.1 1.0
CAZ A:58A311 4.6 68.7 1.0
CB A:ASP91 4.6 57.2 1.0
CA A:ASP66 4.7 61.1 1.0
O A:ASP66 4.8 62.1 1.0
C A:ASP66 4.9 62.1 1.0

Magnesium binding site 4 out of 8 in 5d92

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Magnesium binding site 4 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:61.6
occ:1.00
OD1 A:ASP66 1.8 66.2 1.0
OD1 A:ASP69 2.0 70.7 1.0
OD2 A:ASP87 2.0 64.8 1.0
OD2 A:ASP69 2.2 61.0 1.0
O A:ASP66 2.3 62.1 1.0
CG A:ASP87 2.3 58.9 1.0
OD1 A:ASP87 2.4 59.1 1.0
CG A:ASP69 2.4 58.5 1.0
CA A:ASP66 2.7 61.1 1.0
CG A:ASP66 2.7 61.7 1.0
C A:ASP66 2.8 62.1 1.0
OAW A:58A311 2.8 65.6 1.0
OAT A:58A311 2.9 61.4 1.0
CB A:ASP66 3.2 60.9 1.0
MG A:MG309 3.4 59.6 1.0
CB A:ASP87 3.6 57.7 1.0
OD2 A:ASP66 3.7 60.8 1.0
CB A:ASP69 4.0 58.0 1.0
N A:ASP66 4.0 59.5 1.0
O A:SER65 4.0 59.1 1.0
N A:ILE67 4.1 66.5 1.0
PAR A:58A311 4.1 60.1 1.0
CA A:ASP87 4.3 53.5 1.0
PAV A:58A311 4.3 60.9 1.0
N A:GLY70 4.3 61.3 1.0
O5' A:58A311 4.3 61.1 1.0
C A:SER65 4.5 58.8 1.0
CAG A:58A311 4.5 57.6 1.0
CAF A:58A311 4.6 56.6 1.0
OD2 A:ASP91 4.7 59.2 1.0
CA A:ASP69 4.7 58.9 1.0
N A:ASP69 4.8 60.1 1.0
C A:ASP69 4.8 60.1 1.0
OAU A:58A311 4.8 63.6 1.0
OD1 A:ASP91 4.8 78.8 1.0
CG2 A:THR32 4.9 49.4 1.0
OG1 A:THR32 4.9 51.5 1.0
CA A:ILE67 5.0 66.7 1.0

Magnesium binding site 5 out of 8 in 5d92

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Magnesium binding site 5 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:63.6
occ:1.00
OD1 B:ASP87 1.9 61.3 1.0
OAW B:58A309 2.0 66.6 1.0
OD2 B:ASP66 2.0 64.0 1.0
OD1 B:ASP66 2.1 63.5 1.0
OD2 B:ASP87 2.3 65.3 1.0
OD2 B:ASP91 2.3 64.0 1.0
CG B:ASP87 2.3 61.9 1.0
CG B:ASP66 2.3 63.1 1.0
OAX B:58A309 3.0 69.4 1.0
PAV B:58A309 3.0 76.5 1.0
CG B:ASP91 3.4 63.3 1.0
MG B:MG308 3.6 63.9 1.0
CB B:ASP87 3.7 61.1 1.0
CB B:ASP66 3.9 60.2 1.0
OD1 B:ASP91 3.9 63.9 1.0
OAU B:58A309 4.1 70.4 1.0
OAT B:58A309 4.2 64.8 1.0
OAY B:58A309 4.2 79.5 1.0
O5' B:58A309 4.3 66.9 1.0
O B:ASP87 4.3 64.2 1.0
C B:ASP87 4.4 60.0 1.0
PAR B:58A309 4.4 66.4 1.0
CA B:ASP87 4.5 58.4 1.0
CAZ B:58A309 4.6 78.6 1.0
CB B:ASP91 4.6 63.3 1.0
CA B:ASP66 4.7 57.8 1.0
O B:ASP66 5.0 59.0 1.0
N B:SER88 5.0 58.9 1.0

Magnesium binding site 6 out of 8 in 5d92

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Magnesium binding site 6 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg308

b:63.9
occ:1.00
OAT B:58A309 1.9 64.8 1.0
OD1 B:ASP66 2.0 63.5 1.0
OD1 B:ASP69 2.0 58.3 1.0
OD2 B:ASP87 2.1 65.3 1.0
O B:ASP66 2.1 59.0 1.0
O5' B:58A309 2.7 66.9 1.0
PAR B:58A309 2.8 66.4 1.0
C B:ASP66 3.0 58.9 1.0
OAW B:58A309 3.1 66.6 1.0
CG B:ASP69 3.2 56.6 1.0
CG B:ASP87 3.2 61.9 1.0
CG B:ASP66 3.2 63.1 1.0
N B:GLY70 3.5 60.7 1.0
CA B:ASP66 3.5 57.8 1.0
MG B:MG307 3.6 63.6 1.0
OD2 B:ASP69 3.7 55.7 1.0
OAU B:58A309 3.9 70.4 1.0
CA B:GLY70 3.9 62.4 1.0
OD1 B:ASP87 3.9 61.3 1.0
O4' B:58A309 3.9 66.4 1.0
CB B:ASP66 3.9 60.2 1.0
OAS B:58A309 3.9 71.7 1.0
CAG B:58A309 3.9 62.4 1.0
PAV B:58A309 4.1 76.5 1.0
C5' B:58A309 4.1 85.5 1.0
N B:ILE67 4.1 58.7 1.0
OD2 B:ASP66 4.2 64.0 1.0
CB B:ASP87 4.2 61.1 1.0
C B:ASP69 4.3 59.7 1.0
CB B:ASP69 4.4 56.0 1.0
CAF B:58A309 4.4 58.7 1.0
C4' B:58A309 4.6 71.6 1.0
CA B:ILE67 4.6 59.7 1.0
CA B:ASP69 4.8 57.2 1.0
N B:ASP69 4.9 57.2 1.0
N B:ASP66 4.9 55.4 1.0
O B:SER65 5.0 54.7 1.0
NAH B:58A309 5.0 64.8 1.0
OAX B:58A309 5.0 69.4 1.0

Magnesium binding site 7 out of 8 in 5d92

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Magnesium binding site 7 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg308

b:70.2
occ:1.00
OD1 C:ASP87 1.9 66.5 1.0
OD2 C:ASP66 2.0 71.2 1.0
OD1 C:ASP66 2.2 70.3 1.0
OD2 C:ASP87 2.3 76.1 1.0
CG C:ASP87 2.3 67.2 1.0
OD2 C:ASP91 2.3 67.9 1.0
OAW C:58A310 2.3 69.8 1.0
CG C:ASP66 2.3 70.5 1.0
OAX C:58A310 2.4 70.9 1.0
PAV C:58A310 2.9 72.3 1.0
CG C:ASP91 3.4 69.6 1.0
MG C:MG309 3.6 69.3 1.0
CB C:ASP87 3.7 65.1 1.0
CB C:ASP66 3.9 68.5 1.0
OD1 C:ASP91 3.9 86.2 1.0
OAY C:58A310 4.0 77.8 1.0
OAU C:58A310 4.1 73.6 1.0
O C:ASP87 4.3 62.5 1.0
C C:ASP87 4.4 62.7 1.0
CAZ C:58A310 4.4 78.7 1.0
CA C:ASP87 4.5 63.0 1.0
OAT C:58A310 4.6 70.5 1.0
O5' C:58A310 4.6 71.0 1.0
CB C:ASP91 4.7 67.9 1.0
PAR C:58A310 4.7 70.3 1.0
CA C:ASP66 4.8 67.4 1.0
N C:SER88 5.0 62.4 1.0
O C:ASP66 5.0 68.7 1.0

Magnesium binding site 8 out of 8 in 5d92

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Magnesium binding site 8 out of 8 in the Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Phosphatidylinositolphosphate (Pip) Synthase From Renibacterium Salmoninarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg309

b:69.3
occ:1.00
OD1 C:ASP66 2.0 70.3 1.0
OAT C:58A310 2.0 70.5 1.0
O C:ASP66 2.1 68.7 1.0
OD2 C:ASP87 2.1 76.1 1.0
OD1 C:ASP69 2.1 67.6 1.0
OAW C:58A310 2.5 69.8 1.0
O5' C:58A310 2.8 71.0 1.0
PAR C:58A310 2.9 70.3 1.0
C C:ASP66 3.0 67.9 1.0
CG C:ASP87 3.2 67.2 1.0
CG C:ASP66 3.2 70.5 1.0
CG C:ASP69 3.3 66.2 1.0
N C:GLY70 3.5 70.1 1.0
CA C:ASP66 3.5 67.4 1.0
MG C:MG308 3.6 70.2 1.0
PAV C:58A310 3.7 72.3 1.0
OD2 C:ASP69 3.7 66.5 1.0
OAU C:58A310 3.8 73.6 1.0
CA C:GLY70 3.8 71.6 1.0
OD1 C:ASP87 3.9 66.5 1.0
O4' C:58A310 3.9 72.6 1.0
CB C:ASP66 3.9 68.5 1.0
CAG C:58A310 4.0 69.7 1.0
N C:ILE67 4.1 68.0 1.0
OAS C:58A310 4.2 91.7 1.0
OD2 C:ASP66 4.2 71.2 1.0
CB C:ASP87 4.2 65.1 1.0
C5' C:58A310 4.2 73.8 1.0
C C:ASP69 4.3 70.0 1.0
OAX C:58A310 4.4 70.9 1.0
CB C:ASP69 4.5 67.5 1.0
CA C:ILE67 4.5 69.4 1.0
CAF C:58A310 4.6 68.0 1.0
C4' C:58A310 4.7 73.1 1.0
CA C:ASP69 4.8 68.3 1.0
N C:ASP69 4.8 67.7 1.0
OAY C:58A310 4.9 77.8 1.0
O C:SER65 4.9 64.7 1.0
N C:ASP66 4.9 69.5 1.0
C C:ILE67 4.9 69.1 1.0

Reference:

O.B.Clarke, D.Tomasek, C.D.Jorge, M.B.Dufrisne, M.Kim, S.Banerjee, K.R.Rajashankar, L.Shapiro, W.A.Hendrickson, H.Santos, F.Mancia. Structural Basis For Phosphatidylinositol-Phosphate Biosynthesis. Nat Commun V. 6 8505 2015.
ISSN: ESSN 2041-1723
PubMed: 26510127
DOI: 10.1038/NCOMMS9505
Page generated: Mon Dec 14 20:10:36 2020

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