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Magnesium in PDB 3rbm: Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703

Protein crystallography data

The structure of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703, PDB code: 3rbm was solved by Y.L.Liu, J.H.No, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.58 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.682, 107.952, 140.703, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 (pdb code 3rbm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703, PDB code: 3rbm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3rbm

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Magnesium binding site 1 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:12.8
occ:1.00
 O A:HOH467 1.9 27.3 1.0
OAB A:B732001 2.0 7.0 1.0
OAC A:B732001 2.0 2.0 1.0
OD1 A:ASP287 2.1 27.6 1.0
O A:HOH465 2.1 27.9 1.0
O A:HOH423 2.1 28.5 1.0
CG A:ASP287 3.0 27.6 1.0
PAZ A:B732001 3.2 6.9 1.0
PBA A:B732001 3.3 5.0 1.0
OD2 A:ASP287 3.4 28.1 1.0
O A:HOH464 3.7 26.8 1.0
CAW A:B732001 3.9 4.1 1.0
NZ A:LYS301 4.0 26.9 1.0
OAD A:B732001 4.2 4.0 1.0
NE2 A:GLN284 4.2 27.1 1.0
OD2 A:ASP305 4.3 26.4 1.0
O A:ASP287 4.3 26.8 1.0
CB A:ASP287 4.3 27.1 1.0
OD1 A:ASP305 4.3 26.7 1.0
OAG A:B732001 4.4 5.2 1.0
MG A:MG1003 4.4 4.3 1.0
OD2 A:ASP291 4.4 32.4 1.0
OAE A:B732001 4.5 11.2 1.0
OAF A:B732001 4.5 2.0 1.0
C A:ASP287 4.5 26.6 1.0
OD2 A:ASP288 4.6 26.6 1.0
CG A:ASP305 4.7 26.5 1.0
CAV A:B732001 4.9 9.6 1.0
N A:ASP288 5.0 26.3 1.0
CA A:ASP287 5.0 26.9 1.0

Magnesium binding site 2 out of 12 in 3rbm

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Magnesium binding site 2 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:16.3
occ:1.00
 OAF A:B732001 1.7 2.0 1.0
O A:HOH463 2.0 27.1 1.0
O A:HOH407 2.0 27.6 1.0
OD2 A:ASP130 2.1 27.2 1.0
O A:HOH462 2.2 27.1 1.0
OD1 A:ASP126 2.2 26.7 1.0
CG A:ASP130 2.9 27.3 1.0
OD1 A:ASP130 3.0 27.3 1.0
CG A:ASP126 3.1 26.6 1.0
OD2 A:ASP126 3.2 26.8 1.0
PBA A:B732001 3.2 5.0 1.0
MG A:MG1003 3.3 4.3 1.0
OAG A:B732001 3.6 5.2 1.0
OD2 A:ASP198 4.0 27.3 1.0
CAW A:B732001 4.0 4.1 1.0
NE2 A:GLN195 4.1 27.9 1.0
OAC A:B732001 4.1 2.0 1.0
O A:HOH464 4.3 26.8 1.0
OD1 A:ASP198 4.3 27.4 1.0
CB A:ASP130 4.3 27.3 1.0
CG A:ASP198 4.4 27.1 1.0
OE1 A:GLN195 4.5 27.1 1.0
CB A:ASP126 4.5 26.4 1.0
CE A:LYS310 4.5 27.3 1.0
CAJ A:B732001 4.6 8.1 1.0
NZ A:LYS310 4.6 27.5 1.0
CD A:GLN195 4.7 27.3 1.0
NZ A:LYS243 4.7 26.4 1.0
O A:HOH466 4.7 27.1 1.0
O A:ASP126 4.8 26.7 1.0
NAY A:B732001 4.8 13.7 1.0

Magnesium binding site 3 out of 12 in 3rbm

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Magnesium binding site 3 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:4.3
occ:1.00
 OAE A:B732001 2.1 11.2 1.0
OAF A:B732001 2.3 2.0 1.0
OD2 A:ASP126 2.3 26.8 1.0
O A:HOH466 2.3 27.1 1.0
OD2 A:ASP130 2.4 27.2 1.0
CAW A:B732001 2.7 4.1 1.0
PAZ A:B732001 2.8 6.9 1.0
PBA A:B732001 3.0 5.0 1.0
MG A:MG1002 3.3 16.3 1.0
OAB A:B732001 3.3 7.0 1.0
CG A:ASP126 3.4 26.6 1.0
OAC A:B732001 3.4 2.0 1.0
CG A:ASP130 3.6 27.3 1.0
OD1 A:ASP126 3.8 26.7 1.0
O A:HOH423 3.8 28.5 1.0
CB A:ASP130 4.0 27.3 1.0
CAV A:B732001 4.2 9.6 1.0
O A:HOH407 4.2 27.6 1.0
OAD A:B732001 4.3 4.0 1.0
O A:HOH442 4.4 27.1 1.0
MG A:MG1001 4.4 12.8 1.0
OAG A:B732001 4.5 5.2 1.0
O A:HOH414 4.6 27.6 1.0
O A:HOH464 4.6 26.8 1.0
NH1 A:ARG135 4.6 26.7 1.0
OD1 A:ASP130 4.6 27.3 1.0
CB A:ASP126 4.7 26.4 1.0
O A:HOH462 4.7 27.1 1.0
OD1 A:ASP127 4.8 26.8 1.0
O A:ASP126 4.9 26.7 1.0
NAY A:B732001 4.9 13.7 1.0
O A:HOH463 5.0 27.1 1.0

Magnesium binding site 4 out of 12 in 3rbm

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Magnesium binding site 4 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:9.7
occ:1.00
 O B:HOH477 2.0 27.6 1.0
OAC B:B732001 2.0 5.6 1.0
OD1 B:ASP287 2.1 27.4 1.0
OAB B:B732001 2.2 4.2 1.0
O B:HOH476 2.3 27.6 1.0
CG B:ASP287 3.2 27.4 1.0
PBA B:B732001 3.4 5.7 1.0
O B:HOH412 3.4 27.8 1.0
PAZ B:B732001 3.5 7.6 1.0
OD2 B:ASP287 3.8 27.4 1.0
O B:ASP287 4.0 27.7 1.0
OD2 B:ASP305 4.1 26.8 1.0
NE2 B:GLN284 4.1 27.4 1.0
OD2 B:ASP291 4.1 34.6 1.0
OD1 B:ASP305 4.2 26.8 1.0
CAW B:B732001 4.2 2.0 1.0
CB B:ASP287 4.4 27.4 1.0
C B:ASP287 4.4 27.6 1.0
NZ B:LYS301 4.4 28.2 1.0
OD2 B:ASP288 4.4 27.6 1.0
OAG B:B732001 4.5 2.0 1.0
OAE B:B732001 4.5 13.8 1.0
CG B:ASP305 4.6 26.8 1.0
OAF B:B732001 4.6 6.2 1.0
MG B:MG1003 4.6 6.0 1.0
CB B:ASP291 4.6 28.1 1.0
OAD B:B732001 4.7 6.8 1.0
N B:ASP288 4.7 27.7 1.0
CG B:ASP291 4.8 28.1 1.0
CA B:ASP288 4.9 27.8 1.0
CA B:ASP287 5.0 27.5 1.0

Magnesium binding site 5 out of 12 in 3rbm

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Magnesium binding site 5 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:20.1
occ:1.00
 OD1 B:ASP126 2.1 27.1 1.0
OD2 B:ASP130 2.2 27.5 1.0
OAF B:B732001 2.3 6.2 1.0
O B:HOH478 2.3 28.1 1.0
CG B:ASP130 3.1 27.5 1.0
CG B:ASP126 3.1 27.0 1.0
OD1 B:ASP130 3.2 27.7 1.0
OD2 B:ASP126 3.5 27.1 1.0
NE2 B:GLN195 3.5 27.6 1.0
OD2 B:ASP198 3.7 27.5 1.0
MG B:MG1003 3.7 6.0 1.0
PBA B:B732001 3.7 5.7 1.0
OE1 B:GLN195 3.8 27.2 1.0
OAG B:B732001 3.9 2.0 1.0
CD B:GLN195 4.1 27.2 1.0
CG B:ASP198 4.2 27.4 1.0
OD1 B:ASP198 4.2 27.8 1.0
CB B:ASP126 4.5 26.7 1.0
CAW B:B732001 4.5 2.0 1.0
CE B:LYS310 4.5 27.2 1.0
CB B:ASP130 4.5 27.5 1.0
CAJ B:B732001 4.6 6.6 1.0
NZ B:LYS310 4.6 27.5 1.0
O B:HOH412 4.7 27.8 1.0
OAC B:B732001 4.7 5.6 1.0
NZ B:LYS243 4.8 26.9 1.0
O B:ASP126 4.8 26.9 1.0
NAY B:B732001 4.9 11.1 1.0
CA B:ASP126 4.9 26.6 1.0

Magnesium binding site 6 out of 12 in 3rbm

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Magnesium binding site 6 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:6.0
occ:1.00
 OD2 B:ASP126 2.1 27.1 1.0
OAF B:B732001 2.2 6.2 1.0
OAE B:B732001 2.2 13.8 1.0
O B:HOH475 2.3 27.2 1.0
OD2 B:ASP130 2.5 27.5 1.0
CAW B:B732001 2.9 2.0 1.0
PBA B:B732001 3.0 5.7 1.0
PAZ B:B732001 3.0 7.6 1.0
CG B:ASP126 3.2 27.0 1.0
OAC B:B732001 3.4 5.6 1.0
CG B:ASP130 3.6 27.5 1.0
OD1 B:ASP126 3.6 27.1 1.0
OAB B:B732001 3.7 4.2 1.0
O B:HOH405 3.7 27.6 1.0
MG B:MG1002 3.7 20.1 1.0
CB B:ASP130 3.9 27.5 1.0
O B:HOH478 4.3 28.1 1.0
O B:HOH447 4.3 28.3 1.0
CAV B:B732001 4.3 11.2 1.0
OAD B:B732001 4.4 6.8 1.0
OAG B:B732001 4.5 2.0 1.0
O B:HOH431 4.6 27.6 1.0
CB B:ASP126 4.6 26.7 1.0
MG B:MG1001 4.6 9.7 1.0
O B:HOH412 4.6 27.8 1.0
OD1 B:ASP130 4.7 27.7 1.0
NH1 B:ARG135 4.7 26.9 1.0
O B:ASP126 4.9 26.9 1.0
OD1 B:ASP127 4.9 26.8 1.0

Magnesium binding site 7 out of 12 in 3rbm

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Magnesium binding site 7 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:20.2
occ:1.00
 OAB C:B732001 2.4 9.1 1.0
OAC C:B732001 2.4 2.0 1.0
OD1 C:ASP287 2.5 26.7 1.0
OD2 C:ASP305 3.5 26.5 1.0
CG C:ASP287 3.6 26.6 1.0
OD2 C:ASP291 3.6 33.0 1.0
OD1 C:ASP305 3.7 26.7 1.0
O C:HOH401 3.7 28.0 1.0
PAZ C:B732001 3.8 9.4 1.0
PBA C:B732001 3.8 5.0 1.0
CG C:ASP305 4.0 26.6 1.0
O C:ASP287 4.1 26.3 1.0
OD2 C:ASP287 4.1 26.7 1.0
CB C:ASP291 4.2 26.4 1.0
CG C:ASP291 4.3 26.6 1.0
C C:ASP287 4.5 26.3 1.0
OD2 C:ASP288 4.5 26.6 1.0
MG C:MG1003 4.5 3.2 1.0
NE2 C:GLN284 4.5 26.7 1.0
CAW C:B732001 4.5 2.0 1.0
NZ C:LYS301 4.6 26.6 1.0
CB C:ASP287 4.6 26.5 1.0
OAG C:B732001 4.8 2.0 1.0
OAE C:B732001 4.8 8.7 1.0
N C:ASP288 4.8 26.3 1.0
CA C:ASP288 4.9 26.4 1.0
OAD C:B732001 4.9 8.5 1.0

Magnesium binding site 8 out of 12 in 3rbm

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Magnesium binding site 8 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:13.5
occ:1.00
 O C:HOH452 2.1 28.0 1.0
O C:HOH432 2.2 27.6 1.0
OD1 C:ASP126 2.3 27.1 1.0
OAF C:B732001 2.4 2.0 1.0
OD2 C:ASP130 2.5 27.3 1.0
OD1 C:ASP130 2.9 27.4 1.0
CG C:ASP130 3.1 27.3 1.0
OD2 C:ASP198 3.2 26.0 1.0
NE2 C:GLN195 3.3 26.0 1.0
CG C:ASP126 3.4 26.9 1.0
OE1 C:GLN195 3.7 25.8 1.0
CD C:GLN195 3.8 25.8 1.0
OD2 C:ASP126 3.8 27.0 1.0
CG C:ASP198 3.8 26.1 1.0
OD1 C:ASP198 3.8 26.4 1.0
PBA C:B732001 4.0 5.0 1.0
NZ C:LYS310 4.2 27.3 1.0
MG C:MG1003 4.2 3.2 1.0
OAG C:B732001 4.2 2.0 1.0
CE C:LYS310 4.4 27.1 1.0
CB C:ASP130 4.6 27.1 1.0
CB C:ASP126 4.7 26.7 1.0
O C:HOH401 4.8 28.0 1.0
O C:ASP126 4.8 26.7 1.0
NZ C:LYS243 4.8 27.2 1.0
OAC C:B732001 4.9 2.0 1.0
CAW C:B732001 5.0 2.0 1.0

Magnesium binding site 9 out of 12 in 3rbm

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Magnesium binding site 9 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:3.2
occ:1.00
 OAF C:B732001 2.3 2.0 1.0
O C:HOH451 2.3 27.0 1.0
OAE C:B732001 2.3 8.7 1.0
OD2 C:ASP126 2.4 27.0 1.0
OD2 C:ASP130 2.5 27.3 1.0
PBA C:B732001 2.8 5.0 1.0
CAW C:B732001 2.8 2.0 1.0
PAZ C:B732001 2.9 9.4 1.0
OAC C:B732001 3.1 2.0 1.0
OAB C:B732001 3.2 9.1 1.0
CG C:ASP126 3.5 26.9 1.0
CG C:ASP130 3.6 27.3 1.0
OD1 C:ASP126 3.9 27.1 1.0
CB C:ASP130 4.0 27.1 1.0
O C:HOH452 4.0 28.0 1.0
MG C:MG1002 4.2 13.5 1.0
CAV C:B732001 4.3 7.8 1.0
O C:HOH412 4.4 27.0 1.0
OAG C:B732001 4.4 2.0 1.0
OAD C:B732001 4.4 8.5 1.0
MG C:MG1001 4.5 20.2 1.0
O C:HOH401 4.6 28.0 1.0
OD1 C:ASP130 4.7 27.4 1.0
O C:HOH432 4.7 27.6 1.0
CB C:ASP126 4.8 26.7 1.0
NH1 C:ARG135 4.9 26.9 1.0

Magnesium binding site 10 out of 12 in 3rbm

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Magnesium binding site 10 out of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph -703 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:18.1
occ:1.00
 OAC D:B732001 1.9 5.2 1.0
OAB D:B732001 2.0 6.5 1.0
O D:HOH453 2.1 27.5 1.0
O D:HOH448 2.3 27.6 1.0
OD1 D:ASP287 2.4 27.4 1.0
O D:HOH449 3.1 28.8 1.0
PAZ D:B732001 3.3 10.5 1.0
PBA D:B732001 3.3 7.5 1.0
CG D:ASP287 3.6 27.5 1.0
OD1 D:ASP305 3.7 26.6 1.0
OD2 D:ASP305 3.8 26.7 1.0
OD2 D:ASP291 3.9 33.9 1.0
CAW D:B732001 4.0 7.3 1.0
OD2 D:ASP287 4.0 27.6 1.0
NZ D:LYS301 4.1 27.7 1.0
OAE D:B732001 4.2 16.1 1.0
O D:HOH445 4.2 27.8 1.0
CG D:ASP305 4.2 26.7 1.0
OAF D:B732001 4.3 6.6 1.0
MG D:MG1003 4.4 8.6 1.0
CG D:ASP291 4.6 28.0 1.0
OAG D:B732001 4.6 7.7 1.0
OAD D:B732001 4.6 9.5 1.0
NE2 D:GLN284 4.6 27.4 1.0
O D:ASP287 4.6 27.7 1.0
OD2 D:ASP288 4.8 27.5 1.0
CB D:ASP291 4.8 28.0 1.0
CB D:ASP287 4.8 27.5 1.0
C D:ASP287 4.8 27.6 1.0

Reference:

J.H.No, F.De Macedo Dossin, Y.Zhang, Y.L.Liu, W.Zhu, X.Feng, J.A.Yoo, E.Lee, K.Wang, R.Hui, L.H.Freitas-Junior, E.Oldfield. Lipophilic Analogs of Zoledronate and Risedronate Inhibit Plasmodium Geranylgeranyl Diphosphate Synthase (Ggpps) and Exhibit Potent Antimalarial Activity. Proc.Natl.Acad.Sci.Usa V. 109 4058 2012.
ISSN: ISSN 0027-8424
PubMed: 22392982
DOI: 10.1073/PNAS.1118215109
Page generated: Mon Dec 14 08:44:29 2020

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