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Magnesium in PDB 3iba: Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+

Enzymatic activity of Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+

All present enzymatic activity of Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+, PDB code: 3iba was solved by L.M.Amzel, C.H.Huang, S.B.Gabelli, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.87 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.344, 58.344, 390.404, 90.00, 90.00, 120.00
R / Rfree (%) 22.5 / 29.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+ (pdb code 3iba). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+, PDB code: 3iba:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3iba

Go back to Magnesium Binding Sites List in 3iba
Magnesium binding site 1 out of 3 in the Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+


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 the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:24.1
occ:1.00
 O10 A:ZOL901 2.0 31.1 1.0
O A:HOH450 2.1 31.0 1.0
O17 A:ZOL901 2.1 31.2 1.0
O A:HOH365 2.2 18.8 1.0
OD2 A:ASP98 2.2 30.4 1.0
OD2 A:ASP102 2.4 33.9 1.0
MG A:MG403 3.1 13.1 1.0
CG A:ASP98 3.1 30.9 1.0
P9 A:ZOL901 3.2 31.3 1.0
P14 A:ZOL901 3.4 30.4 1.0
OD1 A:ASP98 3.4 30.3 1.0
CG A:ASP102 3.4 34.3 1.0
C8 A:ZOL901 3.7 30.9 1.0
O A:HOH475 3.8 35.0 1.0
O12 A:ZOL901 3.8 31.5 1.0
CB A:ASP102 3.9 34.6 1.0
O15 A:ZOL901 4.0 30.3 1.0
C7 A:ZOL901 4.0 31.0 1.0
O A:HOH411 4.2 32.0 1.0
OG A:SER104 4.3 36.8 1.0
O A:HOH507 4.3 24.6 1.0
O A:ASP98 4.4 31.2 1.0
O A:HOH422 4.5 26.3 1.0
OD1 A:ASP99 4.5 32.2 1.0
CB A:ASP98 4.5 31.0 1.0
O11 A:ZOL901 4.5 31.0 1.0
OD1 A:ASP102 4.5 33.1 1.0
O16 A:ZOL901 4.6 30.3 1.0
C A:ASP98 4.7 31.3 1.0
O A:HOH375 4.7 28.6 1.0
MG A:MG402 4.9 38.4 1.0
O A:HOH364 4.9 18.0 1.0
NH1 A:ARG107 5.0 37.7 1.0
O A:HOH380 5.0 25.8 1.0

Magnesium binding site 2 out of 3 in 3iba

Go back to Magnesium Binding Sites List in 3iba
Magnesium binding site 2 out of 3 in the Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+


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 the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:38.4
occ:1.00
 O15 A:ZOL901 1.9 30.3 1.0
O A:HOH422 2.0 26.3 1.0
O A:HOH376 2.1 20.5 1.0
O12 A:ZOL901 2.1 31.5 1.0
OD2 A:ASP250 2.3 36.1 1.0
O A:HOH377 2.4 29.2 1.0
P14 A:ZOL901 3.2 30.4 1.0
P9 A:ZOL901 3.3 31.3 1.0
CG A:ASP250 3.4 36.2 1.0
O13 A:ZOL901 3.4 29.9 1.0
C8 A:ZOL901 3.5 30.9 1.0
O A:HOH462 3.7 30.5 1.0
O A:HOH450 3.9 31.0 1.0
NE2 A:GLN247 4.0 32.9 1.0
OD1 A:ASP250 4.0 36.7 1.0
O17 A:ZOL901 4.1 31.2 1.0
OD2 A:ASP268 4.1 39.2 1.0
OD1 A:ASP254 4.2 41.1 1.0
O10 A:ZOL901 4.3 31.1 1.0
O A:ASP250 4.3 36.1 1.0
OD1 A:ASP268 4.3 38.8 1.0
O16 A:ZOL901 4.3 30.3 1.0
O11 A:ZOL901 4.3 31.0 1.0
OD1 A:ASP251 4.4 36.8 1.0
CB A:ASP250 4.4 36.0 1.0
NZ A:LYS264 4.6 42.4 1.0
C A:ASP250 4.6 36.2 1.0
CG A:ASP268 4.7 38.9 1.0
O A:HOH475 4.7 35.0 1.0
CB A:ASP254 4.8 40.6 1.0
CG A:ASP254 4.8 40.8 1.0
MG A:MG401 4.9 24.1 1.0
O A:HOH400 4.9 64.8 1.0

Magnesium binding site 3 out of 3 in 3iba

Go back to Magnesium Binding Sites List in 3iba
Magnesium binding site 3 out of 3 in the Crystal Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+


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 the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Zoledronate, Ipp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:13.1
occ:1.00
 O A:HOH507 1.9 24.6 1.0
O17 A:ZOL901 2.0 31.2 1.0
O A:HOH364 2.1 18.0 1.0
OD1 A:ASP98 2.1 30.3 1.0
O A:HOH380 2.2 25.8 1.0
OD2 A:ASP102 2.2 33.9 1.0
CG A:ASP98 3.1 30.9 1.0
CG A:ASP102 3.1 34.3 1.0
MG A:MG401 3.1 24.1 1.0
P14 A:ZOL901 3.2 30.4 1.0
O16 A:ZOL901 3.3 30.3 1.0
OD1 A:ASP102 3.3 33.1 1.0
OD2 A:ASP98 3.4 30.4 1.0
OD2 A:ASP170 3.6 38.4 1.0
NZ A:LYS273 3.9 37.3 1.0
O A:HOH450 4.0 31.0 1.0
C19 A:ZOL901 4.1 31.6 1.0
O15 A:ZOL901 4.2 30.3 1.0
O A:HOH462 4.3 30.5 1.0
CG A:ASP170 4.3 38.2 1.0
OE1 A:GLN167 4.4 34.3 1.0
C8 A:ZOL901 4.4 30.9 1.0
CB A:ASP98 4.5 31.0 1.0
NE2 A:GLN167 4.5 34.5 1.0
O A:HOH411 4.5 32.0 1.0
C7 A:ZOL901 4.5 31.0 1.0
CB A:ASP102 4.5 34.6 1.0
OD1 A:ASP170 4.6 38.2 1.0
N15 A:ZOL901 4.6 31.3 1.0
O10 A:ZOL901 4.6 31.1 1.0
O A:ASP98 4.7 31.2 1.0
NZ A:LYS207 4.8 29.4 1.0
O A:HOH365 4.9 18.8 1.0
CD A:GLN167 4.9 34.6 1.0

Reference:

C.H.Huang, S.B.Gabelli, E.Oldfield, L.M.Amzel. Binding of Nitrogen-Containing Bisphosphonates (N-Bps) to the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer. Proteins V. 78 888 2010.
ISSN: ISSN 0887-3585
PubMed: 19876942
DOI: 10.1002/PROT.22614
Page generated: Wed Aug 14 16:02:02 2024

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