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Magnesium in PDB 1iv3: Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)

Enzymatic activity of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)

All present enzymatic activity of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms):
4.6.1.12;

Protein crystallography data

The structure of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms), PDB code: 1iv3 was solved by H.Kishida, T.Wada, S.Unzai, T.Kuzuyama, T.Terada, M.Sirouzu, S.Yokoyama, J.R.H.Tame, S.-Y.Park, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.52
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.179, 106.179, 148.811, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms) (pdb code 1iv3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms), PDB code: 1iv3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1iv3

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Magnesium binding site 1 out of 6 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1561

b:23.1
occ:1.00
 OD2 A:ASP8 1.9 16.5 1.0
ND1 A:HIS42 2.0 22.9 1.0
NE2 A:HIS10 2.0 27.1 1.0
O A:HOH1662 2.3 38.4 1.0
CG A:ASP8 2.6 14.3 1.0
OD1 A:ASP8 2.7 16.4 1.0
CE1 A:HIS42 2.8 30.4 1.0
CE1 A:HIS10 2.9 28.9 1.0
CG A:HIS42 3.0 13.5 1.0
CD2 A:HIS10 3.1 30.2 1.0
CB A:HIS42 3.5 9.4 1.0
CB A:ASP8 4.0 14.2 1.0
NE2 A:HIS42 4.0 21.9 1.0
ND1 A:HIS10 4.0 28.6 1.0
CD2 A:HIS42 4.1 16.1 1.0
CG A:HIS10 4.1 29.8 1.0
O A:HOH1617 4.3 25.3 1.0
NZ C:LYS532 4.3 23.7 1.0
O A:SER9 4.5 19.0 1.0
CD1 A:ILE57 4.6 21.3 1.0
OG A:SER35 4.8 59.9 1.0
CA A:ALA39 4.8 14.1 1.0
O A:ASP38 4.8 12.4 1.0
CA A:GLY37 4.9 18.8 1.0
C A:GLY37 4.9 18.8 1.0

Magnesium binding site 2 out of 6 in 1iv3

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Magnesium binding site 2 out of 6 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1562

b:24.4
occ:1.00
 NE2 B:HIS210 1.8 27.8 1.0
O B:HOH1609 1.9 26.7 1.0
ND1 B:HIS242 1.9 24.9 1.0
OD2 B:ASP208 2.1 16.6 1.0
OD1 B:ASP208 2.4 18.8 1.0
CG B:ASP208 2.6 19.1 1.0
CE1 B:HIS210 2.7 36.4 1.0
CE1 B:HIS242 2.8 15.8 1.0
CD2 B:HIS210 3.0 23.6 1.0
CG B:HIS242 3.0 16.6 1.0
CB B:HIS242 3.5 9.2 1.0
ND1 B:HIS210 3.8 34.5 1.0
NE2 B:HIS242 4.0 18.8 1.0
CB B:ASP208 4.0 12.5 1.0
CG B:HIS210 4.0 23.3 1.0
CD2 B:HIS242 4.1 19.2 1.0
NZ A:LYS132 4.2 19.2 1.0
O B:SER209 4.7 14.2 1.0
OG B:SER235 4.7 29.5 1.0
CD1 B:ILE257 4.7 14.5 1.0
CA B:ALA239 4.9 10.2 1.0
O B:HOH1571 4.9 14.8 1.0
O B:ASP238 4.9 9.8 1.0
CA B:GLY237 4.9 16.3 1.0
C B:GLY237 5.0 17.8 1.0

Magnesium binding site 3 out of 6 in 1iv3

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Magnesium binding site 3 out of 6 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1563

b:21.9
occ:1.00
 OD2 C:ASP408 1.9 16.1 1.0
O C:HOH1599 1.9 23.3 1.0
ND1 C:HIS442 2.0 17.8 1.0
NE2 C:HIS410 2.0 22.2 1.0
CE1 C:HIS410 2.5 33.0 1.0
CG C:ASP408 2.5 12.5 1.0
OD1 C:ASP408 2.7 16.2 1.0
CE1 C:HIS442 2.9 24.8 1.0
CG C:HIS442 3.0 14.8 1.0
CD2 C:HIS410 3.2 22.2 1.0
CB C:HIS442 3.5 10.4 1.0
ND1 C:HIS410 3.8 27.3 1.0
NE2 C:HIS442 4.0 20.7 1.0
CB C:ASP408 4.0 11.1 1.0
CD2 C:HIS442 4.1 18.5 1.0
CG C:HIS410 4.1 24.6 1.0
O C:HOH1616 4.2 26.2 1.0
NZ B:LYS332 4.5 24.8 1.0
OG C:SER435 4.7 34.7 1.0
CD1 C:ILE457 4.7 33.1 1.0
CA C:GLY437 4.7 19.9 1.0
O C:SER409 4.7 16.8 1.0
CA C:ALA439 4.8 13.6 1.0
C C:GLY437 4.8 16.9 1.0
O C:ASP438 4.9 13.3 1.0
O C:HOH1584 5.0 17.8 1.0
CA C:HIS442 5.0 13.4 1.0

Magnesium binding site 4 out of 6 in 1iv3

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Magnesium binding site 4 out of 6 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1564

b:27.6
occ:1.00
 NE2 D:HIS1010 1.9 20.7 1.0
O F:HOH500 2.0 39.8 1.0
OD2 D:ASP1008 2.1 24.8 1.0
ND1 D:HIS1042 2.1 21.8 1.0
CE1 D:HIS1010 2.4 28.2 1.0
OD1 D:ASP1008 2.5 20.0 1.0
CG D:ASP1008 2.6 23.9 1.0
CE1 D:HIS1042 3.0 17.7 1.0
CD2 D:HIS1010 3.2 19.2 1.0
CG D:HIS1042 3.2 15.3 1.0
CB D:HIS1042 3.6 9.5 1.0
ND1 D:HIS1010 3.6 33.1 1.0
NZ F:LYS1532 3.9 20.0 1.0
CG D:HIS1010 4.0 28.0 1.0
CB D:ASP1008 4.0 16.3 1.0
NE2 D:HIS1042 4.1 18.0 1.0
CD2 D:HIS1042 4.3 20.2 1.0
O F:HOH151 4.4 20.0 1.0
CD1 D:ILE1057 4.4 17.9 1.0
O D:SER1009 4.5 19.0 1.0
O D:HOH144 4.7 19.9 1.0
OG D:SER1035 4.8 38.5 1.0

Magnesium binding site 5 out of 6 in 1iv3

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Magnesium binding site 5 out of 6 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1565

b:32.0
occ:1.00
 OD2 E:ASP1208 1.9 14.1 1.0
NE2 E:HIS1210 2.0 20.5 1.0
O E:HOH552 2.1 48.2 1.0
ND1 E:HIS1242 2.2 20.1 1.0
CG E:ASP1208 2.4 14.5 1.0
OD1 E:ASP1208 2.5 13.1 1.0
CE1 E:HIS1210 2.6 29.7 1.0
CE1 E:HIS1242 3.1 25.1 1.0
CD2 E:HIS1210 3.2 18.1 1.0
CG E:HIS1242 3.3 12.8 1.0
CB E:HIS1242 3.6 9.8 1.0
CB E:ASP1208 3.8 10.4 1.0
ND1 E:HIS1210 3.8 28.4 1.0
O E:HOH224 4.1 23.6 1.0
NZ D:LYS1132 4.1 17.8 1.0
CG E:HIS1210 4.1 25.7 1.0
NE2 E:HIS1242 4.3 19.2 1.0
CD2 E:HIS1242 4.3 14.3 1.0
O E:SER1209 4.7 19.3 1.0
CA E:ALA1239 4.7 11.0 1.0
CD1 E:ILE1257 4.8 16.9 1.0
N E:SER1209 4.8 14.5 1.0
O E:ASP1238 4.8 12.5 1.0
O E:HOH53 4.9 14.9 1.0
CA E:ASP1208 4.9 12.8 1.0

Magnesium binding site 6 out of 6 in 1iv3

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Magnesium binding site 6 out of 6 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Mg Atoms) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1566

b:24.8
occ:1.00
 NE2 F:HIS1410 1.7 24.3 1.0
OD2 F:ASP1408 2.0 22.9 1.0
ND1 F:HIS1442 2.0 18.4 1.0
O F:HOH490 2.2 38.3 1.0
CE1 F:HIS1410 2.4 27.5 1.0
CG F:ASP1408 2.6 19.0 1.0
OD1 F:ASP1408 2.6 16.5 1.0
CE1 F:HIS1442 2.9 20.7 1.0
CD2 F:HIS1410 2.9 24.5 1.0
CG F:HIS1442 3.1 16.4 1.0
CB F:HIS1442 3.6 10.9 1.0
ND1 F:HIS1410 3.6 31.5 1.0
CG F:HIS1410 3.8 29.7 1.0
CB F:ASP1408 4.0 13.8 1.0
NE2 F:HIS1442 4.1 23.5 1.0
CD2 F:HIS1442 4.2 19.7 1.0
NZ E:LYS1332 4.2 22.8 1.0
O F:HOH240 4.4 24.8 1.0
O F:SER1409 4.5 20.6 1.0
OG F:SER1435 4.5 45.3 1.0
CD1 F:ILE1457 4.7 20.2 1.0
CA F:ALA1439 4.8 9.5 1.0
O F:ASP1438 4.9 11.1 1.0
CA F:GLY1437 4.9 21.2 1.0
O E:HOH156 4.9 20.4 1.0
C F:GLY1437 5.0 26.5 1.0

Reference:

H.Kishida, T.Wada, S.Unzai, T.Kuzuyama, M.Takagi, T.Terada, M.Shirouzu, S.Yokoyama, J.R.Tame, S.Y.Park. Structure and Catalytic Mechanism of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate (Mecdp) Synthase, An Enzyme in the Non-Mevalonate Pathway of Isoprenoid Synthesis. Acta Crystallogr.,Sect.D V. 59 23 2003.
ISSN: ISSN 0907-4449
PubMed: 12499535
DOI: 10.1107/S0907444902017705
Page generated: Mon Dec 14 06:06:52 2020

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