Atomistry » Magnesium » PDB 1it7-1jbz » 1iv3
Atomistry »
  Magnesium »
    PDB 1it7-1jbz »
      1iv3 »

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

Go back to Magnesium Binding Sites List in 1iv3
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

Go back to Magnesium Binding Sites List in 1iv3
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

Go back to Magnesium Binding Sites List in 1iv3
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

Go back to Magnesium Binding Sites List in 1iv3
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

Go back to Magnesium Binding Sites List in 1iv3
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

Go back to Magnesium Binding Sites List in 1iv3
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: Tue Aug 13 05:39:10 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy