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Magnesium in PDB 1iv4: Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)

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

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

Protein crystallography data

The structure of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate), PDB code: 1iv4 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 / 1.55
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.364, 106.364, 149.190, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.7

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate) (pdb code 1iv4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate), PDB code: 1iv4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 1iv4

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Magnesium binding site 1 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


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 Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1561

b:22.8
occ:1.00
 O A:HOH1625 1.9 19.0 1.0
ND1 A:HIS42 1.9 14.9 1.0
OD2 A:ASP8 2.0 14.8 1.0
NE2 A:HIS10 2.1 29.3 1.0
CG A:ASP8 2.7 14.2 1.0
CE1 A:HIS42 2.7 18.7 1.0
OD1 A:ASP8 2.8 14.9 1.0
CE1 A:HIS10 2.9 27.6 1.0
CG A:HIS42 3.1 12.6 1.0
CD2 A:HIS10 3.1 21.9 1.0
MG A:MG1571 3.3 22.2 1.0
O A:HOH1642 3.4 22.7 1.0
CB A:HIS42 3.6 11.1 1.0
NE2 A:HIS42 3.9 20.2 1.0
ND1 A:HIS10 4.0 16.3 1.0
CD2 A:HIS42 4.1 13.4 1.0
CB A:ASP8 4.1 9.9 1.0
CG A:HIS10 4.1 17.1 1.0
NZ C:LYS532 4.4 14.1 1.0
O A:SER9 4.5 14.7 1.0
CD1 A:ILE57 4.6 31.8 1.0
OG A:SER35 4.7 65.7 1.0
O2P C:C5P1601 4.7 15.2 1.0
O A:ASP38 4.8 11.8 1.0
CA A:GLY37 5.0 21.1 1.0
O C:HOH1610 5.0 13.6 1.0
CA A:ALA39 5.0 9.7 1.0
O C:HOH1623 5.0 18.7 1.0

Magnesium binding site 2 out of 12 in 1iv4

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Magnesium binding site 2 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


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 Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1571

b:22.2
occ:1.00
 O C:HOH1623 2.0 18.7 1.0
NZ C:LYS532 2.1 14.1 1.0
OD1 A:ASP8 2.1 14.9 1.0
O2P C:C5P1601 2.2 15.2 1.0
O A:HOH1625 2.2 19.0 1.0
O A:HOH1642 2.4 22.7 1.0
CE C:LYS532 2.7 29.5 1.0
CG A:ASP8 3.2 14.2 1.0
MG A:MG1561 3.3 22.8 1.0
P C:C5P1601 3.3 16.6 1.0
O3P C:C5P1601 3.6 18.0 1.0
OD2 A:ASP8 3.9 14.8 1.0
O A:SER9 4.0 14.7 1.0
CD C:LYS532 4.2 38.9 1.0
O5' C:C5P1601 4.2 16.3 1.0
O C:HOH1610 4.3 13.6 1.0
CB A:ASP8 4.4 9.9 1.0
N A:SER9 4.4 12.0 1.0
O1P C:C5P1601 4.4 21.0 1.0
OE1 C:GLU535 4.5 35.6 1.0
NE2 A:HIS10 4.5 29.3 1.0
CA A:ASP8 4.6 8.8 1.0
CE1 A:HIS10 4.6 27.6 1.0
C5' C:C5P1601 4.9 15.3 1.0
CB C:LYS532 4.9 20.2 1.0
ND1 A:HIS42 4.9 14.9 1.0
CD1 A:ILE57 4.9 31.8 1.0

Magnesium binding site 3 out of 12 in 1iv4

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Magnesium binding site 3 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


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 Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1572

b:22.0
occ:1.00
 O B:HOH1630 1.8 20.0 1.0
O B:HOH1647 2.1 24.6 1.0
NZ A:LYS132 2.1 18.6 1.0
O2P A:C5P1602 2.1 17.1 1.0
OD1 B:ASP208 2.2 15.5 1.0
O A:HOH1643 2.2 23.0 1.0
CE A:LYS132 2.8 29.3 1.0
MG B:MG1562 3.2 23.2 1.0
CG B:ASP208 3.3 11.4 1.0
P A:C5P1602 3.3 19.4 1.0
O3P A:C5P1602 3.5 17.1 1.0
OD2 B:ASP208 3.9 15.8 1.0
O B:SER209 4.1 13.4 1.0
O B:HOH1677 4.2 35.2 1.0
CD A:LYS132 4.2 37.4 1.0
O5' A:C5P1602 4.3 20.1 1.0
NE2 B:HIS210 4.3 19.3 1.0
O A:HOH1612 4.3 13.9 1.0
OE1 A:GLU135 4.3 28.5 1.0
CE1 B:HIS210 4.3 32.4 1.0
O1P A:C5P1602 4.3 24.0 1.0
CB B:ASP208 4.4 9.0 1.0
N B:SER209 4.5 11.9 1.0
CD1 B:ILE257 4.7 21.2 1.0
CA B:ASP208 4.7 10.2 1.0
ND1 B:HIS242 4.8 17.5 1.0
C5' A:C5P1602 4.9 20.5 1.0
CB A:LYS132 5.0 18.5 1.0

Magnesium binding site 4 out of 12 in 1iv4

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Magnesium binding site 4 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


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 Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1562

b:23.2
occ:1.00
 O B:HOH1630 1.9 20.0 1.0
NE2 B:HIS210 1.9 19.3 1.0
ND1 B:HIS242 2.0 17.5 1.0
OD2 B:ASP208 2.0 15.8 1.0
CE1 B:HIS210 2.6 32.4 1.0
CG B:ASP208 2.7 11.4 1.0
OD1 B:ASP208 2.8 15.5 1.0
CE1 B:HIS242 2.8 15.5 1.0
O B:HOH1647 3.1 24.6 1.0
CD2 B:HIS210 3.1 21.0 1.0
O B:HOH1677 3.1 35.2 1.0
CG B:HIS242 3.1 15.0 1.0
MG A:MG1572 3.2 22.0 1.0
CB B:HIS242 3.6 10.5 1.0
ND1 B:HIS210 3.8 22.2 1.0
NE2 B:HIS242 4.0 13.9 1.0
CG B:HIS210 4.1 17.0 1.0
CB B:ASP208 4.1 9.0 1.0
CD2 B:HIS242 4.2 14.6 1.0
NZ A:LYS132 4.3 18.6 1.0
CD1 B:ILE257 4.5 21.2 1.0
O B:SER209 4.5 13.4 1.0
OG B:SER235 4.6 73.9 1.0
O2P A:C5P1602 4.7 17.1 1.0
O A:HOH1643 4.9 23.0 1.0
O A:HOH1612 4.9 13.9 1.0
O B:ASP238 5.0 10.7 1.0
CA B:ALA239 5.0 10.0 1.0
CA B:GLY237 5.0 14.1 1.0
N B:SER209 5.0 11.9 1.0

Magnesium binding site 5 out of 12 in 1iv4

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Magnesium binding site 5 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


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 Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1573

b:20.9
occ:1.00
 O C:HOH1632 2.0 20.5 1.0
O C:HOH1622 2.0 18.7 1.0
OD1 C:ASP408 2.1 14.6 1.0
NZ B:LYS332 2.1 14.9 1.0
O2P B:C5P1603 2.2 18.8 1.0
O B:HOH1640 2.4 22.6 1.0
CE B:LYS332 2.8 27.8 1.0
CG C:ASP408 3.2 13.6 1.0
MG C:MG1563 3.2 21.4 1.0
P B:C5P1603 3.4 18.4 1.0
O3P B:C5P1603 3.7 15.4 1.0
OD2 C:ASP408 3.7 17.3 1.0
O C:SER409 4.1 15.0 1.0
CD B:LYS332 4.2 32.5 1.0
NE2 C:HIS410 4.2 19.3 1.0
O C:HOH1615 4.2 16.4 1.0
O5' B:C5P1603 4.4 18.4 1.0
CE1 C:HIS410 4.4 20.3 1.0
CB C:ASP408 4.4 8.5 1.0
N C:SER409 4.5 8.8 1.0
O1P B:C5P1603 4.5 20.6 1.0
OE1 B:GLU335 4.6 35.9 1.0
CA C:ASP408 4.7 11.0 1.0
CD1 C:ILE457 4.7 25.5 1.0
ND1 C:HIS442 4.8 22.4 1.0
CD2 C:HIS410 5.0 24.9 1.0

Magnesium binding site 6 out of 12 in 1iv4

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Magnesium binding site 6 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


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 Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1563

b:21.4
occ:1.00
 O C:HOH1632 1.9 20.5 1.0
OD2 C:ASP408 1.9 17.3 1.0
ND1 C:HIS442 2.0 22.4 1.0
NE2 C:HIS410 2.1 19.3 1.0
CG C:ASP408 2.7 13.6 1.0
CE1 C:HIS442 2.8 26.0 1.0
CE1 C:HIS410 2.8 20.3 1.0
OD1 C:ASP408 2.9 14.6 1.0
CG C:HIS442 3.1 9.9 1.0
CD2 C:HIS410 3.2 24.9 1.0
MG B:MG1573 3.2 20.9 1.0
O C:HOH1622 3.3 18.7 1.0
CB C:HIS442 3.6 13.2 1.0
NE2 C:HIS442 4.0 20.3 1.0
ND1 C:HIS410 4.0 19.8 1.0
CB C:ASP408 4.1 8.5 1.0
CD2 C:HIS442 4.2 14.1 1.0
CG C:HIS410 4.2 24.0 1.0
NZ B:LYS332 4.4 14.9 1.0
CD1 C:ILE457 4.5 25.5 1.0
O C:SER409 4.6 15.0 1.0
OG C:SER435 4.7 54.6 1.0
O C:ASP438 4.7 12.9 1.0
O2P B:C5P1603 4.8 18.8 1.0
CA C:ALA439 4.8 14.1 1.0
O C:HOH1615 4.8 16.4 1.0
CA C:GLY437 4.9 25.6 1.0
C C:GLY437 5.0 23.5 1.0
C C:ASP438 5.0 16.1 1.0

Magnesium binding site 7 out of 12 in 1iv4

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Magnesium binding site 7 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1564

b:21.5
occ:1.00
 O F:HOH154 1.8 20.0 1.0
ND1 D:HIS1042 2.0 21.3 1.0
NE2 D:HIS1010 2.0 27.3 1.0
OD2 D:ASP1008 2.1 15.9 1.0
CG D:ASP1008 2.7 13.1 1.0
CE1 D:HIS1010 2.7 25.5 1.0
OD1 D:ASP1008 2.8 13.9 1.0
CE1 D:HIS1042 2.9 18.1 1.0
MG D:MG1574 3.1 24.0 1.0
CG D:HIS1042 3.1 14.8 1.0
O D:HOH234 3.1 23.5 1.0
CD2 D:HIS1010 3.2 24.9 1.0
CB D:HIS1042 3.5 9.7 1.0
ND1 D:HIS1010 3.9 25.7 1.0
NE2 D:HIS1042 4.0 19.2 1.0
CB D:ASP1008 4.1 10.3 1.0
CG D:HIS1010 4.1 21.9 1.0
NZ F:LYS1532 4.2 14.6 1.0
CD2 D:HIS1042 4.2 18.5 1.0
CD1 D:ILE1057 4.5 30.2 1.0
O D:SER1009 4.5 14.0 1.0
OG D:SER1035 4.6 55.3 1.0
O2P F:C5P1604 4.6 20.4 1.0
O F:HOH416 4.8 34.7 1.0
O D:HOH74 4.9 16.1 1.0
CA D:ALA1039 5.0 9.9 1.0
O D:ASP1038 5.0 11.0 1.0

Magnesium binding site 8 out of 12 in 1iv4

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Magnesium binding site 8 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1574

b:24.0
occ:1.00
 NZ F:LYS1532 2.0 14.6 1.0
O F:HOH154 2.0 20.0 1.0
OD1 D:ASP1008 2.1 13.9 1.0
O2P F:C5P1604 2.2 20.4 1.0
O F:HOH416 2.2 34.7 1.0
O D:HOH234 2.2 23.5 1.0
CE F:LYS1532 2.7 25.0 1.0
MG D:MG1564 3.1 21.5 1.0
CG D:ASP1008 3.3 13.1 1.0
P F:C5P1604 3.4 19.0 1.0
O3P F:C5P1604 3.7 15.2 1.0
OD2 D:ASP1008 3.8 15.9 1.0
O D:SER1009 4.1 14.0 1.0
CD F:LYS1532 4.1 27.7 1.0
NE2 D:HIS1010 4.3 27.3 1.0
O5' F:C5P1604 4.3 18.3 1.0
O D:HOH74 4.4 16.1 1.0
O D:HOH438 4.4 36.6 1.0
CE1 D:HIS1010 4.4 25.5 1.0
CB D:ASP1008 4.4 10.3 1.0
O1P F:C5P1604 4.5 18.7 1.0
N D:SER1009 4.6 9.7 1.0
OE2 F:GLU1535 4.6 29.9 1.0
CA D:ASP1008 4.7 8.8 1.0
ND1 D:HIS1042 4.7 21.3 1.0
CD1 D:ILE1057 4.8 30.2 1.0
C5' F:C5P1604 5.0 16.5 1.0

Magnesium binding site 9 out of 12 in 1iv4

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Magnesium binding site 9 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1575

b:19.9
occ:1.00
 O D:HOH157 1.9 20.0 1.0
O E:HOH204 2.0 21.8 1.0
O D:HOH161 2.1 20.1 1.0
NZ D:LYS1132 2.1 14.4 1.0
O2P D:C5P1605 2.1 18.4 1.0
OD1 E:ASP1208 2.2 15.5 1.0
CE D:LYS1132 2.8 28.6 1.0
MG E:MG1565 3.0 25.9 1.0
CG E:ASP1208 3.3 15.9 1.0
P D:C5P1605 3.4 17.7 1.0
O3P D:C5P1605 3.7 17.1 1.0
OD2 E:ASP1208 3.8 13.6 1.0
O E:SER1209 4.2 13.7 1.0
NE2 E:HIS1210 4.3 16.9 1.0
CE1 E:HIS1210 4.3 22.4 1.0
CD D:LYS1132 4.3 30.4 1.0
O5' D:C5P1605 4.4 14.8 1.0
O E:HOH54 4.4 15.0 1.0
O D:HOH459 4.4 37.7 1.0
O1P D:C5P1605 4.4 18.2 1.0
CB E:ASP1208 4.4 12.6 1.0
N E:SER1209 4.6 13.3 1.0
CA E:ASP1208 4.7 9.2 1.0
ND1 E:HIS1242 4.7 17.6 1.0

Magnesium binding site 10 out of 12 in 1iv4

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Magnesium binding site 10 out of 12 in the Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase (Bound Form Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1565

b:25.9
occ:1.00
 OD2 E:ASP1208 1.8 13.6 1.0
O D:HOH157 1.9 20.0 1.0
ND1 E:HIS1242 2.1 17.6 1.0
NE2 E:HIS1210 2.2 16.9 1.0
CG E:ASP1208 2.4 15.9 1.0
OD1 E:ASP1208 2.5 15.5 1.0
CE1 E:HIS1210 2.9 22.4 1.0
CE1 E:HIS1242 3.0 17.3 1.0
MG D:MG1575 3.0 19.9 1.0
CG E:HIS1242 3.1 12.6 1.0
O E:HOH204 3.1 21.8 1.0
CD2 E:HIS1210 3.3 19.1 1.0
CB E:HIS1242 3.5 10.8 1.0
CB E:ASP1208 3.9 12.6 1.0
ND1 E:HIS1210 4.0 24.6 1.0
NE2 E:HIS1242 4.1 18.3 1.0
NZ D:LYS1132 4.2 14.4 1.0
CD2 E:HIS1242 4.2 16.1 1.0
CG E:HIS1210 4.2 16.6 1.0
O E:SER1209 4.6 13.7 1.0
O2P D:C5P1605 4.7 18.4 1.0
CD1 E:ILE1257 4.7 19.8 1.0
O D:HOH161 4.7 20.1 1.0
O E:ASP1238 4.7 12.9 1.0
O E:HOH54 4.8 15.0 1.0
CA E:ALA1239 4.8 10.4 1.0
N E:SER1209 4.9 13.3 1.0
CA E:ASP1208 5.0 9.2 1.0
CA E:HIS1242 5.0 11.7 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

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