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Magnesium in PDB 9hjs: Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C

Enzymatic activity of Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C

All present enzymatic activity of Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C:
2.5.1.1; 2.5.1.10; 2.5.1.29;

Protein crystallography data

The structure of Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C, PDB code: 9hjs was solved by R.Yehia, M.Giladi, Y.Haitin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.19 / 2.51
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.623, 69.081, 154.987, 90, 97.39, 90
R / Rfree (%) 22.7 / 27.1

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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C (pdb code 9hjs). 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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C, PDB code: 9hjs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 9hjs

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Magnesium binding site 1 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:71.6
occ:1.00
 OD2 A:ASP68 1.9 76.2 1.0
O3A A:GRG501 2.2 75.3 1.0
O A:HOH604 2.4 70.6 1.0
O2B A:GRG501 2.4 81.8 1.0
OD2 A:ASP64 2.6 75.6 1.0
O A:HOH603 2.6 73.8 1.0
PB A:GRG501 2.8 81.1 1.0
CG A:ASP68 3.0 71.0 1.0
MG A:MG503 3.4 72.2 1.0
CB A:ASP68 3.5 70.4 1.0
O3B A:GRG501 3.5 83.1 1.0
PA A:GRG501 3.5 80.4 1.0
CG A:ASP64 3.6 73.4 1.0
O1A A:GRG501 3.6 80.8 1.0
OD1 A:ASP64 3.8 74.1 1.0
OE1 A:GLU210 3.9 73.9 1.0
OD1 A:ASP68 4.1 69.0 1.0
NZ A:LYS212 4.1 82.6 1.0
O2A A:GRG501 4.1 77.6 1.0
OG A:SER70 4.1 74.6 1.0
O1B A:GRG501 4.1 78.4 1.0
NZ A:LYS202 4.2 88.7 1.0
OE2 A:GLU210 4.5 72.4 1.0
O A:HOH602 4.5 72.4 1.0
NH1 A:ARG73 4.6 79.0 1.0
CD A:GLU210 4.6 71.8 1.0
O A:ASP64 4.7 74.4 1.0
NH2 A:ARG73 4.7 80.1 1.0
CE A:LYS202 4.8 89.6 1.0
O1 A:GRG501 4.8 83.5 1.0
CB A:ASP64 4.9 71.8 1.0
OD1 A:ASP65 4.9 78.3 1.0
CA A:ASP68 5.0 69.9 1.0

Magnesium binding site 2 out of 12 in 9hjs

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Magnesium binding site 2 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:72.2
occ:1.00
 OD1 A:ASP64 1.8 74.1 1.0
O1A A:GRG501 2.1 80.8 1.0
O A:HOH601 2.1 67.8 1.0
OD2 A:ASP68 2.2 76.2 1.0
O A:HOH602 2.3 72.4 1.0
OD1 A:ASP68 2.8 69.0 1.0
CG A:ASP64 2.8 73.4 1.0
CG A:ASP68 2.8 71.0 1.0
OE1 A:GLN126 3.1 74.8 1.0
OD2 A:ASP64 3.2 75.6 1.0
PA A:GRG501 3.2 80.4 1.0
O3A A:GRG501 3.4 75.3 1.0
MG A:MG502 3.4 71.6 1.0
NE2 A:GLN126 3.8 78.0 1.0
CD A:GLN126 3.9 72.6 1.0
C1 A:GRG501 4.0 81.3 1.0
NZ A:LYS212 4.1 82.6 1.0
O1 A:GRG501 4.2 83.5 1.0
CB A:ASP64 4.2 71.8 1.0
OE2 A:GLU210 4.3 72.4 1.0
CB A:ASP68 4.3 70.4 1.0
O2A A:GRG501 4.4 77.6 1.0
OD2 A:ASP129 4.4 74.3 1.0
O A:ASP64 4.5 74.4 1.0
CA A:ASP64 4.8 70.4 1.0
NZ A:LYS151 4.8 78.3 1.0
O A:HOH604 4.9 70.6 1.0
C A:ASP64 4.9 72.3 1.0
O A:HOH603 4.9 73.8 1.0
PB A:GRG501 5.0 81.1 1.0

Magnesium binding site 3 out of 12 in 9hjs

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Magnesium binding site 3 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:71.7
occ:1.00
 OD2 B:ASP68 2.0 76.1 1.0
O2B B:GRG401 2.0 78.9 1.0
OD2 B:ASP64 2.2 72.2 1.0
O B:HOH505 2.4 81.2 1.0
O1A B:GRG401 2.9 76.1 1.0
CG B:ASP68 3.0 74.2 1.0
O B:HOH501 3.1 72.6 1.0
CG B:ASP64 3.3 72.2 1.0
PB B:GRG401 3.3 75.4 1.0
CB B:ASP68 3.4 70.1 1.0
O3A B:GRG401 3.6 77.2 1.0
PA B:GRG401 3.8 76.7 1.0
OD1 B:ASP64 3.8 73.0 1.0
OG B:SER70 4.0 67.2 1.0
OD1 B:ASP68 4.1 73.3 1.0
O B:HOH502 4.2 70.2 1.0
OD1 B:ASP65 4.2 78.4 1.0
MG B:MG403 4.2 67.8 1.0
O B:ASP64 4.2 69.9 1.0
O3B B:GRG401 4.3 73.3 1.0
O1B B:GRG401 4.3 80.5 1.0
OE1 B:GLU210 4.4 76.4 1.0
C B:ASP64 4.5 70.0 1.0
CB B:ASP64 4.5 70.5 1.0
N B:ASP65 4.8 67.5 1.0
NH2 B:ARG73 4.9 74.4 1.0
O1 B:GRG401 4.9 76.0 1.0
C1 B:GRG401 4.9 75.3 1.0
O2A B:GRG401 4.9 80.0 1.0
CA B:ASP68 4.9 69.0 1.0
CA B:ASP65 4.9 69.9 1.0
OE2 B:GLU210 4.9 77.3 1.0

Magnesium binding site 4 out of 12 in 9hjs

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Magnesium binding site 4 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:67.8
occ:1.00
 OD1 B:ASP64 2.3 73.0 1.0
O B:HOH502 2.4 70.2 1.0
O1A B:GRG401 2.6 76.1 1.0
OD2 B:ASP68 2.7 76.1 1.0
OD1 B:ASP68 2.8 73.3 1.0
CG B:ASP68 3.1 74.2 1.0
OE1 B:GLN126 3.2 75.4 1.0
OD2 B:ASP129 3.2 80.4 1.0
CG B:ASP64 3.3 72.2 1.0
OD2 B:ASP64 3.7 72.2 1.0
PA B:GRG401 3.8 76.7 1.0
CD B:GLN126 3.9 75.1 1.0
NE2 B:GLN126 4.0 74.0 1.0
O2A B:GRG401 4.0 80.0 1.0
OE2 B:GLU210 4.2 77.3 1.0
MG B:MG402 4.2 71.7 1.0
CG B:ASP129 4.3 79.0 1.0
O1 B:GRG401 4.6 76.0 1.0
CB B:ASP64 4.6 70.5 1.0
CB B:ASP68 4.7 70.1 1.0
C1 B:GRG401 4.7 75.3 1.0
O B:HOH505 4.7 81.2 1.0
CB B:ASP129 4.7 79.1 1.0
OE1 B:GLU67 4.8 76.8 1.0
O B:HOH507 4.9 74.4 1.0
O B:ASP64 4.9 69.9 1.0

Magnesium binding site 5 out of 12 in 9hjs

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Magnesium binding site 5 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:55.5
occ:1.00
 OD1 C:ASP64 2.1 52.6 1.0
O C:HOH503 2.3 60.1 1.0
O C:HOH501 2.4 56.2 1.0
OD2 C:ASP68 2.6 57.8 1.0
OD1 C:ASP68 2.7 50.9 1.0
CG C:ASP68 3.0 53.7 1.0
O1A C:GRG401 3.2 58.0 1.0
CG C:ASP64 3.2 54.2 1.0
OE1 C:GLN126 3.2 55.1 1.0
OD2 C:ASP129 3.8 59.6 1.0
OD2 C:ASP64 3.8 54.5 1.0
NE2 C:GLN126 3.8 57.8 1.0
CD C:GLN126 3.9 54.5 1.0
MG C:MG403 3.9 56.2 1.0
OE2 C:GLU210 4.3 59.1 1.0
PA C:GRG401 4.3 62.8 1.0
O1 C:GRG401 4.3 58.8 1.0
CB C:ASP64 4.4 48.2 1.0
C1 C:GRG401 4.5 58.4 1.0
O C:ASP64 4.5 51.2 1.0
OE1 C:GLU67 4.5 52.8 1.0
CB C:ASP68 4.5 54.2 1.0
CA C:ASP64 4.7 49.0 1.0
NH1 C:ARG133 4.8 52.1 1.0
CG C:ASP129 4.8 61.3 1.0
CG1 C:ILE130 4.9 52.0 1.0
O2A C:GRG401 4.9 56.7 1.0
C C:ASP64 5.0 50.2 1.0

Magnesium binding site 6 out of 12 in 9hjs

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Magnesium binding site 6 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:56.2
occ:1.00
 O1A C:GRG401 1.9 58.0 1.0
OD2 C:ASP68 2.1 57.8 1.0
O2B C:GRG401 2.1 60.0 1.0
O C:HOH508 2.3 53.8 1.0
O C:HOH512 2.4 63.6 1.0
OD2 C:ASP64 2.5 54.5 1.0
O C:HOH501 3.1 56.2 1.0
PB C:GRG401 3.1 62.1 1.0
PA C:GRG401 3.2 62.8 1.0
CG C:ASP68 3.2 53.7 1.0
CG C:ASP64 3.5 54.2 1.0
O3B C:GRG401 3.5 58.0 1.0
O3A C:GRG401 3.6 56.1 1.0
OD1 C:ASP64 3.6 52.6 1.0
CB C:ASP68 3.7 54.2 1.0
O2A C:GRG401 3.9 56.7 1.0
MG C:MG402 3.9 55.5 1.0
OE1 C:GLU210 4.0 59.4 1.0
OD1 C:ASP68 4.2 50.9 1.0
CE C:LYS202 4.4 58.1 1.0
O1B C:GRG401 4.4 59.2 1.0
O1 C:GRG401 4.4 58.8 1.0
O C:HOH503 4.5 60.1 1.0
NH2 C:ARG73 4.6 54.3 1.0
OE2 C:GLU210 4.6 59.1 1.0
OG C:SER70 4.6 59.9 1.0
C1 C:GRG401 4.6 58.4 1.0
NZ C:LYS212 4.6 61.5 1.0
CD C:GLU210 4.7 59.1 1.0
O C:ASP64 4.8 51.2 1.0
CB C:ASP64 4.9 48.2 1.0

Magnesium binding site 7 out of 12 in 9hjs

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Magnesium binding site 7 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:53.9
occ:1.00
 OD2 D:ASP68 1.9 52.3 1.0
OD1 D:ASP64 2.0 51.6 1.0
O D:HOH504 2.0 48.5 1.0
O1A D:GRG401 2.1 52.6 1.0
O D:HOH512 2.1 50.1 1.0
O D:HOH510 2.5 49.2 1.0
CG D:ASP68 2.7 50.8 1.0
CG D:ASP64 2.8 53.1 1.0
OD2 D:ASP64 2.9 50.4 1.0
MG D:MG403 2.9 52.2 1.0
OD1 D:ASP68 2.9 51.1 1.0
PA D:GRG401 3.4 53.5 1.0
O2A D:GRG401 3.7 52.4 1.0
OE1 D:GLN126 3.9 50.2 1.0
OD2 D:ASP129 4.1 50.2 1.0
C1 D:GRG401 4.1 52.5 1.0
OE2 D:GLU210 4.1 54.1 1.0
CB D:ASP68 4.1 53.6 1.0
O1 D:GRG401 4.1 50.7 1.0
CB D:ASP64 4.2 47.6 1.0
O2B D:GRG401 4.2 55.7 1.0
NE2 D:GLN126 4.4 47.7 1.0
O D:ASP64 4.5 53.6 1.0
CD D:GLN126 4.5 44.6 1.0
O3A D:GRG401 4.6 53.5 1.0
O D:HOH507 4.6 55.2 1.0
CA D:ASP64 4.8 48.9 1.0
C D:ASP64 4.9 51.5 1.0

Magnesium binding site 8 out of 12 in 9hjs

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Magnesium binding site 8 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:52.2
occ:1.00
 OD2 D:ASP68 1.9 52.3 1.0
O2B D:GRG401 2.1 55.7 1.0
O D:HOH507 2.1 55.2 1.0
O1A D:GRG401 2.4 52.6 1.0
OD2 D:ASP64 2.6 50.4 1.0
MG D:MG402 2.9 53.9 1.0
CG D:ASP68 3.0 50.8 1.0
PB D:GRG401 3.2 73.3 1.0
PA D:GRG401 3.4 53.5 1.0
O3A D:GRG401 3.4 53.5 1.0
CB D:ASP68 3.5 53.6 1.0
CG D:ASP64 3.6 53.1 1.0
OE1 D:GLU210 3.8 55.8 1.0
OD1 D:ASP64 3.8 51.6 1.0
O D:HOH512 3.9 50.1 1.0
O3B D:GRG401 4.0 59.3 1.0
O2A D:GRG401 4.0 52.4 1.0
OD1 D:ASP68 4.1 51.1 1.0
NH2 D:ARG73 4.3 52.6 1.0
OE2 D:GLU210 4.3 54.1 1.0
CE D:LYS202 4.4 58.8 1.0
OG D:SER70 4.4 59.8 1.0
O1B D:GRG401 4.4 51.6 1.0
CD D:GLU210 4.5 53.0 1.0
NZ D:LYS202 4.5 57.3 1.0
O D:HOH504 4.7 48.5 1.0
NZ D:LYS212 4.8 53.4 1.0
O1 D:GRG401 4.8 50.7 1.0
O D:ASP64 4.8 53.6 1.0
O D:HOH510 4.8 49.2 1.0
CB D:ASP64 4.9 47.6 1.0
C1 D:GRG401 4.9 52.5 1.0

Magnesium binding site 9 out of 12 in 9hjs

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Magnesium binding site 9 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:66.9
occ:1.00
 OD2 E:ASP64 2.1 67.9 1.0
OD2 E:ASP68 2.1 74.8 1.0
O2B E:GRG401 2.2 79.3 1.0
O1A E:GRG401 2.9 73.7 1.0
CG E:ASP68 3.0 69.6 1.0
CG E:ASP64 3.2 68.9 1.0
CB E:ASP68 3.3 70.7 1.0
PB E:GRG401 3.6 73.5 1.0
OD1 E:ASP64 3.7 67.1 1.0
OG E:SER70 3.8 72.8 1.0
O E:ASP64 3.9 70.8 1.0
O1B E:GRG401 3.9 69.5 1.0
MG E:MG403 4.0 73.4 1.0
CE E:LYS202 4.1 69.2 1.0
OD1 E:ASP65 4.1 66.7 1.0
PA E:GRG401 4.1 73.6 1.0
OD1 E:ASP68 4.1 69.4 1.0
C E:ASP64 4.2 66.4 1.0
O3A E:GRG401 4.3 74.7 1.0
OE1 E:GLU210 4.3 71.5 1.0
NH2 E:ARG73 4.3 69.5 1.0
CB E:ASP64 4.4 68.6 1.0
N E:ASP65 4.5 63.7 1.0
NZ E:LYS202 4.5 69.8 1.0
O E:HOH504 4.6 70.8 1.0
CA E:ASP65 4.6 62.9 1.0
O3B E:GRG401 4.7 71.4 1.0
C1 E:GRG401 4.7 73.2 1.0
CA E:ASP68 4.8 67.9 1.0
CB E:SER70 4.8 68.9 1.0
CA E:ASP64 4.9 65.4 1.0
O1 E:GRG401 4.9 72.8 1.0

Magnesium binding site 10 out of 12 in 9hjs

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Magnesium binding site 10 out of 12 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C


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 Human Geranylgeranyl Diphosphate Synthase Mutant R235C within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:73.4
occ:1.00
 O E:HOH502 2.0 69.4 1.0
OD1 E:ASP64 2.1 67.1 1.0
O1A E:GRG401 2.2 73.7 1.0
O E:HOH504 2.2 70.8 1.0
OD2 E:ASP68 2.6 74.8 1.0
OE1 E:GLN126 3.0 71.6 1.0
CG E:ASP64 3.1 68.9 1.0
PA E:GRG401 3.1 73.6 1.0
OD1 E:ASP68 3.3 69.4 1.0
CG E:ASP68 3.4 69.6 1.0
O1 E:GRG401 3.4 72.8 1.0
OD2 E:ASP64 3.5 67.9 1.0
O2A E:GRG401 3.5 75.5 1.0
NE2 E:GLN126 3.6 70.6 1.0
CD E:GLN126 3.7 71.0 1.0
OD2 E:ASP129 3.8 80.8 1.0
C1 E:GRG401 4.0 73.2 1.0
MG E:MG402 4.0 66.9 1.0
OE2 E:GLU210 4.3 76.7 1.0
CB E:ASP64 4.4 68.6 1.0
O3A E:GRG401 4.7 74.7 1.0
CB E:ASP68 4.8 70.7 1.0
O2B E:GRG401 4.8 79.3 1.0
CG E:ASP129 4.9 80.0 1.0
O E:ASP64 4.9 70.8 1.0
NZ E:LYS151 4.9 79.2 1.0

Reference:

R.Yehia, A.Kadek, J.M.Portasikova, P.Man, M.Giladi, Y.Haitin. Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant R235C To Be Published.
Page generated: Sat Aug 16 04:03:56 2025

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