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Calcium in PDB 3q2q: Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate

Enzymatic activity of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate

All present enzymatic activity of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate:
2.5.1.30;

Protein crystallography data

The structure of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate, PDB code: 3q2q was solved by Y.Patskovsky, R.Toro, M.Rutter, J.M.Sauder, C.D.Poulter, J.A.Gerlt, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.659, 71.659, 150.919, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate (pdb code 3q2q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate, PDB code: 3q2q:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3q2q

Go back to Calcium Binding Sites List in 3q2q
Calcium binding site 1 out of 3 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca360

b:52.8
occ:0.50
 O A:HOH552 2.2 67.5 1.0
O1A A:DMA359 2.3 69.1 0.5
O3B A:DMA359 2.3 51.1 0.5
OD2 A:ASP113 2.4 62.9 1.0
OD1 A:ASP117 2.6 83.1 1.0
OD1 A:ASP113 2.7 59.0 1.0
OD2 A:ASP117 2.7 93.4 1.0
O A:HOH553 2.8 71.8 1.0
CG A:ASP113 2.9 64.5 1.0
CG A:ASP117 3.0 85.5 1.0
O A:HOH565 3.3 67.8 1.0
PA A:DMA359 3.5 65.2 0.5
PB A:DMA359 3.6 67.9 0.5
O3A A:DMA359 3.8 63.8 0.5
O1 A:DMA359 3.9 64.7 0.5
NZ A:LYS197 4.1 62.5 1.0
O2B A:DMA359 4.2 60.2 0.5
C1 A:DMA359 4.3 55.2 0.5
CB A:ASP113 4.4 50.7 1.0
O A:ASP113 4.4 57.7 1.0
CB A:ASP117 4.5 85.2 1.0
O1B A:DMA359 4.8 56.2 0.5
O2A A:DMA359 4.8 56.0 0.5
C A:ASP113 4.9 55.3 1.0
C2 A:DMA359 5.0 57.7 0.5
O A:HOH555 5.0 84.3 1.0

Calcium binding site 2 out of 3 in 3q2q

Go back to Calcium Binding Sites List in 3q2q
Calcium binding site 2 out of 3 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca361

b:0.1
occ:1.00
 O A:HOH549 2.4 62.7 1.0
OD2 A:ASP238 2.4 42.2 0.5
O A:HOH557 2.5 80.5 1.0
O A:HOH548 2.6 60.3 1.0
O A:HOH550 2.9 76.3 1.0
O A:HOH562 3.1 90.0 1.0
CG A:ASP238 3.3 41.8 0.5
OD1 A:ASP238 3.5 49.4 0.5
O A:HOH545 4.1 55.9 1.0
O A:HOH554 4.4 83.8 1.0
CB A:ASP238 4.7 36.2 0.5
CB A:ASP238 4.7 35.2 0.5
OD2 A:ASP257 4.8 57.9 1.0
O A:ASP238 4.9 36.2 1.0
OD2 A:ASP238 4.9 51.2 0.5
OD1 A:ASP242 4.9 65.1 1.0
CB A:ASP242 5.0 40.9 1.0
O A:HOH544 5.0 71.2 1.0

Calcium binding site 3 out of 3 in 3q2q

Go back to Calcium Binding Sites List in 3q2q
Calcium binding site 3 out of 3 in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Complexed with Calcium and Isoprenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca364

b:43.5
occ:1.00
 O A:HOH402 2.3 69.2 1.0
O A:HOH437 2.4 58.6 1.0
OG A:SER303 2.5 44.9 1.0
OE2 A:GLU300 2.5 60.2 1.0
OE1 A:GLU300 3.0 83.6 1.0
CD A:GLU300 3.1 80.4 1.0
CB A:SER303 3.5 41.7 1.0
CG A:GLU300 4.5 64.7 1.0
O A:GLU300 4.6 42.8 1.0
C A:SER303 4.7 39.4 1.0
CA A:SER303 4.7 37.9 1.0
O A:SER303 4.8 37.7 1.0
CG A:GLN304 4.8 38.4 1.0

Reference:

F.H.Wallrapp, J.J.Pan, G.Ramamoorthy, D.E.Almonacid, B.S.Hillerich, R.Seidel, Y.Patskovsky, P.C.Babbitt, S.C.Almo, M.P.Jacobson, C.D.Poulter. Prediction of Function For the Polyprenyl Transferase Subgroup in the Isoprenoid Synthase Superfamily. Proc.Natl.Acad.Sci.Usa V. 110 E1196 2013.
ISSN: ISSN 0027-8424
PubMed: 23493556
DOI: 10.1073/PNAS.1300632110
Page generated: Tue Jul 8 15:45:32 2025

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