Calcium in PDB 9c7i: Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site

Enzymatic activity of Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site

All present enzymatic activity of Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site:
4.2.1.138; 4.2.3.89;

Protein crystallography data

The structure of Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site, PDB code: 9c7i was solved by R.Prem Kumar, J.O.Matos, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.57 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.522, 89.804, 114.11, 90, 90.82, 90
R / Rfree (%) 21.1 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site (pdb code 9c7i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site, PDB code: 9c7i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 9c7i

Go back to Calcium Binding Sites List in 9c7i
Calcium binding site 1 out of 6 in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site


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 Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:32.3
occ:1.00
 OE1 A:GLN268 2.3 24.4 1.0
OD2 D:ASP254 2.4 24.3 1.0
OE2 A:GLU265 2.5 22.4 1.0
O A:HOH637 2.5 24.5 1.0
O A:HOH640 2.6 21.9 1.0
OE1 A:GLU265 2.7 24.1 1.0
O A:HOH611 2.7 21.5 1.0
CD A:GLU265 2.9 27.7 1.0
CD A:GLN268 3.3 23.7 1.0
CG D:ASP254 3.4 26.0 1.0
NE2 A:GLN268 3.8 22.5 1.0
CB D:ASP254 3.9 26.0 1.0
O A:HOH556 3.9 28.8 1.0
NE2 A:HIS10 4.3 27.3 1.0
CG A:GLU265 4.4 20.4 1.0
O A:HOH524 4.4 21.9 1.0
OD1 D:ASP254 4.5 29.9 1.0
CG A:GLN268 4.7 21.8 1.0
O D:HOH670 4.7 33.5 1.0
O A:HOH510 4.8 20.0 1.0
CB A:GLN268 4.9 21.1 1.0
CE1 A:HIS10 4.9 26.3 1.0

Calcium binding site 2 out of 6 in 9c7i

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Calcium binding site 2 out of 6 in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site


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 Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:33.1
occ:1.00
 OD2 C:ASP254 2.4 27.1 1.0
O C:HOH577 2.4 20.5 1.0
OE1 B:GLN268 2.4 29.0 1.0
OE1 B:GLU265 2.4 24.8 1.0
O B:HOH576 2.5 30.0 1.0
O C:HOH659 2.6 26.0 1.0
OE2 B:GLU265 2.6 31.3 1.0
CD B:GLU265 2.8 31.2 1.0
CG C:ASP254 3.4 28.8 1.0
CD B:GLN268 3.5 29.9 1.0
CB C:ASP254 3.8 28.7 1.0
O C:HOH513 3.9 31.3 1.0
NE2 B:GLN268 3.9 32.9 1.0
CG B:GLU265 4.3 20.4 1.0
O B:HOH675 4.4 33.4 1.0
OD1 C:ASP254 4.5 34.7 1.0
O B:HOH517 4.6 22.5 1.0
O C:HOH679 4.6 23.6 1.0
CG B:GLN268 4.8 26.6 1.0
NE2 B:HIS10 4.8 28.0 1.0
O B:HOH683 4.9 42.4 1.0
CB B:GLN268 5.0 21.7 1.0
CB B:GLU265 5.0 21.9 1.0

Calcium binding site 3 out of 6 in 9c7i

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Calcium binding site 3 out of 6 in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site


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 Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:33.3
occ:1.00
 O B:HOH606 2.3 40.3 1.0
O A:HOH520 2.4 36.9 1.0
OE1 B:GLU169 2.6 35.8 1.0
O B:VAL164 2.6 38.6 1.0
O B:HOH648 2.8 29.4 1.0
CD B:GLU169 3.5 42.9 1.0
O D:HOH584 3.6 37.7 1.0
C B:VAL164 3.7 39.4 1.0
OE2 B:GLU169 3.8 50.3 1.0
CA B:PRO165 3.9 34.2 1.0
OE2 A:GLU273 4.1 35.3 1.0
N B:SER166 4.2 38.4 1.0
N B:PRO165 4.3 38.3 1.0
OE2 B:GLU158 4.4 33.8 1.0
C B:PRO165 4.5 41.9 1.0
O B:HOH652 4.5 32.1 1.0
N B:VAL164 4.6 36.9 1.0
OE1 A:GLU273 4.6 29.9 1.0
NH2 A:ARG269 4.7 33.7 1.0
O A:HOH642 4.7 31.1 1.0
CD A:GLU273 4.8 34.4 1.0
CA B:VAL164 4.8 38.6 1.0
CG B:GLU169 4.9 38.8 1.0

Calcium binding site 4 out of 6 in 9c7i

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Calcium binding site 4 out of 6 in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:23.7
occ:1.00
 OE1 C:GLN268 2.3 26.8 1.0
O B:HOH619 2.3 27.8 1.0
O C:HOH643 2.3 24.1 1.0
OE1 C:GLU265 2.4 21.3 1.0
OD2 B:ASP254 2.5 24.2 1.0
OE2 C:GLU265 2.5 19.6 1.0
O B:HOH629 2.6 27.7 1.0
CD C:GLU265 2.8 23.8 1.0
CD C:GLN268 3.3 28.1 1.0
CG B:ASP254 3.5 25.4 1.0
NE2 C:GLN268 3.7 27.9 1.0
CB B:ASP254 3.9 27.2 1.0
O C:HOH618 4.1 29.4 1.0
CG C:GLU265 4.3 16.0 1.0
O B:HOH634 4.4 27.7 1.0
O C:HOH535 4.5 20.8 1.0
O C:HOH678 4.5 29.8 1.0
OD1 B:ASP254 4.5 25.6 1.0
CG C:GLN268 4.7 23.0 1.0
NE2 C:HIS10 4.7 24.4 1.0
O C:HOH559 4.8 22.0 1.0
O B:HOH680 4.9 30.6 1.0
CB C:GLN268 4.9 25.2 1.0

Calcium binding site 5 out of 6 in 9c7i

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Calcium binding site 5 out of 6 in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:35.8
occ:1.00
 O C:VAL164 2.4 40.3 1.0
O D:HOH507 2.4 34.0 1.0
O C:HOH585 2.5 31.9 1.0
O C:HOH658 2.7 34.3 1.0
OE1 C:GLU169 2.8 39.6 1.0
O C:HOH648 2.9 31.3 1.0
O D:HOH512 3.3 31.5 1.0
C C:VAL164 3.5 37.5 1.0
O C:HOH634 3.7 34.6 1.0
CD C:GLU169 3.7 39.1 1.0
CA C:PRO165 3.8 32.9 1.0
OE2 C:GLU169 3.9 42.3 1.0
NH1 D:ARG269 4.0 40.1 1.0
N C:SER166 4.1 35.3 1.0
N C:PRO165 4.1 35.1 1.0
OE2 C:GLU158 4.2 43.6 1.0
OE2 D:GLU273 4.3 33.7 1.0
C C:PRO165 4.3 36.5 1.0
N C:VAL164 4.5 36.9 1.0
CA C:VAL164 4.7 40.7 1.0
OE1 D:GLU273 4.7 30.3 1.0
O D:HOH638 4.9 22.2 1.0
O C:HOH576 4.9 34.7 1.0
CD D:GLU273 4.9 29.1 1.0

Calcium binding site 6 out of 6 in 9c7i

Go back to Calcium Binding Sites List in 9c7i
Calcium binding site 6 out of 6 in the Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Caryolan-1-Ol Synthase From S. Griseus with Peg Molecule in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:24.2
occ:1.00
 OD2 A:ASP254 2.3 29.3 1.0
O D:HOH620 2.3 21.1 1.0
OE2 D:GLU265 2.4 25.2 1.0
OE1 D:GLN268 2.4 27.8 1.0
O D:HOH577 2.5 26.9 1.0
O A:HOH646 2.5 27.9 1.0
OE1 D:GLU265 2.5 20.6 1.0
CD D:GLU265 2.8 27.1 1.0
CG A:ASP254 3.3 27.5 1.0
CD D:GLN268 3.5 28.2 1.0
CB A:ASP254 3.7 29.8 1.0
NE2 D:GLN268 3.9 28.9 1.0
CG D:GLU265 4.3 18.3 1.0
O A:HOH648 4.3 29.6 1.0
OD1 A:ASP254 4.3 32.6 1.0
O D:HOH673 4.3 28.4 1.0
O D:HOH566 4.5 19.2 1.0
O D:HOH651 4.6 28.4 1.0
NE2 D:HIS10 4.6 25.5 1.0
CG D:GLN268 4.8 25.1 1.0
O A:HOH687 4.8 24.2 1.0
O A:HOH679 4.9 35.2 1.0
O A:HOH569 4.9 35.5 1.0
CB D:GLN268 4.9 20.2 1.0

Reference:

R.P.Kumar, J.O.Matos, B.Y.Black, W.H.Ellenburg, J.Chen, M.Patterson, J.A.Gehtman, D.L.Theobald, I.J.Krauss, D.D.Oprian. Crystal Structure of Caryolan-1-Ol Synthase, A Sesquiterpene Synthase Catalyzing An Initial Anti-Markovnikov Cyclization Reaction. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39400323
DOI: 10.1021/ACS.BIOCHEM.4C00547
Page generated: Wed Nov 13 07:23:37 2024

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