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Calcium in PDB 4lls: Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site

Enzymatic activity of Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site

All present enzymatic activity of Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site, PDB code: 4lls was solved by J.Kim, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, M.Stead, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.50 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.095, 83.032, 71.386, 90.00, 108.87, 90.00
R / Rfree (%) 16.9 / 19.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site (pdb code 4lls). 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site, PDB code: 4lls:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4lls

Go back to Calcium Binding Sites List in 4lls
Calcium binding site 1 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:17.7
occ:1.00
 OD1 A:ASP216 2.3 16.8 1.0
O A:HOH486 2.3 19.8 1.0
O2A A:GST302 2.3 21.2 1.0
O A:HOH523 2.3 22.0 1.0
O A:HOH522 2.5 19.9 1.0
O2B A:GST302 2.5 17.8 1.0
CG A:ASP216 3.4 16.4 1.0
PB A:GST302 3.5 18.9 1.0
PA A:GST302 3.6 17.8 1.0
O A:HOH627 3.7 35.7 1.0
O1B A:GST302 3.7 18.1 1.0
OD2 A:ASP216 3.8 17.3 1.0
O3B A:GST302 4.3 19.8 1.0
O A:ASP216 4.3 17.0 1.0
NZ A:LYS230 4.4 15.3 1.0
O A:HOH510 4.4 28.7 1.0
O1A A:GST302 4.5 18.4 1.0
O A:HOH477 4.5 30.0 1.0
OD1 A:ASP235 4.5 28.3 1.0
O A:HOH581 4.5 37.8 1.0
OD2 A:ASP235 4.5 26.0 1.0
CB A:ASP216 4.6 15.1 1.0
O3A A:GST302 4.7 17.8 1.0
NE2 A:GLN213 4.7 26.3 1.0
OD1 A:ASP217 4.7 19.8 1.0
CE A:LYS230 4.7 19.1 1.0
C A:ASP216 4.7 16.9 1.0
O A:HOH616 4.8 30.9 1.0
CB A:ASP220 4.9 23.3 1.0
CG A:ASP235 5.0 26.1 1.0
C5 A:IPE301 5.0 20.4 1.0

Calcium binding site 2 out of 6 in 4lls

Go back to Calcium Binding Sites List in 4lls
Calcium binding site 2 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:18.1
occ:0.90
 O3B A:GST302 2.2 19.8 1.0
OD2 A:ASP80 2.3 21.6 1.0
OD2 A:ASP86 2.3 20.2 1.0
O3A A:GST302 2.3 17.8 1.0
O A:HOH616 2.4 30.9 1.0
O A:HOH456 2.4 22.5 1.0
CG A:ASP86 3.3 19.7 1.0
CG A:ASP80 3.4 18.8 1.0
PA A:GST302 3.5 17.8 1.0
PB A:GST302 3.5 18.9 1.0
O1B A:GST302 3.7 18.1 1.0
CB A:ASP86 3.7 19.1 1.0
OD1 A:ASP80 3.9 22.2 1.0
O A:HOH527 3.9 24.4 1.0
O A:HOH632 4.1 31.5 1.0
O2A A:GST302 4.1 21.2 1.0
O A:HOH526 4.2 22.3 1.0
NH1 A:ARG91 4.2 16.8 1.0
C1 A:GST302 4.3 25.7 1.0
OD1 A:ASP88 4.4 28.6 1.0
O A:HOH627 4.4 35.7 1.0
OD1 A:ASP86 4.4 23.5 1.0
CA A:CA305 4.5 26.3 1.0
O2B A:GST302 4.6 17.8 1.0
CB A:ASP80 4.6 17.3 1.0
OD2 A:ASP81 4.7 19.7 1.0
O1A A:GST302 4.8 18.4 1.0
S1 A:GST302 4.8 22.9 1.0
O A:ASP80 4.9 16.7 1.0

Calcium binding site 3 out of 6 in 4lls

Go back to Calcium Binding Sites List in 4lls
Calcium binding site 3 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:26.3
occ:1.00
 O A:HOH632 2.2 31.5 1.0
O A:HOH527 2.4 24.4 1.0
OE1 A:GLU160 2.5 42.9 1.0
O A:HOH528 2.5 33.6 1.0
OD1 A:ASP86 2.6 23.5 1.0
O A:HOH529 2.6 46.9 1.0
OD2 A:ASP86 2.7 20.2 1.0
CG A:ASP86 3.0 19.7 1.0
OD2 A:ASP156 3.1 35.3 1.0
CD A:GLU160 3.6 59.6 1.0
O A:HOH586 4.0 36.7 1.0
O3B A:GST302 4.1 19.8 1.0
OD1 A:ASP80 4.2 22.2 1.0
OE2 A:GLU160 4.2 75.5 1.0
CG A:ASP156 4.2 31.7 1.0
CD A:LYS240 4.4 54.2 1.0
NZ A:LYS178 4.4 31.0 1.0
CA A:CA304 4.5 18.1 0.9
CB A:ASP86 4.5 19.1 1.0
CG A:GLU160 4.6 43.9 1.0
CE A:LYS240 4.7 61.1 1.0
CE A:LYS178 4.7 34.7 1.0
O A:HOH581 4.9 37.8 1.0
OE1 A:GLN153 4.9 24.4 1.0
O A:HOH616 4.9 30.9 1.0
OD1 A:ASP156 4.9 39.3 1.0
OD2 A:ASP80 5.0 21.6 1.0

Calcium binding site 4 out of 6 in 4lls

Go back to Calcium Binding Sites List in 4lls
Calcium binding site 4 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:24.6
occ:0.80
 O B:HOH601 2.2 47.8 1.0
O2A B:GST302 2.3 21.5 0.8
O2B B:GST302 2.3 24.0 0.8
OD2 B:ASP86 2.3 35.1 1.0
OD2 B:ASP80 2.3 29.3 1.0
O B:HOH512 2.6 30.9 1.0
CG B:ASP86 3.3 29.3 1.0
CG B:ASP80 3.5 25.9 1.0
PB B:GST302 3.5 27.1 0.8
PA B:GST302 3.5 22.0 0.8
O1B B:GST302 3.6 24.8 0.8
CB B:ASP86 3.7 25.2 1.0
OD1 B:ASP80 4.0 23.6 1.0
O B:HOH569 4.0 38.7 1.0
O1A B:GST302 4.1 24.3 0.8
NH1 B:ARG91 4.2 24.9 1.0
C1 B:GST302 4.2 36.8 0.8
O B:HOH599 4.2 39.0 1.0
OD2 B:ASP88 4.3 32.0 1.0
CA B:CA305 4.3 40.7 0.8
OD1 B:ASP86 4.4 29.3 1.0
O B:HOH598 4.6 35.5 1.0
O3B B:GST302 4.7 28.8 0.8
S1 B:GST302 4.7 34.4 0.8
CB B:ASP80 4.7 20.6 1.0
O3A B:GST302 4.7 20.3 0.8
OD2 B:ASP81 4.8 25.5 1.0

Calcium binding site 5 out of 6 in 4lls

Go back to Calcium Binding Sites List in 4lls
Calcium binding site 5 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:19.8
occ:0.80
 O B:HOH602 2.3 28.6 1.0
O1A B:GST302 2.3 24.3 0.8
O3B B:GST302 2.3 28.8 0.8
O B:HOH510 2.3 27.1 1.0
OD2 B:ASP216 2.3 25.2 1.0
O B:HOH509 2.4 24.1 1.0
CG B:ASP216 3.4 25.8 1.0
PB B:GST302 3.5 27.1 0.8
PA B:GST302 3.6 22.0 0.8
O1B B:GST302 3.8 24.8 0.8
OD1 B:ASP216 3.9 23.9 1.0
O2B B:GST302 4.2 24.0 0.8
O B:HOH588 4.4 34.2 1.0
O B:ASP216 4.4 24.3 1.0
NZ B:LYS230 4.4 24.4 1.0
O3A B:GST302 4.5 20.3 0.8
OD1 B:ASP235 4.5 37.6 1.0
NE2 B:GLN213 4.6 30.9 1.0
OD2 B:ASP235 4.6 34.3 1.0
CB B:ASP216 4.6 21.9 1.0
O2A B:GST302 4.7 21.5 0.8
CE B:LYS230 4.7 28.8 1.0
C B:ASP216 4.8 23.5 1.0
OD1 B:ASP217 4.8 28.2 1.0
CB B:ASP220 5.0 26.3 1.0

Calcium binding site 6 out of 6 in 4lls

Go back to Calcium Binding Sites List in 4lls
Calcium binding site 6 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp, and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:40.7
occ:0.80
 O B:HOH599 2.1 39.0 1.0
O B:HOH598 2.3 35.5 1.0
O B:HOH508 2.5 50.1 1.0
OD2 B:ASP86 2.5 35.1 1.0
OD1 B:ASP86 2.6 29.3 1.0
CG B:ASP86 2.9 29.3 1.0
OD2 B:ASP156 3.1 33.4 1.0
O2B B:GST302 3.9 24.0 0.8
O B:HOH600 3.9 37.0 1.0
NZ B:LYS178 4.0 37.8 1.0
CG B:ASP156 4.2 32.4 1.0
CA B:CA303 4.3 24.6 0.8
OE1 B:GLU160 4.3 72.2 1.0
OD1 B:ASP80 4.3 23.6 1.0
CB B:ASP86 4.4 25.2 1.0
CE B:LYS240 4.6 55.8 1.0
OD1 B:ASP156 4.9 36.1 1.0
OD2 B:ASP80 4.9 29.3 1.0
O B:HOH601 4.9 47.8 1.0

Reference:

J.Kim, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, M.Stead, J.A.Gerlt, S.C.Almo. Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Ipp, Gspp and Calcium Bound in Active Site To Be Published.
Page generated: Sun Jul 14 09:35:54 2024

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