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Calcium in PDB 8dk0: Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone

Enzymatic activity of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone

All present enzymatic activity of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone:
3.1.1.17;

Protein crystallography data

The structure of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone, PDB code: 8dk0 was solved by C.A.Bingman, B.W.Hall, R.W.Smith, B.G.Fox, T.J.Donohue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.03 / 1.55
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 47.51, 47.51, 199.02, 90, 90, 120
R / Rfree (%) 17.6 / 21

Other elements in 8dk0:

The structure of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone (pdb code 8dk0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone, PDB code: 8dk0:

Calcium binding site 1 out of 1 in 8dk0

Go back to Calcium Binding Sites List in 8dk0
Calcium binding site 1 out of 1 in the Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone


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 RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound (S)Gamma- Valerolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:24.6
occ:1.00
 OD1 A:ASN172 2.3 23.2 1.0
O A:HOH563 2.3 25.6 1.0
OD1 A:ASN123 2.4 25.8 1.0
OD1 A:ASP229 2.4 27.1 1.0
OE2 A:GLU15 2.4 29.0 1.0
OG A:SER230 2.5 25.2 1.0
O A:HOH504 2.7 28.6 1.0
HD21 A:ASN123 3.4 29.5 1.0
CG A:ASN172 3.4 23.5 1.0
CG A:ASN123 3.4 23.9 1.0
HD21 A:ASN55 3.4 35.7 1.0
HD21 A:ASN172 3.4 31.4 1.0
CD A:GLU15 3.5 30.4 1.0
CG A:ASP229 3.6 37.9 1.0
CB A:SER230 3.7 26.9 1.0
HB2 A:SER230 3.7 32.2 1.0
ND2 A:ASN123 3.8 24.6 1.0
ND2 A:ASN172 3.8 26.2 1.0
OE1 A:GLU15 3.8 28.1 1.0
HB2 A:ASP124 3.8 26.6 1.0
O6 A:YVR403 3.9 54.6 1.0
ND2 A:ASN55 3.9 29.8 1.0
HD22 A:ASN55 3.9 35.7 1.0
H A:SER230 3.9 28.6 1.0
N A:SER230 4.0 23.8 1.0
C5 A:YVR403 4.2 52.6 1.0
CA A:SER230 4.3 21.0 1.0
HA A:SER230 4.3 25.1 1.0
OD2 A:ASP229 4.3 37.9 1.0
HB3 A:SER230 4.4 32.2 1.0
HD22 A:ASN271 4.5 25.9 1.0
C A:ASP229 4.5 25.7 1.0
O A:THR270 4.5 25.4 1.0
OD2 A:ASP124 4.5 24.7 1.0
O1 A:YVR403 4.6 96.3 1.0
HA A:ASN172 4.6 30.9 1.0
H1 A:YVR403 4.6 76.0 1.0
HA A:ASP229 4.6 29.1 1.0
HD22 A:ASN123 4.6 29.5 1.0
O A:ASN123 4.7 22.2 1.0
CB A:ASN172 4.7 24.4 1.0
HD22 A:ASN172 4.7 31.4 1.0
HB A:THR270 4.7 36.2 1.0
HG3 A:GLU15 4.7 34.8 1.0
CB A:ASP229 4.7 23.5 1.0
CG A:GLU15 4.7 29.0 1.0
CB A:ASP124 4.7 22.2 1.0
CB A:ASN123 4.8 26.0 1.0
O A:ASN55 4.8 25.6 1.0
H4 A:YVR403 4.8 69.2 1.0
ND2 A:ASN271 4.8 21.6 1.0
C A:ASN172 4.8 22.4 1.0
CA A:ASP229 4.9 24.2 1.0
C A:ASN123 4.9 26.4 1.0
HD21 A:ASN271 4.9 25.9 1.0
HB3 A:ASP229 4.9 28.2 1.0
HB3 A:ASN123 4.9 31.2 1.0
C4 A:YVR403 4.9 63.4 1.0
H5 A:YVR403 5.0 102.5 1.0
CA A:ASN172 5.0 25.8 1.0
HA2 A:GLY173 5.0 28.7 1.0
CG A:ASP124 5.0 24.5 1.0
HB3 A:ASN172 5.0 29.3 1.0
CG A:ASN55 5.0 31.3 1.0

Reference:

B.W.Hall, C.A.Bingman, B.G.Fox, D.R.Noguera, T.J.Donohue. A Broad Specificity Beta-Propeller Enzyme From Rhodopseudomonas Palustris That Hydrolyzes Many Lactones Including Gamma-Valerolactone. J.Biol.Chem. 02782 2022.
ISSN: ESSN 1083-351X
PubMed: 36502920
DOI: 10.1016/J.JBC.2022.102782
Page generated: Thu Jul 10 03:57:49 2025

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