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Sodium in PDB 8djf: Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Tetrahedral Intermediate

Enzymatic activity of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Tetrahedral Intermediate

All present enzymatic activity of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Tetrahedral Intermediate:
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 Tetrahedral Intermediate, PDB code: 8djf 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 (%) 17.8 / 21.2

Other elements in 8djf:

The structure of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Tetrahedral Intermediate also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 8djf

Go back to Sodium Binding Sites List in 8djf
Sodium binding site 1 out of 1 in the Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Tetrahedral Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Tetrahedral Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.7
occ:1.00
 O A:HOH598 2.3 28.3 1.0
O A:ILE272 2.3 25.1 1.0
OD1 A:ASN271 2.5 23.4 1.0
O A:HOH551 2.6 27.8 1.0
O A:HOH608 2.6 24.8 1.0
O A:LEU231 2.7 24.7 1.0
HB2 A:ALA232 3.2 30.1 1.0
H A:ILE272 3.4 30.0 1.0
C A:ILE272 3.5 22.9 1.0
CG A:ASN271 3.5 23.0 1.0
HB2 A:ALA273 3.6 32.4 1.0
HD21 A:ASN271 3.7 26.1 1.0
C A:LEU231 3.7 23.1 1.0
HA A:ALA273 3.9 32.9 1.0
ND2 A:ASN271 4.0 21.8 1.0
H A:LEU231 4.0 28.1 1.0
O A:HOH613 4.1 28.1 1.0
CB A:ALA232 4.1 25.1 1.0
N A:ILE272 4.1 25.0 1.0
HB3 A:SER230 4.1 30.8 1.0
HA A:ALA232 4.2 29.1 1.0
HG23 A:ILE272 4.2 32.6 1.0
HG2 A:PRO17 4.3 30.1 1.0
O A:HOH552 4.3 22.8 1.0
N A:ALA273 4.3 25.8 1.0
CB A:ALA273 4.4 27.0 1.0
O A:HOH568 4.4 22.9 1.0
CA A:ALA273 4.4 27.4 1.0
N A:ALA232 4.4 23.5 1.0
CA A:ALA232 4.5 24.2 1.0
CA A:ILE272 4.5 27.4 1.0
N A:LEU231 4.5 23.4 1.0
HD2 A:PRO17 4.5 29.7 1.0
HB1 A:ALA232 4.6 30.1 1.0
O A:HOH518 4.6 29.3 1.0
OD2 A:ASP124 4.6 24.1 1.0
O A:HOH538 4.6 26.0 1.0
HB3 A:ALA232 4.7 30.1 1.0
CA A:LEU231 4.7 22.0 1.0
HG22 A:ILE272 4.8 32.6 1.0
HB1 A:ALA273 4.8 32.4 1.0
CB A:ASN271 4.8 26.2 1.0
HD22 A:ASN271 4.8 26.1 1.0
O A:PRO17 4.9 25.2 1.0
CG2 A:ILE272 4.9 27.2 1.0
HB3 A:ASN271 4.9 31.4 1.0
HA A:ASN271 5.0 29.8 1.0
HA A:LEU231 5.0 26.4 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: Wed Oct 9 11:29:42 2024

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