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Praseodymium in PDB 5avk: Crystal Structure of Proteinase K From Engyodontium Album

Enzymatic activity of Crystal Structure of Proteinase K From Engyodontium Album

All present enzymatic activity of Crystal Structure of Proteinase K From Engyodontium Album:
3.4.21.64;

Protein crystallography data

The structure of Crystal Structure of Proteinase K From Engyodontium Album, PDB code: 5avk was solved by M.Sugahara, K.Numata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.55 / 1.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.480, 67.480, 107.128, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.4

Praseodymium Binding Sites:

The binding sites of Praseodymium atom in the Crystal Structure of Proteinase K From Engyodontium Album (pdb code 5avk). This binding sites where shown within 5.0 Angstroms radius around Praseodymium atom.
In total 2 binding sites of Praseodymium where determined in the Crystal Structure of Proteinase K From Engyodontium Album, PDB code: 5avk:
Jump to Praseodymium binding site number: 1; 2;

Praseodymium binding site 1 out of 2 in 5avk

Go back to Praseodymium Binding Sites List in 5avk
Praseodymium binding site 1 out of 2 in the Crystal Structure of Proteinase K From Engyodontium Album


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 1 of Crystal Structure of Proteinase K From Engyodontium Album within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr1006

b:10.1
occ:0.72
O A:HOH1325 2.4 13.9 1.0
O A:PRO175 2.4 9.6 1.0
O A:HOH1121 2.4 20.0 1.0
OD2 A:ASP200 2.4 10.0 1.0
O A:VAL177 2.4 9.9 1.0
O A:HOH1197 2.4 9.8 1.0
O A:HOH1188 2.4 12.0 1.0
OD1 A:ASP200 2.5 13.1 1.0
O A:HOH1150 2.5 20.1 1.0
CG A:ASP200 2.8 12.8 1.0
C A:PRO175 3.5 8.9 1.0
C A:VAL177 3.6 7.5 1.0
N A:VAL177 4.1 9.3 1.0
CB A:ASP200 4.3 9.6 1.0
CA A:PRO175 4.3 10.1 1.0
O A:HOH1414 4.3 26.7 1.0
C A:SER176 4.4 10.9 1.0
O A:VAL198 4.4 11.0 1.0
N A:SER176 4.5 9.2 1.0
CA A:VAL177 4.5 9.0 1.0
N A:CYS178 4.6 7.5 1.0
CA A:CYS178 4.6 7.7 1.0
CA A:SER176 4.7 9.6 1.0
O A:GLU174 4.7 8.6 1.0
O A:HOH1151 4.7 25.6 1.0
N A:THR179 4.7 7.3 1.0
O A:HOH1413 4.8 28.6 1.0
O A:HOH1351 4.9 21.3 1.0
O A:HOH1166 5.0 23.6 1.0

Praseodymium binding site 2 out of 2 in 5avk

Go back to Praseodymium Binding Sites List in 5avk
Praseodymium binding site 2 out of 2 in the Crystal Structure of Proteinase K From Engyodontium Album


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 2 of Crystal Structure of Proteinase K From Engyodontium Album within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr1007

b:16.5
occ:0.66
O A:HOH1335 2.3 27.1 1.0
O A:HOH1289 2.4 20.2 1.0
O A:HOH1309 2.4 21.4 1.0
O A:HOH1370 2.4 24.9 1.0
OD1 A:ASP260 2.5 18.8 1.0
O A:THR16 2.5 15.4 1.0
O A:HOH1315 2.5 18.5 1.0
O A:HOH1356 2.5 25.4 1.0
OD2 A:ASP260 2.6 19.5 1.0
CG A:ASP260 2.9 22.6 1.0
O A:HOH1365 3.6 23.4 1.0
C A:THR16 3.7 13.9 1.0
CB A:ASP260 4.4 17.4 1.0
O A:HOH1110 4.4 27.2 1.0
CB A:THR16 4.5 13.6 1.0
CA A:THR16 4.6 12.7 1.0
N A:SER17 4.6 13.2 1.0
O A:HOH1463 4.6 30.7 1.0
CA A:SER17 4.7 15.1 1.0
O A:HOH1369 4.9 34.8 1.0
OD1 A:ASN257 4.9 16.4 1.0
O A:HOH1123 4.9 17.6 1.0
NH2 A:ARG12 5.0 11.9 1.0
OG1 A:THR16 5.0 17.4 1.0

Reference:

K.Yazawa, M.Sugahara, K.Yutani, M.Takehira, K.Numata. Derivatization of Proteinase K with Heavy Atoms Enhances Its Thermal Stability. Acs Catalysis V. 6 3036 2016.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.6B00100
Page generated: Thu Oct 29 06:39:29 2020

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