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Sodium in PDB 5m99: Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization

Enzymatic activity of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization

All present enzymatic activity of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization:
3.2.1.1;

Protein crystallography data

The structure of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization, PDB code: 5m99 was solved by U.Hameed, I.Price, O.A.Mirza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.16 / 1.96
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 153.237, 153.237, 143.056, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 18.4

Other elements in 5m99:

The structure of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization also contains other interesting chemical elements:

Potassium (K) 2 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization (pdb code 5m99). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization, PDB code: 5m99:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 1 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:38.3
occ:1.00
 O A:GLY401 2.3 44.2 1.0
O A:ASP411 2.4 36.1 1.0
O A:CYS408 2.4 31.8 1.0
OD2 A:ASP406 2.5 46.6 1.0
OD1 A:ASP406 2.7 46.8 1.0
CG A:ASP406 2.9 53.6 1.0
OD1 A:ASP412 3.0 50.4 1.0
C A:ASP411 3.5 35.4 1.0
C A:GLY401 3.5 44.5 1.0
C A:CYS408 3.6 34.3 1.0
O A:HOH890 4.1 42.6 1.0
CG A:ASP412 4.2 46.0 1.0
CB A:CYS408 4.2 33.4 1.0
CA A:ASP412 4.2 33.5 1.0
C A:ASN402 4.3 46.0 1.0
N A:ASP412 4.3 33.7 1.0
CA A:CYS408 4.3 31.1 1.0
O A:ASN402 4.3 47.4 1.0
CA A:GLY401 4.4 42.2 1.0
N A:ASP411 4.4 34.0 1.0
CB A:ASP406 4.4 52.8 1.0
O A:HOH813 4.4 48.2 1.0
N A:CYS408 4.5 30.5 1.0
N A:ASN402 4.5 41.0 1.0
CB A:ASN402 4.5 46.6 1.0
O A:HOH968 4.5 50.6 1.0
N A:ALA403 4.5 42.4 1.0
CA A:ASP411 4.5 35.3 1.0
O A:ILE409 4.6 25.0 1.0
C A:ILE409 4.6 30.4 1.0
CA A:ASN402 4.6 41.5 1.0
N A:ILE409 4.6 28.8 1.0
CA A:ALA403 4.7 41.0 1.0
CB A:ASP412 4.8 36.5 1.0
CA A:ILE409 4.8 26.7 1.0

Sodium binding site 2 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 2 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:34.5
occ:1.00
 O A:VAL48 2.3 28.6 1.0
OD1 A:ASP46 2.3 35.7 1.0
OD1 A:ASP42 2.4 33.2 1.0
OD2 A:ASP50 2.4 33.5 1.0
O A:HOH867 2.4 34.8 1.0
OD1 A:ASP44 2.5 40.0 1.0
CG A:ASP46 3.2 39.0 1.0
CG A:ASP42 3.3 29.2 1.0
C A:VAL48 3.5 30.3 1.0
CG A:ASP50 3.5 32.3 1.0
OD2 A:ASP46 3.5 35.7 1.0
CG A:ASP44 3.5 43.8 1.0
N A:VAL48 3.9 29.1 1.0
CB A:ASP50 4.0 30.1 1.0
CB A:ASP42 4.0 29.1 1.0
CA A:ASP42 4.0 30.8 1.0
OD2 A:ASP44 4.0 47.1 1.0
O A:HOH897 4.1 41.1 1.0
CA A:VAL48 4.1 24.4 1.0
N A:ASP44 4.1 38.6 1.0
N A:SER43 4.1 33.0 1.0
CB A:VAL48 4.2 30.2 1.0
OD2 A:ASP42 4.2 33.8 1.0
N A:ASP46 4.3 39.8 1.0
C A:ASP42 4.4 33.1 1.0
N A:GLY45 4.5 35.1 1.0
CB A:ASP46 4.5 38.1 1.0
N A:GLY49 4.6 25.4 1.0
N A:ASP50 4.6 25.3 1.0
C A:GLY49 4.6 26.3 1.0
OD1 A:ASP50 4.6 35.0 1.0
CB A:ASP44 4.6 38.1 1.0
N A:GLY47 4.7 34.5 1.0
CA A:ASP44 4.7 41.5 1.0
CA A:GLY49 4.8 20.3 1.0
C A:ASP44 4.8 40.4 1.0
CA A:ASP46 4.8 36.5 1.0
CA A:ASP50 4.9 28.8 1.0
CG1 A:VAL48 4.9 25.6 1.0
O A:GLY49 4.9 28.9 1.0
O A:HOH866 5.0 46.3 1.0
O A:ASP94 5.0 29.5 1.0

Sodium binding site 3 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 3 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:26.8
occ:1.00
 O A:HOH778 2.3 23.2 1.0
O A:HIS217 2.3 23.1 1.0
O A:HOH701 2.4 34.4 1.0
OD1 A:ASN122 2.4 24.6 1.0
O A:HOH729 2.6 34.0 1.0
O A:ILE218 2.8 24.8 1.0
C A:ILE218 3.3 22.3 1.0
C A:HIS217 3.4 23.9 1.0
CG A:ASN122 3.5 25.9 1.0
OD2 A:ASP183 3.5 43.5 1.0
CA A:ILE218 3.6 24.9 1.0
O A:HOH801 3.7 20.6 1.0
ND2 A:ASN122 3.9 25.2 1.0
N A:ILE218 3.9 20.4 1.0
CG A:ASP183 4.0 33.4 1.0
O A:ASN122 4.1 21.8 1.0
O A:HOH955 4.1 28.9 1.0
N A:TYR219 4.2 20.6 1.0
CB A:ASP183 4.3 25.2 1.0
O A:LEU184 4.6 21.0 1.0
CA A:HIS217 4.6 23.7 1.0
CB A:HIS217 4.6 23.0 1.0
CA A:TYR219 4.6 23.7 1.0
O2 A:EDO612 4.6 35.2 1.0
OD1 A:ASP183 4.7 39.6 1.0
CB A:ASN122 4.7 20.0 1.0
C A:ASN122 4.9 21.8 1.0
CA A:ASN122 4.9 21.1 1.0
C A:TYR219 4.9 26.2 1.0

Sodium binding site 4 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 4 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:31.9
occ:1.00
 O A:ASP225 2.3 35.4 1.0
O A:HOH787 2.3 32.7 1.0
O A:LYS216 2.4 22.7 1.0
O A:TYR219 2.4 22.2 1.0
O A:HOH826 2.5 24.1 1.0
C A:ASP225 3.5 38.0 1.0
C A:LYS216 3.5 29.1 1.0
CA A:HIS217 3.5 23.7 1.0
C A:TYR219 3.6 26.2 1.0
C A:GLY226 3.7 35.9 1.0
O A:GLY226 3.8 28.5 1.0
OG A:SER230 3.9 22.8 1.0
N A:ILE227 3.9 29.2 1.0
N A:HIS217 4.0 21.6 1.0
CA A:GLY220 4.0 29.3 1.0
CA A:GLY226 4.0 31.2 1.0
ND1 A:HIS217 4.1 24.5 1.0
O A:HOH801 4.1 20.6 1.0
N A:GLY226 4.2 29.5 1.0
C A:HIS217 4.2 23.9 1.0
O A:TRP223 4.3 30.9 1.0
N A:GLY220 4.3 26.3 1.0
N A:ASP225 4.4 31.4 1.0
CA A:ILE227 4.5 28.8 1.0
O A:SER222 4.5 28.2 1.0
CB A:HIS217 4.5 23.0 1.0
CA A:ASP225 4.5 33.5 1.0
CG A:LYS216 4.6 32.8 1.0
O A:HIS217 4.6 23.1 1.0
CG A:HIS217 4.7 24.3 1.0
CA A:LYS216 4.7 21.8 1.0
N A:TYR219 4.8 20.6 1.0
CA A:TYR219 4.8 23.7 1.0
N A:ILE218 4.9 20.4 1.0
CB A:SER230 5.0 21.1 1.0
CE1 A:HIS217 5.0 26.2 1.0

Sodium binding site 5 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 5 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:34.7
occ:1.00
 O B:GLY401 2.3 35.8 1.0
O B:ASP411 2.3 30.8 1.0
O B:CYS408 2.4 26.6 1.0
OD2 B:ASP406 2.5 42.7 1.0
OD1 B:ASP406 2.6 39.7 1.0
OD1 B:ASP412 2.9 40.3 1.0
CG B:ASP406 3.0 47.2 1.0
C B:ASP411 3.4 32.0 1.0
C B:GLY401 3.5 39.5 1.0
C B:CYS408 3.6 28.9 1.0
O B:HOH938 3.6 38.3 1.0
CG B:ASP412 4.1 37.1 1.0
CA B:ASP412 4.2 28.6 1.0
N B:ASP412 4.2 29.3 1.0
N B:ASP411 4.2 25.1 1.0
CB B:CYS408 4.3 29.4 1.0
CA B:GLY401 4.3 37.0 1.0
C B:ASN402 4.3 41.4 1.0
CA B:CYS408 4.3 29.0 1.0
O B:ASN402 4.4 41.1 1.0
N B:CYS408 4.4 28.8 1.0
CA B:ASP411 4.4 29.2 1.0
O B:HOH1027 4.4 40.7 1.0
O B:ILE409 4.4 24.4 1.0
N B:ASN402 4.5 37.9 1.0
N B:ALA403 4.5 37.4 1.0
CB B:ASN402 4.5 44.4 1.0
CB B:ASP406 4.5 47.1 1.0
C B:ILE409 4.5 28.3 1.0
N B:ILE409 4.6 25.7 1.0
CA B:ASN402 4.6 38.4 1.0
CA B:ALA403 4.7 34.3 1.0
CA B:ILE409 4.7 27.4 1.0
CB B:ASP412 4.7 25.8 1.0
O B:HOH803 4.8 42.5 1.0
OD2 B:ASP412 5.0 44.4 1.0
N B:TYR410 5.0 25.3 1.0

Sodium binding site 6 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 6 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:26.2
occ:1.00
 OD1 B:ASP42 2.3 27.6 1.0
O B:VAL48 2.4 25.6 1.0
OD2 B:ASP50 2.4 24.4 1.0
OD1 B:ASP46 2.4 31.2 1.0
OD1 B:ASP44 2.4 34.9 1.0
O B:HOH809 2.5 28.4 1.0
CG B:ASP46 3.3 31.7 1.0
CG B:ASP42 3.3 30.0 1.0
CG B:ASP50 3.5 24.0 1.0
CG B:ASP44 3.5 40.0 1.0
C B:VAL48 3.5 25.4 1.0
OD2 B:ASP46 3.7 30.0 1.0
CB B:ASP50 3.9 26.1 1.0
CB B:ASP42 4.0 23.5 1.0
N B:VAL48 4.0 27.0 1.0
N B:ASP44 4.0 30.9 1.0
CA B:ASP42 4.0 23.6 1.0
O B:HOH977 4.1 36.9 1.0
OD2 B:ASP44 4.1 42.0 1.0
CA B:VAL48 4.1 25.2 1.0
N B:SER43 4.1 24.2 1.0
CB B:VAL48 4.2 24.4 1.0
OD2 B:ASP42 4.2 27.4 1.0
N B:ASP46 4.3 28.1 1.0
C B:ASP42 4.4 28.3 1.0
N B:GLY45 4.4 31.0 1.0
CB B:ASP44 4.6 30.2 1.0
OD1 B:ASP50 4.6 28.6 1.0
N B:ASP50 4.6 24.0 1.0
N B:GLY49 4.6 22.2 1.0
CB B:ASP46 4.6 30.1 1.0
C B:GLY49 4.6 21.4 1.0
CA B:ASP44 4.6 33.4 1.0
C B:ASP44 4.8 38.4 1.0
O B:HOH787 4.8 42.4 1.0
N B:GLY47 4.8 28.6 1.0
CA B:GLY49 4.8 19.4 1.0
CA B:ASP50 4.9 24.9 1.0
CA B:ASP46 4.9 27.5 1.0
CG1 B:VAL48 4.9 27.5 1.0
O B:GLY49 4.9 20.9 1.0
O B:HOH1158 4.9 40.5 1.0
O B:ASP94 5.0 29.3 1.0

Sodium binding site 7 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 7 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:29.7
occ:1.00
 O B:HIS217 2.3 23.3 1.0
O B:HOH757 2.3 24.1 1.0
OD1 B:ASN122 2.4 28.4 1.0
O B:HOH710 2.5 34.5 1.0
O B:HOH712 2.6 36.3 1.0
O B:ILE218 2.8 26.0 1.0
C B:ILE218 3.3 29.7 1.0
C B:HIS217 3.3 25.0 1.0
CG B:ASN122 3.4 27.1 1.0
CA B:ILE218 3.6 27.2 1.0
O B:HOH813 3.6 24.9 1.0
OD2 B:ASP183 3.6 47.2 1.0
ND2 B:ASN122 3.8 24.4 1.0
N B:ILE218 3.9 25.7 1.0
O B:ASN122 4.1 23.7 1.0
CG B:ASP183 4.1 30.6 1.0
O B:HOH1000 4.2 27.0 1.0
N B:TYR219 4.3 24.3 1.0
CB B:ASP183 4.4 26.1 1.0
CA B:HIS217 4.5 21.9 1.0
CB B:HIS217 4.6 19.6 1.0
O B:LEU184 4.6 24.6 1.0
CB B:ASN122 4.6 25.4 1.0
CA B:TYR219 4.7 26.5 1.0
CA B:ASN122 4.9 22.2 1.0
C B:ASN122 4.9 23.6 1.0
O1 B:EDO610 4.9 47.0 1.0
OD1 B:ASP183 4.9 42.6 1.0
C B:TYR219 4.9 32.4 1.0

Sodium binding site 8 out of 8 in 5m99

Go back to Sodium Binding Sites List in 5m99
Sodium binding site 8 out of 8 in the Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Archaic Form of Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:34.2
occ:1.00
 O B:ASP225 2.3 34.4 1.0
O B:HOH879 2.4 33.7 1.0
O B:HOH877 2.4 26.7 1.0
O B:LYS216 2.4 25.3 1.0
O B:TYR219 2.5 24.9 1.0
C B:ASP225 3.5 35.3 1.0
C B:LYS216 3.5 24.8 1.0
CA B:HIS217 3.6 21.9 1.0
C B:TYR219 3.7 32.4 1.0
C B:GLY226 3.7 35.2 1.0
O B:GLY226 3.7 32.6 1.0
OG B:SER230 4.0 24.4 1.0
CA B:GLY220 4.0 30.7 1.0
N B:HIS217 4.0 21.0 1.0
CA B:GLY226 4.1 32.1 1.0
N B:ILE227 4.1 27.9 1.0
ND1 B:HIS217 4.1 26.4 1.0
O B:TRP223 4.2 31.8 1.0
N B:GLY226 4.2 33.3 1.0
O B:HOH813 4.3 24.9 1.0
C B:HIS217 4.3 25.0 1.0
N B:GLY220 4.3 29.9 1.0
O B:SER222 4.4 32.6 1.0
N B:ASP225 4.5 29.8 1.0
CA B:ASP225 4.6 32.0 1.0
CA B:ILE227 4.6 29.1 1.0
CB B:HIS217 4.6 19.6 1.0
CG B:LYS216 4.6 31.8 1.0
O B:HIS217 4.7 23.3 1.0
CG B:HIS217 4.7 29.4 1.0
CA B:LYS216 4.8 24.9 1.0
N B:TYR219 4.8 24.3 1.0
CA B:TYR219 4.8 26.5 1.0
CB B:SER230 4.9 22.6 1.0
C B:TRP223 4.9 30.4 1.0
C B:ASP224 5.0 29.9 1.0
N B:ILE218 5.0 25.7 1.0
CE1 B:HIS217 5.0 28.6 1.0

Reference:

U.Hameed, I.Price, A.Ke, D.B.Wilson, O.Mirza. Functional Characterization and Crystal Structure of Thermostable Amylase From Thermotoga Petrophila, Reveals High Thermostability and An Unusual Form of Dimerization. Biochim. Biophys. Acta V.1865 1237 2017.
ISSN: ISSN 0006-3002
PubMed: 28648523
DOI: 10.1016/J.BBAPAP.2017.06.015
Page generated: Mon Oct 7 22:31:18 2024

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