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Calcium in PDB 1jg8: Crystal Structure of Threonine Aldolase (Low-Specificity)

Enzymatic activity of Crystal Structure of Threonine Aldolase (Low-Specificity)

All present enzymatic activity of Crystal Structure of Threonine Aldolase (Low-Specificity):
4.1.2.5;

Protein crystallography data

The structure of Crystal Structure of Threonine Aldolase (Low-Specificity), PDB code: 1jg8 was solved by C.L.Kielkopf, J.Bonanno, S.Ray, S.K.Burley, New York Sgx Research Centerfor Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.890, 100.600, 149.820, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 22.2

Other elements in 1jg8:

The structure of Crystal Structure of Threonine Aldolase (Low-Specificity) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Threonine Aldolase (Low-Specificity) (pdb code 1jg8). 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 Threonine Aldolase (Low-Specificity), PDB code: 1jg8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1jg8

Go back to Calcium Binding Sites List in 1jg8
Calcium binding site 1 out of 6 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:15.7
occ:1.00
 OE1 D:GLN236 2.5 11.8 1.0
O A:SER202 2.6 11.6 1.0
OG1 A:THR14 2.7 9.9 1.0
O A:THR14 2.7 11.7 1.0
O A:THR12 3.0 13.6 1.0
O A:ALA207 3.1 11.3 1.0
CD D:GLN236 3.4 13.4 1.0
O A:HOH910 3.4 13.1 1.0
C A:SER202 3.5 11.2 1.0
C A:THR14 3.7 12.8 1.0
NE2 D:GLN236 3.8 12.3 1.0
N A:THR14 3.9 11.9 1.0
C A:THR12 3.9 12.3 1.0
CB A:THR14 3.9 11.1 1.0
CA A:SER202 4.0 11.6 1.0
CA A:THR14 4.0 11.4 1.0
C A:ALA207 4.1 11.5 1.0
CB A:SER202 4.2 13.0 1.0
CA A:PRO208 4.4 11.3 1.0
C A:VAL13 4.5 12.4 1.0
CB D:ARG235 4.5 11.2 1.0
O A:LLP203 4.5 13.0 1.0
C A:CYS206 4.5 11.1 1.0
N A:LLP203 4.6 10.8 1.0
O A:ASP11 4.6 11.2 1.0
CG D:GLN236 4.6 12.4 1.0
CA A:THR12 4.6 13.0 1.0
O A:PRO208 4.6 11.6 1.0
O A:CYS206 4.7 10.6 1.0
CA A:CYS206 4.7 10.9 1.0
N A:PRO208 4.7 11.8 1.0
N A:VAL13 4.8 13.4 1.0
N A:ALA207 4.8 10.6 1.0
C A:PRO208 4.8 12.7 1.0
N A:LYS15 4.9 13.0 1.0
CA A:LLP203 4.9 11.8 1.0
CG D:ARG235 4.9 11.5 1.0
CA A:VAL13 5.0 12.6 1.0

Calcium binding site 2 out of 6 in 1jg8

Go back to Calcium Binding Sites List in 1jg8
Calcium binding site 2 out of 6 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:15.9
occ:1.00
 O B:SER202 2.6 10.8 1.0
OE1 C:GLN236 2.6 13.9 1.0
O B:THR14 2.7 13.5 1.0
OG1 B:THR14 2.7 12.2 1.0
O B:ALA207 2.9 10.9 1.0
O B:THR12 3.0 13.5 1.0
C B:SER202 3.5 11.5 1.0
CD C:GLN236 3.5 14.8 1.0
O B:HOH935 3.5 13.2 1.0
C B:THR14 3.7 13.7 1.0
N B:THR14 3.8 12.5 1.0
C B:THR12 3.9 12.9 1.0
NE2 C:GLN236 3.9 11.9 1.0
CB B:THR14 3.9 12.1 1.0
CA B:SER202 4.0 11.5 1.0
C B:ALA207 4.0 11.3 1.0
CA B:THR14 4.0 12.6 1.0
CB B:SER202 4.2 13.7 1.0
O B:LLP203 4.4 11.3 1.0
CA B:PRO208 4.4 11.9 1.0
C B:CYS206 4.4 11.4 1.0
C B:VAL13 4.5 13.4 1.0
N B:LLP203 4.5 12.1 1.0
O B:ASP11 4.5 11.1 1.0
CA B:THR12 4.5 13.2 1.0
CB C:ARG235 4.6 13.6 1.0
N B:ALA207 4.6 11.6 1.0
O B:CYS206 4.6 10.5 1.0
N B:PRO208 4.6 11.2 1.0
O B:PRO208 4.6 12.3 1.0
CA B:CYS206 4.7 10.8 1.0
CG C:GLN236 4.7 13.2 1.0
N B:VAL13 4.8 12.9 1.0
C B:PRO208 4.8 11.5 1.0
CA B:LLP203 4.8 11.9 1.0
N B:LYS15 4.8 14.0 1.0
CG C:ARG235 5.0 14.2 1.0
CA B:VAL13 5.0 13.4 1.0

Calcium binding site 3 out of 6 in 1jg8

Go back to Calcium Binding Sites List in 1jg8
Calcium binding site 3 out of 6 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:19.9
occ:1.00
 OD1 B:ASN330 2.4 16.1 1.0
O B:HOH992 2.5 22.4 1.0
OE1 B:GLU333 2.6 24.5 1.0
CD B:GLU333 3.5 24.0 1.0
CG B:ASN330 3.5 17.1 1.0
OE2 B:GLU333 3.6 24.2 1.0
ND2 B:ASN330 4.3 16.9 1.0
CA B:ASN330 4.5 15.3 1.0
CB B:ASN330 4.6 15.1 1.0
O B:HOH1098 4.6 26.2 1.0
CG B:GLU333 4.9 21.9 1.0
N B:ASN330 4.9 14.6 1.0

Calcium binding site 4 out of 6 in 1jg8

Go back to Calcium Binding Sites List in 1jg8
Calcium binding site 4 out of 6 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca904

b:16.7
occ:1.00
 OE1 B:GLN236 2.5 13.2 1.0
O C:SER202 2.7 12.5 1.0
O C:THR14 2.8 14.5 1.0
OG1 C:THR14 2.8 11.7 1.0
O C:ALA207 2.9 12.7 1.0
O C:THR12 2.9 12.3 1.0
CD B:GLN236 3.4 13.2 1.0
O C:HOH939 3.5 15.6 1.0
C C:SER202 3.6 12.8 1.0
C C:THR14 3.8 13.7 1.0
NE2 B:GLN236 3.8 11.0 1.0
C C:THR12 3.8 12.3 1.0
N C:THR14 3.9 12.9 1.0
C C:ALA207 4.0 13.0 1.0
CB C:THR14 4.0 13.1 1.0
CA C:SER202 4.0 12.3 1.0
CA C:THR14 4.1 13.8 1.0
CB C:SER202 4.2 12.8 1.0
CA C:PRO208 4.3 12.2 1.0
CA C:THR12 4.4 12.8 1.0
C C:CYS206 4.4 13.6 1.0
O C:PRO208 4.5 12.5 1.0
CB B:ARG235 4.5 10.9 1.0
O C:LLP203 4.6 13.1 1.0
C C:VAL13 4.6 12.6 1.0
O C:ASP11 4.6 14.7 1.0
O C:CYS206 4.6 13.1 1.0
N C:LLP203 4.6 12.1 1.0
N C:PRO208 4.6 12.4 1.0
C C:PRO208 4.6 13.1 1.0
CG B:GLN236 4.7 12.0 1.0
N C:ALA207 4.7 13.6 1.0
CA C:CYS206 4.7 13.0 1.0
N C:VAL13 4.8 12.8 1.0
CG B:ARG235 4.9 14.3 1.0
CA C:LLP203 4.9 12.9 1.0
N C:LYS15 5.0 13.3 1.0

Calcium binding site 5 out of 6 in 1jg8

Go back to Calcium Binding Sites List in 1jg8
Calcium binding site 5 out of 6 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca903

b:15.4
occ:1.00
 OE1 A:GLN236 2.6 12.9 1.0
O D:SER202 2.6 12.4 1.0
O D:THR14 2.7 14.2 1.0
OG1 D:THR14 2.8 13.9 1.0
O D:ALA207 2.9 13.1 1.0
O D:THR12 3.1 13.5 1.0
O D:HOH946 3.4 13.5 1.0
CD A:GLN236 3.5 12.5 1.0
C D:SER202 3.5 12.9 1.0
C D:THR14 3.7 15.5 1.0
NE2 A:GLN236 3.9 12.7 1.0
N D:THR14 3.9 13.9 1.0
CB D:THR14 3.9 14.1 1.0
C D:ALA207 3.9 12.0 1.0
C D:THR12 4.0 14.4 1.0
CA D:SER202 4.0 11.4 1.0
CA D:THR14 4.0 14.3 1.0
CB D:SER202 4.2 14.6 1.0
C D:CYS206 4.3 12.1 1.0
CA D:PRO208 4.4 12.8 1.0
O D:LLP203 4.4 13.2 1.0
O D:CYS206 4.5 13.6 1.0
O D:PRO208 4.5 12.4 1.0
N D:LLP203 4.5 13.3 1.0
C D:VAL13 4.6 14.8 1.0
N D:PRO208 4.6 12.6 1.0
N D:ALA207 4.6 12.2 1.0
O D:ASP11 4.6 11.4 1.0
CA D:CYS206 4.6 12.1 1.0
CA D:THR12 4.6 13.7 1.0
CB A:ARG235 4.7 12.1 1.0
C D:PRO208 4.7 12.2 1.0
CG A:GLN236 4.7 13.6 1.0
N D:VAL13 4.8 13.4 1.0
CA D:LLP203 4.8 13.1 1.0
N D:LYS15 4.9 15.0 1.0
CA D:ALA207 5.0 11.9 1.0

Calcium binding site 6 out of 6 in 1jg8

Go back to Calcium Binding Sites List in 1jg8
Calcium binding site 6 out of 6 in the Crystal Structure of Threonine Aldolase (Low-Specificity)


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 Threonine Aldolase (Low-Specificity) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca906

b:15.3
occ:1.00
 OE1 D:GLU333 2.2 14.9 1.0
OD1 D:ASN330 2.4 19.6 1.0
O D:HOH970 2.4 16.2 1.0
CG D:ASN330 3.4 19.8 1.0
CD D:GLU333 3.5 15.3 1.0
CB D:GLU333 3.9 13.5 1.0
ND2 D:ASN330 4.0 21.2 1.0
CG D:GLU333 4.3 13.9 1.0
O D:ASN330 4.4 13.6 1.0
OE2 D:GLU333 4.4 16.1 1.0
CA D:ASN330 4.4 15.3 1.0
CB D:ASN330 4.5 17.4 1.0
C D:ASN330 4.9 15.5 1.0

Reference:

C.L.Kielkopf, J.Bonanno, S.Ray, S.K.Burley. Crystal Structure of Low-Specificity Threonine Aldolase, A Key Enzyme in Glycine Biosynthesis To Be Published.
Page generated: Thu Jul 11 10:45:13 2024

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