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Calcium in PDB 1m6s: Crystal Structure of Threonine Aldolase

Enzymatic activity of Crystal Structure of Threonine Aldolase

All present enzymatic activity of Crystal Structure of Threonine Aldolase:
4.1.2.5;

Protein crystallography data

The structure of Crystal Structure of Threonine Aldolase, PDB code: 1m6s was solved by S.K.Burley, C.L.Kielkopf, 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 / 21.3

Other elements in 1m6s:

The structure of Crystal Structure of Threonine Aldolase also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Threonine Aldolase (pdb code 1m6s). 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, PDB code: 1m6s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1m6s

Go back to Calcium Binding Sites List in 1m6s
Calcium binding site 1 out of 6 in the Crystal Structure of Threonine Aldolase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1301

b:15.9
occ:1.00
 O A:SER198 2.5 12.2 1.0
OE1 D:GLN232 2.5 11.9 1.0
OG1 A:THR10 2.7 10.5 1.0
O A:THR10 2.8 11.4 1.0
O A:THR8 3.0 13.7 1.0
O A:ALA203 3.0 11.2 1.0
CD D:GLN232 3.4 13.2 1.0
O A:HOH1313 3.4 13.2 1.0
C A:SER198 3.5 11.7 1.0
C A:THR10 3.7 12.9 1.0
NE2 D:GLN232 3.8 12.8 1.0
N A:THR10 3.9 11.8 1.0
C A:THR8 3.9 12.6 1.0
CB A:THR10 3.9 11.2 1.0
CA A:SER198 4.0 11.9 1.0
CA A:THR10 4.0 11.7 1.0
C A:ALA203 4.1 11.5 1.0
CB A:SER198 4.2 13.1 1.0
CA A:PRO204 4.4 11.7 1.0
O A:LLP199 4.5 13.3 1.0
C A:CYS202 4.5 11.1 1.0
C A:VAL9 4.5 12.6 1.0
N A:LLP199 4.5 11.4 1.0
CB D:ARG231 4.5 11.2 1.0
O A:ASP7 4.6 11.5 1.0
CA A:THR8 4.6 13.1 1.0
CG D:GLN232 4.6 12.1 1.0
O A:PRO204 4.6 12.1 1.0
O A:CYS202 4.7 10.4 1.0
CA A:CYS202 4.7 10.9 1.0
N A:PRO204 4.7 11.8 1.0
N A:ALA203 4.7 10.4 1.0
N A:VAL9 4.8 13.4 1.0
C A:PRO204 4.8 13.2 1.0
CA A:LLP199 4.8 12.2 1.0
N A:LYS11 4.9 12.8 1.0
CG D:ARG231 4.9 11.6 1.0
CA A:VAL9 5.0 12.5 1.0

Calcium binding site 2 out of 6 in 1m6s

Go back to Calcium Binding Sites List in 1m6s
Calcium binding site 2 out of 6 in the Crystal Structure of Threonine Aldolase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:15.8
occ:1.00
 OE1 A:GLN232 2.5 13.4 1.0
O D:SER198 2.6 12.8 1.0
O D:THR10 2.7 14.3 1.0
OG1 D:THR10 2.8 13.9 1.0
O D:ALA203 2.9 11.9 1.0
O D:THR8 3.1 13.5 1.0
O D:HOH1348 3.4 13.7 1.0
CD A:GLN232 3.5 13.6 1.0
C D:SER198 3.5 13.6 1.0
C D:THR10 3.7 15.8 1.0
NE2 A:GLN232 3.8 14.0 1.0
N D:THR10 3.9 14.3 1.0
C D:THR8 3.9 14.5 1.0
CB D:THR10 3.9 14.2 1.0
C D:ALA203 4.0 11.4 1.0
CA D:SER198 4.0 12.2 1.0
CA D:THR10 4.1 14.5 1.0
CB D:SER198 4.2 15.0 1.0
CA D:PRO204 4.4 12.7 1.0
C D:CYS202 4.4 11.9 1.0
O D:LLP199 4.5 13.3 1.0
O D:PRO204 4.5 12.4 1.0
N D:LLP199 4.5 13.7 1.0
O D:CYS202 4.5 13.4 1.0
C D:VAL9 4.5 15.1 1.0
CA D:THR8 4.6 13.7 1.0
O D:ASP7 4.6 10.9 1.0
N D:PRO204 4.6 12.5 1.0
CB A:ARG231 4.6 12.5 1.0
N D:ALA203 4.6 11.6 1.0
CA D:CYS202 4.6 12.0 1.0
CG A:GLN232 4.7 14.3 1.0
C D:PRO204 4.7 12.1 1.0
N D:VAL9 4.8 13.8 1.0
CA D:LLP199 4.8 13.5 1.0
N D:LYS11 4.9 15.3 1.0

Calcium binding site 3 out of 6 in 1m6s

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Calcium binding site 3 out of 6 in the Crystal Structure of Threonine Aldolase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1303

b:16.6
occ:1.00
 OE1 B:GLN232 2.5 13.4 1.0
O C:SER198 2.7 12.5 1.0
OG1 C:THR10 2.8 11.8 1.0
O C:THR10 2.8 14.8 1.0
O C:ALA203 2.9 12.4 1.0
O C:THR8 2.9 11.8 1.0
CD B:GLN232 3.4 13.4 1.0
O C:HOH1339 3.5 15.6 1.0
C C:SER198 3.5 12.8 1.0
C C:THR10 3.8 14.4 1.0
C C:THR8 3.8 12.3 1.0
NE2 B:GLN232 3.8 11.8 1.0
N C:THR10 3.9 12.9 1.0
CB C:THR10 4.0 13.4 1.0
C C:ALA203 4.0 12.9 1.0
CA C:SER198 4.0 12.4 1.0
CA C:THR10 4.1 13.9 1.0
CB C:SER198 4.3 12.3 1.0
CA C:PRO204 4.3 12.2 1.0
C C:CYS202 4.4 13.6 1.0
CA C:THR8 4.4 12.9 1.0
O C:PRO204 4.5 12.4 1.0
CB B:ARG231 4.5 11.0 1.0
O C:ASP7 4.5 15.1 1.0
O C:LLP199 4.5 13.2 1.0
C C:VAL9 4.5 12.6 1.0
O C:CYS202 4.6 13.1 1.0
N C:LLP199 4.6 11.8 1.0
N C:PRO204 4.6 12.5 1.0
N C:ALA203 4.6 13.0 1.0
CA C:CYS202 4.7 13.0 1.0
C C:PRO204 4.7 13.4 1.0
CG B:GLN232 4.7 12.3 1.0
N C:VAL9 4.7 12.4 1.0
CA C:LLP199 4.9 12.7 1.0
CG B:ARG231 4.9 14.5 1.0
N C:LYS11 4.9 13.8 1.0
CA C:VAL9 5.0 12.3 1.0

Calcium binding site 4 out of 6 in 1m6s

Go back to Calcium Binding Sites List in 1m6s
Calcium binding site 4 out of 6 in the Crystal Structure of Threonine Aldolase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1304

b:19.7
occ:1.00
 OD1 B:ASN326 2.3 16.5 1.0
O B:HOH1579 2.4 35.3 1.0
O B:HOH1578 2.4 30.8 1.0
O B:HOH1580 2.4 22.9 1.0
O B:HOH1395 2.5 23.8 1.0
OE1 B:GLU329 2.6 24.4 1.0
CD B:GLU329 3.5 24.1 1.0
CG B:ASN326 3.5 17.4 1.0
OE2 B:GLU329 3.6 24.4 1.0
ND2 B:ASN326 4.3 16.9 1.0
O B:HOH1581 4.4 36.5 1.0
CA B:ASN326 4.5 15.8 1.0
CB B:ASN326 4.6 15.4 1.0
O B:HOH1501 4.7 26.2 1.0
O B:HOH1582 4.9 39.1 1.0
CG B:GLU329 4.9 22.0 1.0
N B:ASN326 4.9 14.5 1.0

Calcium binding site 5 out of 6 in 1m6s

Go back to Calcium Binding Sites List in 1m6s
Calcium binding site 5 out of 6 in the Crystal Structure of Threonine Aldolase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1300

b:16.1
occ:1.00
 OE1 C:GLN232 2.6 13.4 1.0
O B:SER198 2.6 10.8 1.0
O B:THR10 2.7 13.6 1.0
OG1 B:THR10 2.8 11.9 1.0
O B:ALA203 3.0 10.9 1.0
O B:THR8 3.0 13.8 1.0
CD C:GLN232 3.5 14.8 1.0
C B:SER198 3.5 11.7 1.0
O B:HOH1339 3.5 13.8 1.0
C B:THR10 3.6 13.6 1.0
N B:THR10 3.8 12.4 1.0
C B:THR8 3.9 13.1 1.0
NE2 C:GLN232 3.9 11.8 1.0
CB B:THR10 3.9 12.0 1.0
CA B:THR10 4.0 12.6 1.0
CA B:SER198 4.0 11.8 1.0
C B:ALA203 4.0 11.5 1.0
CB B:SER198 4.2 13.9 1.0
CA B:PRO204 4.4 11.9 1.0
C B:VAL9 4.4 13.3 1.0
C B:CYS202 4.5 11.4 1.0
O B:LLP199 4.5 11.8 1.0
CA B:THR8 4.5 13.5 1.0
O B:ASP7 4.5 11.4 1.0
N B:LLP199 4.5 12.0 1.0
CB C:ARG231 4.6 12.3 1.0
O B:PRO204 4.7 12.0 1.0
O B:CYS202 4.7 10.6 1.0
N B:ALA203 4.7 11.2 1.0
N B:PRO204 4.7 11.3 1.0
CA B:CYS202 4.7 10.7 1.0
CG C:GLN232 4.7 13.7 1.0
N B:VAL9 4.7 12.9 1.0
C B:PRO204 4.8 11.7 1.0
N B:LYS11 4.8 13.9 1.0
CA B:LLP199 4.8 12.1 1.0
CG C:ARG231 4.9 13.4 1.0
CA B:VAL9 4.9 13.3 1.0

Calcium binding site 6 out of 6 in 1m6s

Go back to Calcium Binding Sites List in 1m6s
Calcium binding site 6 out of 6 in the Crystal Structure of Threonine Aldolase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1305

b:13.5
occ:1.00
 OE1 D:GLU329 2.3 14.7 1.0
OD1 D:ASN326 2.4 20.3 1.0
O D:HOH1372 2.4 15.7 1.0
CG D:ASN326 3.4 20.6 1.0
CD D:GLU329 3.5 15.5 1.0
CB D:GLU329 3.9 13.4 1.0
ND2 D:ASN326 4.1 22.1 1.0
CG D:GLU329 4.3 14.2 1.0
O D:ASN326 4.4 13.8 1.0
OE2 D:GLU329 4.4 15.7 1.0
CA D:ASN326 4.5 15.6 1.0
CB D:ASN326 4.5 17.9 1.0
C D:ASN326 4.9 15.6 1.0

Reference:

C.L.Kielkopf, S.K.Burley. X-Ray Structures of Threonine Aldolase Complexes: Structural Basis of Substrate Recognition Biochemistry V. 41 11711 2002.
ISSN: ISSN 0006-2960
PubMed: 12269813
DOI: 10.1021/BI020393+
Page generated: Thu Jul 11 12:17:50 2024

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