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Calcium in PDB 1lw4: X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine

Enzymatic activity of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine

All present enzymatic activity of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine:
4.1.2.5;

Protein crystallography data

The structure of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine, PDB code: 1lw4 was solved by C.L.Kielkopf, S.K.Burley, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.900, 100.500, 150.320, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.6

Other elements in 1lw4:

The structure of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine (pdb code 1lw4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine, PDB code: 1lw4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1lw4

Go back to Calcium Binding Sites List in 1lw4
Calcium binding site 1 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1056

b:19.7
occ:1.00
 OE1 A:GLN232 2.5 18.7 1.0
O D:SER198 2.6 12.4 1.0
O D:THR10 2.7 16.6 1.0
OG1 D:THR10 2.8 15.7 1.0
O D:ALA203 3.0 11.7 1.0
O D:THR8 3.1 15.1 1.0
CD A:GLN232 3.4 17.7 1.0
O D:HOH1068 3.4 14.8 1.0
C D:SER198 3.6 12.2 1.0
C D:THR10 3.7 17.6 1.0
NE2 A:GLN232 3.8 14.9 1.0
N D:THR10 3.9 13.4 1.0
C D:THR8 3.9 15.5 1.0
CB D:THR10 4.0 15.5 1.0
C D:ALA203 4.0 12.1 1.0
CA D:THR10 4.0 14.6 1.0
CA D:SER198 4.1 13.5 1.0
CB D:SER198 4.2 16.1 1.0
CA D:PRO204 4.4 14.0 1.0
C D:CYS202 4.4 13.6 1.0
O D:PRO204 4.5 14.6 1.0
C D:VAL9 4.5 16.8 1.0
CG A:GLN232 4.6 18.5 1.0
O D:LLP199 4.6 15.3 1.0
CA D:THR8 4.6 14.3 1.0
CB A:ARG231 4.6 14.3 1.0
N D:LLP199 4.6 13.1 1.0
O D:ASP7 4.6 13.4 1.0
O D:CYS202 4.6 15.1 1.0
N D:PRO204 4.6 15.1 1.0
N D:ALA203 4.7 12.2 1.0
CA D:CYS202 4.7 12.7 1.0
C D:PRO204 4.7 14.3 1.0
N D:VAL9 4.8 14.5 1.0
N D:LYS11 4.8 15.6 1.0
CA D:LLP199 4.9 14.1 1.0
CG A:ARG231 5.0 14.0 1.0
CA D:VAL9 5.0 15.0 1.0

Calcium binding site 2 out of 6 in 1lw4

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Calcium binding site 2 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1054

b:17.6
occ:1.00
 OE1 C:GLN232 2.6 18.1 1.0
O B:SER198 2.6 14.0 1.0
O B:THR10 2.7 13.2 1.0
OG1 B:THR10 2.8 15.6 1.0
O B:THR8 3.0 16.0 1.0
O B:ALA203 3.0 16.3 1.0
CD C:GLN232 3.5 19.2 1.0
C B:SER198 3.5 16.9 1.0
O B:HOH1117 3.6 17.6 1.0
C B:THR10 3.6 16.2 1.0
N B:THR10 3.8 15.2 1.0
C B:THR8 3.9 16.2 1.0
CB B:THR10 3.9 15.0 1.0
NE2 C:GLN232 3.9 16.3 1.0
CA B:THR10 4.0 14.1 1.0
CA B:SER198 4.0 14.4 1.0
C B:ALA203 4.1 15.2 1.0
CB B:SER198 4.2 16.6 1.0
CA B:PRO204 4.5 14.5 1.0
C B:VAL9 4.5 16.1 1.0
O B:LLP199 4.5 14.9 0.2
CA B:THR8 4.5 16.6 1.0
C B:CYS202 4.5 17.0 1.0
O B:LLP199 4.5 17.4 0.5
O B:ASP7 4.5 16.3 1.0
N B:LLP199 4.5 16.4 0.5
N B:LLP199 4.6 13.8 0.2
CB C:ARG231 4.6 14.9 1.0
O B:PRO204 4.6 14.2 1.0
CG C:GLN232 4.6 18.7 1.0
N B:ALA203 4.7 13.9 1.0
O B:CYS202 4.7 15.6 1.0
N B:PRO204 4.7 13.8 1.0
CA B:CYS202 4.7 15.0 1.0
N B:VAL9 4.7 14.7 1.0
C B:PRO204 4.8 14.2 1.0
CA B:LLP199 4.8 18.3 0.5
N B:LYS11 4.8 14.8 1.0
CA B:LLP199 4.8 15.4 0.2
CG C:ARG231 4.9 18.2 1.0
CA B:VAL9 5.0 15.7 1.0

Calcium binding site 3 out of 6 in 1lw4

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Calcium binding site 3 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1057

b:19.0
occ:1.00
 OE1 B:GLN232 2.6 13.6 1.0
O C:SER198 2.7 14.3 1.0
O C:THR10 2.8 17.1 1.0
OG1 C:THR10 2.8 14.9 1.0
O C:ALA203 2.8 14.7 1.0
O C:THR8 3.0 12.9 1.0
CD B:GLN232 3.5 13.3 1.0
O C:HOH1066 3.5 17.4 1.0
C C:SER198 3.6 14.4 1.0
C C:THR10 3.7 16.2 1.0
C C:THR8 3.9 15.1 1.0
N C:THR10 3.9 16.4 1.0
NE2 B:GLN232 3.9 14.2 1.0
C C:ALA203 3.9 16.7 1.0
CB C:THR10 4.0 17.4 1.0
CA C:SER198 4.1 16.3 1.0
CA C:THR10 4.1 15.8 1.0
CA C:PRO204 4.3 16.4 1.0
CB C:SER198 4.3 15.6 1.0
C C:CYS202 4.4 18.0 1.0
CA C:THR8 4.5 15.0 1.0
O C:PRO204 4.5 16.4 1.0
C C:VAL9 4.5 14.9 1.0
CB B:ARG231 4.5 13.4 1.0
O C:ASP7 4.5 17.9 1.0
O C:LLP199 4.6 14.8 1.0
O C:CYS202 4.6 15.9 1.0
N C:PRO204 4.6 15.3 1.0
N C:ALA203 4.6 17.0 1.0
N C:LLP199 4.6 13.7 1.0
C C:PRO204 4.6 18.1 1.0
CA C:CYS202 4.7 14.4 1.0
CG B:GLN232 4.7 15.7 1.0
N C:VAL9 4.8 13.4 1.0
N C:LYS11 4.9 16.5 1.0
CG B:ARG231 4.9 15.7 1.0
CA C:LLP199 4.9 14.4 1.0
CA C:ALA203 5.0 17.4 1.0

Calcium binding site 4 out of 6 in 1lw4

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Calcium binding site 4 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1058

b:27.1
occ:1.00
 OD1 B:ASN326 2.3 27.9 1.0
O B:HOH1280 2.4 39.1 1.0
OE1 B:GLU329 2.5 33.9 1.0
O B:HOH1138 2.5 26.7 1.0
O B:HOH1278 2.5 40.6 1.0
O B:HOH1279 2.5 40.0 1.0
CD B:GLU329 3.4 33.1 1.0
CG B:ASN326 3.5 29.4 1.0
OE2 B:GLU329 3.6 34.5 1.0
ND2 B:ASN326 4.2 30.4 1.0
CA B:ASN326 4.4 22.6 1.0
CB B:ASN326 4.5 25.7 1.0
O B:HOH1285 4.7 40.0 1.0
CG B:GLU329 4.8 31.1 1.0
N B:ASN326 4.9 20.5 1.0
O B:HOH1284 5.0 40.1 1.0

Calcium binding site 5 out of 6 in 1lw4

Go back to Calcium Binding Sites List in 1lw4
Calcium binding site 5 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1055

b:17.4
occ:1.00
 OE1 D:GLN232 2.5 16.9 1.0
O A:SER198 2.6 13.3 1.0
O A:THR10 2.7 15.2 1.0
OG1 A:THR10 2.8 10.8 1.0
O A:ALA203 3.0 14.5 1.0
O A:THR8 3.0 14.5 1.0
CD D:GLN232 3.4 17.7 1.0
O A:HOH1069 3.4 16.0 1.0
C A:SER198 3.5 14.6 1.0
C A:THR10 3.7 17.5 1.0
NE2 D:GLN232 3.8 17.2 1.0
N A:THR10 3.8 15.7 1.0
C A:THR8 3.9 15.5 1.0
CB A:THR10 3.9 15.4 1.0
C A:ALA203 4.0 16.6 1.0
CA A:THR10 4.0 14.4 1.0
CA A:SER198 4.0 14.1 1.0
CB A:SER198 4.2 16.9 1.0
CA A:PRO204 4.4 15.9 1.0
C A:CYS202 4.5 14.4 1.0
C A:VAL9 4.5 14.4 1.0
O A:LLP199 4.5 16.0 1.0
CG D:GLN232 4.5 16.5 1.0
N A:LLP199 4.6 14.1 1.0
CB D:ARG231 4.6 15.2 1.0
O A:PRO204 4.6 14.3 1.0
O A:ASP7 4.6 13.9 1.0
CA A:THR8 4.6 15.7 1.0
O A:CYS202 4.6 13.4 1.0
N A:PRO204 4.6 15.1 1.0
CA A:CYS202 4.7 13.5 1.0
N A:ALA203 4.7 15.0 1.0
C A:PRO204 4.7 17.4 1.0
N A:VAL9 4.8 15.8 1.0
N A:LYS11 4.8 15.4 1.0
CA A:LLP199 4.9 15.8 1.0
CG D:ARG231 4.9 14.0 1.0
CA A:VAL9 5.0 14.6 1.0

Calcium binding site 6 out of 6 in 1lw4

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Calcium binding site 6 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with L-Allo-Threonine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1059

b:18.2
occ:1.00
 OE1 D:GLU329 2.3 18.6 1.0
OD1 D:ASN326 2.4 22.8 1.0
O D:HOH1305 2.4 38.2 1.0
O D:HOH1306 2.5 38.1 1.0
CG D:ASN326 3.4 25.9 1.0
CD D:GLU329 3.5 19.7 1.0
CB D:GLU329 3.9 14.8 1.0
ND2 D:ASN326 4.0 29.6 1.0
CG D:GLU329 4.3 18.6 1.0
O D:ASN326 4.5 13.7 1.0
O D:HOH1307 4.5 40.2 1.0
OE2 D:GLU329 4.5 19.7 1.0
CA D:ASN326 4.5 17.7 1.0
CB D:ASN326 4.5 20.3 1.0
C D:ASN326 5.0 17.0 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: Mon Jul 7 17:02:09 2025

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