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Calcium in PDB 1lw5: X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine

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

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

Protein crystallography data

The structure of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine, PDB code: 1lw5 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 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.020, 100.710, 150.200, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.7

Other elements in 1lw5:

The structure of X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine 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 Glycine (pdb code 1lw5). 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 Glycine, PDB code: 1lw5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1lw5

Go back to Calcium Binding Sites List in 1lw5
Calcium binding site 1 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:23.9
occ:1.00
 O A:SER198 2.4 17.6 1.0
OE1 D:GLN232 2.6 18.1 1.0
OG1 A:THR10 2.9 16.2 1.0
O A:THR8 2.9 16.9 1.0
O A:ALA203 2.9 20.0 1.0
O A:THR10 3.0 19.5 1.0
C A:SER198 3.3 19.0 1.0
CD D:GLN232 3.5 19.0 1.0
O A:HOH1015 3.7 19.8 1.0
C A:THR8 3.8 20.1 1.0
CA A:SER198 3.9 19.1 1.0
C A:THR10 3.9 19.0 1.0
NE2 D:GLN232 3.9 18.6 1.0
N A:THR10 3.9 18.7 1.0
C A:ALA203 4.0 21.1 1.0
CB A:THR10 4.1 19.8 1.0
CB A:SER198 4.1 20.7 1.0
CA A:THR10 4.2 18.6 1.0
N A:LLP199 4.4 18.2 1.0
CB D:ARG231 4.4 18.5 1.0
O A:LLP199 4.4 17.9 1.0
CA A:THR8 4.5 19.6 1.0
CA A:PRO204 4.5 20.1 1.0
C A:CYS202 4.5 19.8 1.0
O A:ASP7 4.6 19.6 1.0
C A:VAL9 4.6 20.8 1.0
O A:PRO204 4.6 16.5 1.0
N A:ALA203 4.7 21.7 1.0
CA A:LLP199 4.7 19.9 1.0
N A:PRO204 4.7 20.2 1.0
CG D:ARG231 4.7 15.8 1.0
CG D:GLN232 4.7 20.5 1.0
N A:VAL9 4.7 20.5 1.0
C A:PRO204 4.7 21.8 1.0
CA A:CYS202 4.8 19.1 1.0
O A:CYS202 4.8 18.7 1.0
CA A:VAL9 5.0 20.6 1.0

Calcium binding site 2 out of 6 in 1lw5

Go back to Calcium Binding Sites List in 1lw5
Calcium binding site 2 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:22.0
occ:1.00
 OE1 A:GLN232 2.4 22.4 1.0
O D:SER198 2.7 20.3 1.0
O D:THR10 2.7 22.0 1.0
O D:THR8 2.8 20.1 1.0
OG1 D:THR10 3.0 21.8 1.0
O D:ALA203 3.1 16.9 1.0
CD A:GLN232 3.3 22.7 1.0
O D:HOH1020 3.6 15.7 1.0
C D:SER198 3.6 21.6 1.0
C D:THR10 3.7 23.7 1.0
C D:THR8 3.7 21.6 1.0
NE2 A:GLN232 3.8 22.5 1.0
N D:THR10 3.8 20.4 1.0
CA D:THR10 4.1 21.9 1.0
CB D:THR10 4.1 22.7 1.0
CA D:SER198 4.1 21.3 1.0
C D:ALA203 4.1 20.1 1.0
CB D:SER198 4.3 21.1 1.0
C D:VAL9 4.4 21.2 1.0
CB A:ARG231 4.4 21.1 1.0
CA D:PRO204 4.4 22.0 1.0
CA D:THR8 4.4 20.8 1.0
O D:PRO204 4.5 19.6 1.0
CG A:GLN232 4.5 24.2 1.0
O D:ASP7 4.6 19.8 1.0
C D:CYS202 4.6 20.5 1.0
N D:VAL9 4.6 19.8 1.0
N D:LLP199 4.7 21.3 1.0
O D:LLP199 4.7 24.3 1.0
C D:PRO204 4.7 22.4 1.0
N D:PRO204 4.7 22.4 1.0
O D:CYS202 4.8 22.3 1.0
CG A:ARG231 4.8 21.4 1.0
N D:ALA203 4.8 19.3 1.0
CA D:CYS202 4.8 19.9 1.0
CA D:VAL9 4.8 21.1 1.0
N D:LYS11 4.9 21.5 1.0
CA D:LLP199 4.9 23.0 1.0
O D:VAL9 5.0 21.1 1.0

Calcium binding site 3 out of 6 in 1lw5

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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 Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1007

b:22.1
occ:1.00
 OE1 B:GLN232 2.5 20.5 1.0
O C:THR10 2.7 18.8 1.0
O C:SER198 2.7 16.2 1.0
O C:ALA203 2.8 20.2 1.0
OG1 C:THR10 2.8 17.5 1.0
O C:THR8 2.9 18.5 1.0
CD B:GLN232 3.4 19.2 1.0
O C:HOH1028 3.5 22.2 1.0
C C:SER198 3.6 18.1 1.0
C C:THR10 3.7 19.1 1.0
C C:THR8 3.8 19.3 1.0
NE2 B:GLN232 3.8 18.3 1.0
N C:THR10 3.9 18.5 1.0
C C:ALA203 3.9 22.3 1.0
CB C:THR10 3.9 18.5 1.0
CA C:THR10 4.0 18.4 1.0
CA C:SER198 4.1 20.5 1.0
CA C:PRO204 4.2 21.1 1.0
CB C:SER198 4.3 19.4 1.0
C C:CYS202 4.4 23.0 1.0
CA C:THR8 4.4 19.4 1.0
C C:VAL9 4.5 18.9 1.0
O C:PRO204 4.5 20.6 1.0
O C:CYS202 4.5 22.5 1.0
CB B:ARG231 4.5 16.4 1.0
N C:PRO204 4.5 21.9 1.0
CG B:GLN232 4.6 18.4 1.0
O C:ASP7 4.6 20.3 1.0
C C:PRO204 4.6 21.1 1.0
N C:ALA203 4.6 21.8 1.0
CA C:CYS202 4.7 21.2 1.0
O C:LLP199 4.7 21.7 1.0
N C:LLP199 4.7 17.0 1.0
N C:VAL9 4.8 19.5 1.0
N C:LYS11 4.8 19.3 1.0
CG B:ARG231 5.0 16.9 1.0
CA C:VAL9 5.0 19.4 1.0

Calcium binding site 4 out of 6 in 1lw5

Go back to Calcium Binding Sites List in 1lw5
Calcium binding site 4 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1008

b:31.3
occ:1.00
 O B:HOH1203 2.2 33.5 1.0
OD1 B:ASN326 2.4 31.2 1.0
O B:HOH1038 2.5 29.6 1.0
O B:HOH1142 2.5 33.1 1.0
O B:HOH1146 2.6 28.9 1.0
OE1 B:GLU329 2.7 38.1 1.0
CD B:GLU329 3.5 36.9 1.0
CG B:ASN326 3.6 31.1 1.0
OE2 B:GLU329 3.7 37.4 1.0
ND2 B:ASN326 4.3 30.9 1.0
O B:HOH1211 4.6 42.9 1.0
CA B:ASN326 4.6 27.6 1.0
CB B:ASN326 4.7 28.3 1.0
CG B:GLU329 4.9 34.5 1.0

Calcium binding site 5 out of 6 in 1lw5

Go back to Calcium Binding Sites List in 1lw5
Calcium binding site 5 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1004

b:22.8
occ:1.00
 OE1 C:GLN232 2.5 21.2 1.0
O B:THR10 2.6 17.8 1.0
OG1 B:THR10 2.7 19.3 1.0
O B:SER198 2.7 17.1 1.0
O B:ALA203 2.9 16.0 1.0
O B:THR8 2.9 21.4 1.0
CD C:GLN232 3.4 20.2 1.0
O B:HOH1039 3.5 19.4 1.0
C B:THR10 3.6 19.1 1.0
C B:SER198 3.6 20.9 1.0
N B:THR10 3.8 18.5 1.0
CB B:THR10 3.9 18.0 1.0
C B:THR8 3.9 21.8 1.0
NE2 C:GLN232 3.9 19.2 1.0
CA B:THR10 3.9 18.5 1.0
C B:ALA203 4.0 19.5 1.0
CA B:SER198 4.1 20.5 1.0
CB B:SER198 4.3 21.1 1.0
CA B:PRO204 4.4 17.9 1.0
C B:VAL9 4.4 20.8 1.0
C B:CYS202 4.4 20.2 1.0
CA B:THR8 4.5 21.2 1.0
O B:ASP7 4.5 19.7 1.0
O B:LLP199 4.6 18.9 0.5
O B:LLP199 4.6 17.9 0.5
CB C:ARG231 4.6 22.3 1.0
O B:PRO204 4.6 17.7 1.0
N B:LLP199 4.6 19.4 0.5
N B:LLP199 4.6 19.9 0.5
O B:CYS202 4.6 19.9 1.0
CG C:GLN232 4.6 21.2 1.0
N B:PRO204 4.6 18.5 1.0
N B:ALA203 4.6 19.8 1.0
CA B:CYS202 4.7 19.2 1.0
C B:PRO204 4.7 18.8 1.0
N B:VAL9 4.7 21.1 1.0
N B:LYS11 4.8 18.5 1.0
CA B:LLP199 4.9 22.2 0.5
CA B:LLP199 4.9 21.8 0.5
CA B:VAL9 4.9 19.9 1.0
CG C:ARG231 5.0 20.1 1.0

Calcium binding site 6 out of 6 in 1lw5

Go back to Calcium Binding Sites List in 1lw5
Calcium binding site 6 out of 6 in the X-Ray Structure of L-Threonine Aldolase (Low-Specificity) in Complex with Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1009

b:25.4
occ:1.00
 OE1 D:GLU329 2.3 26.6 1.0
O D:HOH1215 2.4 37.0 1.0
OD1 D:ASN326 2.4 28.1 1.0
O D:HOH1214 2.5 37.2 1.0
CG D:ASN326 3.4 28.8 1.0
CD D:GLU329 3.5 26.6 1.0
CB D:GLU329 3.8 21.4 1.0
ND2 D:ASN326 4.1 30.3 1.0
CG D:GLU329 4.3 23.0 1.0
O D:ASN326 4.4 22.8 1.0
OE2 D:GLU329 4.4 24.6 1.0
CA D:ASN326 4.5 23.6 1.0
CB D:ASN326 4.5 26.0 1.0
O D:HOH1222 4.6 41.1 1.0
C D:ASN326 4.9 24.3 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 17:02:19 2025

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