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Sodium in PDB 4rjy: Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate

Protein crystallography data

The structure of Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate, PDB code: 4rjy was solved by M.K.Safo, N.Chowdhury, A.K.Gandhi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.160, 104.880, 84.910, 90.00, 92.49, 90.00
R / Rfree (%) 21.2 / 27.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate (pdb code 4rjy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate, PDB code: 4rjy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4rjy

Go back to Sodium Binding Sites List in 4rjy
Sodium binding site 1 out of 6 in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:23.4
occ:1.00
 OG1 A:THR10 2.5 9.6 1.0
O A:SER196 2.6 25.4 1.0
NE2 B:GLN230 2.6 14.7 1.0
O A:THR10 2.6 16.2 1.0
O A:THR8 2.8 19.9 1.0
O A:THR201 3.0 20.9 1.0
CD B:GLN230 3.4 18.5 1.0
N A:THR10 3.4 22.4 1.0
C A:THR10 3.4 23.2 1.0
OE1 B:GLN230 3.5 22.6 1.0
C A:SER196 3.5 19.0 1.0
C A:THR8 3.6 19.2 1.0
CB A:THR10 3.6 17.4 1.0
CA A:THR10 3.6 15.3 1.0
CA A:SER196 4.0 16.3 1.0
C A:THR201 4.1 22.5 1.0
C A:VAL9 4.1 18.9 1.0
CB A:SER196 4.1 12.6 1.0
CA A:THR8 4.3 19.8 1.0
O A:ASP7 4.3 15.6 1.0
N A:VAL9 4.4 21.7 1.0
O A:LLP197 4.4 20.3 1.0
N A:ARG11 4.5 27.0 1.0
N A:LLP197 4.6 20.5 1.0
CA A:VAL9 4.6 15.3 1.0
C A:GLY200 4.6 25.2 1.0
N A:THR201 4.6 27.9 1.0
CG B:GLN230 4.6 24.5 1.0
O A:PRO202 4.7 31.6 1.0
CG2 A:THR10 4.8 17.3 1.0
CA A:LLP197 4.8 20.2 1.0
CA A:PRO202 4.8 20.8 1.0
N A:PRO202 4.8 20.3 1.0
O A:VAL9 4.8 27.6 1.0
O A:GLY200 4.8 21.4 1.0
CA A:GLY200 4.9 22.0 1.0
CB B:ARG229 4.9 19.2 1.0
CA A:THR201 5.0 22.1 1.0

Sodium binding site 2 out of 6 in 4rjy

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Sodium binding site 2 out of 6 in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:14.0
occ:1.00
 O A:HOH679 2.7 24.3 1.0
O C:HOH641 2.7 16.3 1.0
OG B:SER97 2.8 19.4 1.0
OG C:SER97 2.9 16.5 1.0
O B:ALA93 3.0 19.3 1.0
O B:VAL94 3.2 26.6 1.0
O C:ALA93 3.2 26.1 1.0
O C:VAL94 3.3 19.9 1.0
CA C:SER97 3.5 21.9 1.0
CA B:SER97 3.5 20.1 1.0
N B:SER97 3.7 21.2 1.0
CB C:SER97 3.7 20.7 1.0
CB B:SER97 3.7 21.9 1.0
N C:SER97 3.7 23.9 1.0
C B:VAL94 3.9 22.4 1.0
C C:VAL94 4.1 12.5 1.0
C B:ALA93 4.2 21.3 1.0
C C:ALA93 4.4 25.2 1.0
CA B:VAL94 4.6 21.3 1.0
O C:HOH501 4.6 20.8 1.0
CA C:VAL94 4.6 19.4 1.0
O A:HOH517 4.6 18.7 1.0
O B:LEU95 4.6 19.3 1.0
C B:LEU95 4.6 18.0 1.0
N B:LEU95 4.7 11.7 1.0
O D:HOH572 4.8 30.1 1.0
OG D:SER97 4.8 17.1 1.0
OG A:SER97 4.8 18.5 1.0
C B:GLY96 4.8 18.9 1.0
O D:HOH501 4.8 21.4 1.0
C C:GLY96 4.8 24.5 1.0
N B:VAL94 4.8 22.0 1.0
C C:SER97 4.9 25.4 1.0
CA B:LEU95 4.9 10.7 1.0
NA D:NA401 4.9 22.5 1.0
C B:SER97 4.9 20.8 1.0
N C:VAL94 5.0 23.3 1.0
N B:GLY96 5.0 19.3 1.0

Sodium binding site 3 out of 6 in 4rjy

Go back to Sodium Binding Sites List in 4rjy
Sodium binding site 3 out of 6 in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:19.5
occ:1.00
 O B:SER196 2.5 20.9 1.0
O B:THR10 2.6 29.5 1.0
NE2 A:GLN230 2.6 17.0 1.0
OG1 B:THR10 2.8 28.1 1.0
O B:THR201 2.8 27.8 1.0
O B:THR8 3.0 31.4 1.0
CD A:GLN230 3.4 33.0 1.0
C B:THR10 3.5 27.7 1.0
OE1 A:GLN230 3.6 29.0 1.0
C B:SER196 3.6 26.6 1.0
N B:THR10 3.7 24.1 1.0
CB B:THR10 3.9 21.8 1.0
CA B:THR10 3.9 21.7 1.0
C B:THR201 3.9 28.6 1.0
C B:THR8 4.0 26.4 1.0
O B:HOH510 4.0 29.4 1.0
CA B:SER196 4.0 25.9 1.0
CB B:SER196 4.1 28.1 1.0
C B:VAL9 4.4 28.1 1.0
CA B:PRO202 4.4 24.5 1.0
O B:PRO202 4.5 26.5 1.0
N B:THR201 4.5 21.7 1.0
N B:PRO202 4.6 27.9 1.0
C B:GLY200 4.6 21.4 1.0
C B:PRO202 4.7 25.4 1.0
CG A:GLN230 4.7 27.2 1.0
CA B:THR8 4.7 22.6 1.0
O B:ASP7 4.7 17.4 1.0
N B:LLP197 4.7 22.6 1.0
N B:ARG11 4.7 25.2 1.0
CB A:ARG229 4.7 29.7 1.0
O B:LLP197 4.8 23.6 1.0
N B:VAL9 4.8 26.2 1.0
CA B:THR201 4.9 24.0 1.0
CA B:GLY200 4.9 16.6 1.0
O B:GLY200 4.9 22.9 1.0
CA B:VAL9 5.0 27.4 1.0
CA B:LLP197 5.0 20.9 1.0

Sodium binding site 4 out of 6 in 4rjy

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Sodium binding site 4 out of 6 in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:23.8
occ:1.00
 O C:THR10 2.5 25.2 1.0
O C:SER196 2.6 25.2 1.0
NE2 D:GLN230 2.7 20.4 1.0
OG1 C:THR10 2.7 27.2 1.0
O C:THR201 2.9 23.1 1.0
O C:THR8 2.9 25.2 1.0
CD D:GLN230 3.3 26.5 1.0
OE1 D:GLN230 3.4 30.6 1.0
C C:THR10 3.5 21.9 1.0
N C:THR10 3.6 22.6 1.0
C C:SER196 3.6 28.0 1.0
C C:THR8 3.8 24.6 1.0
CB C:THR10 3.8 19.4 1.0
CA C:THR10 3.8 22.3 1.0
C C:THR201 4.0 26.5 1.0
C C:VAL9 4.1 26.2 1.0
CA C:SER196 4.2 26.0 1.0
CG D:GLN230 4.4 27.3 1.0
O C:GLY200 4.4 27.0 1.0
CA C:PRO202 4.4 28.1 1.0
CB C:SER196 4.5 22.0 1.0
C C:GLY200 4.5 27.9 1.0
O C:ASP7 4.5 27.7 1.0
CA C:THR8 4.5 24.5 1.0
N C:VAL9 4.5 21.5 1.0
N C:ARG11 4.6 25.6 1.0
N C:PRO202 4.6 30.4 1.0
O C:VAL9 4.7 30.3 1.0
N C:LLP197 4.7 23.2 1.0
CB D:ARG229 4.7 17.9 1.0
CA C:VAL9 4.7 26.1 1.0
O C:LLP197 4.7 21.5 1.0
O C:PRO202 4.7 26.0 1.0
N C:THR201 4.8 29.2 1.0
C C:PRO202 4.8 30.4 1.0
CA C:LLP197 4.9 17.1 1.0
CA C:GLY200 4.9 26.2 1.0
CG2 C:THR10 5.0 16.6 1.0

Sodium binding site 5 out of 6 in 4rjy

Go back to Sodium Binding Sites List in 4rjy
Sodium binding site 5 out of 6 in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:22.5
occ:1.00
 OG D:SER97 2.8 17.1 1.0
OG A:SER97 2.8 18.5 1.0
O C:HOH641 3.0 16.3 1.0
O D:ALA93 3.0 30.6 1.0
O A:ALA93 3.1 25.4 1.0
O A:HOH679 3.2 24.3 1.0
O D:VAL94 3.3 19.5 1.0
CA D:SER97 3.3 15.2 1.0
N D:SER97 3.4 19.7 1.0
O A:VAL94 3.5 21.9 1.0
CA A:SER97 3.5 17.4 1.0
CB D:SER97 3.5 17.4 1.0
CB A:SER97 3.6 23.3 1.0
N A:SER97 3.8 25.2 1.0
C D:VAL94 3.9 12.2 1.0
C D:ALA93 4.1 23.4 1.0
C A:VAL94 4.2 20.0 1.0
O D:HOH572 4.3 30.1 1.0
C A:ALA93 4.4 24.4 1.0
CA D:VAL94 4.4 17.4 1.0
C D:LEU95 4.5 22.8 1.0
C D:GLY96 4.5 15.3 1.0
O D:LEU95 4.5 23.3 1.0
N D:LEU95 4.6 14.1 1.0
O A:HOH517 4.7 18.7 1.0
O C:HOH501 4.7 20.8 1.0
CA A:VAL94 4.7 21.4 1.0
N D:VAL94 4.7 16.6 1.0
N D:GLY96 4.7 20.1 1.0
O A:LEU95 4.8 29.9 1.0
C D:SER97 4.8 17.5 1.0
O D:HOH501 4.8 21.4 1.0
CA D:LEU95 4.9 17.4 1.0
C A:SER97 4.9 24.9 1.0
OG B:SER97 4.9 19.4 1.0
OG C:SER97 4.9 16.5 1.0
NA B:NA401 4.9 14.0 1.0
C A:GLY96 5.0 19.1 1.0
C A:LEU95 5.0 27.5 1.0

Sodium binding site 6 out of 6 in 4rjy

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Sodium binding site 6 out of 6 in the Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of E. Coli L-Threonine Aldolase in Complex with A Non-Covalently Uncleaved Bound L-Serine Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:28.1
occ:1.00
 O D:SER196 2.7 23.7 1.0
O D:THR10 2.7 23.6 1.0
O D:THR201 2.8 14.5 1.0
NE2 C:GLN230 2.9 46.4 1.0
O D:THR8 2.9 33.9 1.0
OG1 D:THR10 3.0 18.8 1.0
CD C:GLN230 3.4 36.0 1.0
OE1 C:GLN230 3.5 36.4 1.0
C D:SER196 3.6 28.6 1.0
C D:THR10 3.7 24.6 1.0
C D:THR8 3.8 28.3 1.0
N D:THR10 3.9 29.4 1.0
C D:THR201 3.9 26.3 1.0
CA D:SER196 4.1 26.3 1.0
CA D:THR10 4.1 20.9 1.0
CB D:THR10 4.1 17.4 1.0
CB D:SER196 4.2 29.3 1.0
C D:VAL9 4.4 30.3 1.0
N D:THR201 4.4 22.2 1.0
CA D:PRO202 4.4 26.8 1.0
O D:PRO202 4.5 33.6 1.0
CA D:THR8 4.5 24.7 1.0
CB C:ARG229 4.5 26.9 1.0
CG C:GLN230 4.6 33.5 1.0
O D:ASP7 4.6 25.3 1.0
N D:VAL9 4.6 32.4 1.0
C D:GLY200 4.7 19.6 1.0
N D:PRO202 4.7 27.3 1.0
N D:LLP197 4.7 21.0 1.0
C D:PRO202 4.7 28.9 1.0
CA D:GLY200 4.7 20.3 1.0
CG C:ARG229 4.8 21.5 1.0
N D:ARG11 4.8 23.7 1.0
CA D:VAL9 4.8 27.4 1.0
CA D:THR201 4.9 20.2 1.0
O D:LLP197 5.0 27.5 1.0

Reference:

M.K.Safo, N.Chowdhury, A.K.Gandhi. Molecular Basis of E. Coli L-Threonine Aldolase Catalytic Inactivation at Low pH To Be Published.
Page generated: Mon Oct 7 18:16:08 2024

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