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Sodium in PDB 3b1d: Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form

Enzymatic activity of Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form

All present enzymatic activity of Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form:
4.4.1.8;

Protein crystallography data

The structure of Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form, PDB code: 3b1d was solved by Y.Kezuka, Y.Yoshida, T.Nonaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.84 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.965, 111.302, 217.193, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form (pdb code 3b1d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form, PDB code: 3b1d:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3b1d

Go back to Sodium Binding Sites List in 3b1d
Sodium binding site 1 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form


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 Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:14.2
occ:1.00
 O A:HOH1025 2.3 19.5 1.0
O A:HOH895 2.4 11.3 1.0
O A:HOH1157 2.4 26.9 1.0
O A:HOH970 2.5 15.4 1.0
O A:HOH1037 2.5 21.9 1.0
OG A:SER358 2.5 10.9 1.0
CB A:SER358 3.5 9.2 1.0
N A:SER358 4.0 9.1 1.0
OE1 A:GLU359 4.3 8.7 1.0
CA A:SER358 4.4 8.9 1.0
O A:HOH1034 4.4 24.6 1.0
O A:HOH930 4.4 16.0 1.0
OE2 A:GLU359 4.4 10.8 1.0
O A:HOH886 4.5 9.5 1.0
O A:HOH1065 4.6 30.0 1.0
CD A:GLU359 4.6 9.9 1.0
O A:HOH902 4.7 21.3 1.0
O A:HOH978 4.7 20.8 1.0
O A:HOH1221 4.9 26.2 1.0
CB A:SER135 4.9 7.9 1.0
O A:HOH1101 5.0 21.2 1.0

Sodium binding site 2 out of 4 in 3b1d

Go back to Sodium Binding Sites List in 3b1d
Sodium binding site 2 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form


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 Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:20.5
occ:1.00
 O B:HOH1185 2.4 20.7 1.0
O B:HOH970 2.4 16.9 1.0
O B:HOH1059 2.4 21.9 1.0
O B:HOH939 2.4 11.4 1.0
OG B:SER358 2.5 11.9 1.0
O B:HOH1070 2.7 22.7 1.0
CB B:SER358 3.5 9.9 1.0
N B:SER358 4.0 9.3 1.0
O B:HOH949 4.3 15.7 1.0
OE2 B:GLU359 4.4 12.9 1.0
OE1 B:GLU359 4.4 11.5 1.0
CA B:SER358 4.4 9.6 1.0
O B:HOH839 4.5 9.9 1.0
O B:HOH1019 4.6 22.5 1.0
CD B:GLU359 4.6 11.9 1.0
O B:HOH978 4.7 21.0 1.0
O B:HOH812 4.9 17.1 1.0
CB B:SER135 4.9 8.8 1.0

Sodium binding site 3 out of 4 in 3b1d

Go back to Sodium Binding Sites List in 3b1d
Sodium binding site 3 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form


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 Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na701

b:20.2
occ:1.00
 O C:HOH1058 2.3 28.1 1.0
O C:HOH923 2.4 16.9 1.0
O C:HOH949 2.5 21.6 1.0
O C:HOH1114 2.6 23.1 1.0
OG C:SER358 2.7 14.8 1.0
CB C:SER358 3.5 11.8 1.0
N C:SER358 4.1 11.2 1.0
O C:HOH929 4.3 24.7 1.0
OE1 C:GLU359 4.4 11.6 1.0
CA C:SER358 4.5 11.8 1.0
OE2 C:GLU359 4.5 14.3 1.0
O C:HOH906 4.5 13.3 1.0
O C:HOH927 4.7 20.9 1.0
CD C:GLU359 4.7 12.0 1.0
O C:HOH1122 4.8 23.4 1.0
CB C:SER135 4.9 13.6 1.0
O C:HOH1032 4.9 26.5 1.0

Sodium binding site 4 out of 4 in 3b1d

Go back to Sodium Binding Sites List in 3b1d
Sodium binding site 4 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form


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 Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: External Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na701

b:15.8
occ:1.00
 O D:HOH966 2.3 21.9 1.0
O D:HOH964 2.4 17.8 1.0
O D:HOH827 2.4 12.7 1.0
O D:HOH1017 2.5 17.5 1.0
OG D:SER358 2.5 11.0 1.0
O D:HOH939 2.6 21.2 1.0
CB D:SER358 3.5 8.8 1.0
N D:SER358 4.1 8.4 1.0
OE1 D:GLU359 4.3 9.7 1.0
O D:HOH1083 4.4 28.0 1.0
OE2 D:GLU359 4.4 9.7 1.0
CA D:SER358 4.4 9.2 1.0
O D:HOH904 4.4 19.5 1.0
O D:HOH829 4.4 9.5 1.0
O D:HOH1036 4.5 17.2 1.0
CD D:GLU359 4.6 8.6 1.0
O D:HOH990 4.7 20.2 1.0
O D:HOH935 4.9 20.8 1.0
O D:HOH1157 4.9 25.4 1.0
CB D:SER135 5.0 8.3 1.0

Reference:

Y.Kezuka, Y.Yoshida, T.Nonaka. Structural Insights Into Catalysis By Beta C-S Lyase From Streptococcus Anginosus Proteins V. 80 2447 2012.
ISSN: ISSN 0887-3585
PubMed: 22674431
DOI: 10.1002/PROT.24129
Page generated: Mon Oct 7 05:54:23 2024

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