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Sodium in PDB 3b1e: Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: Alpha-Aminoacrylate Form

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

All present enzymatic activity of Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: Alpha-Aminoacrylate 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: Alpha-Aminoacrylate Form, PDB code: 3b1e 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) 49.27 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.204, 111.212, 217.353, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 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: Alpha-Aminoacrylate Form (pdb code 3b1e). 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: Alpha-Aminoacrylate Form, PDB code: 3b1e:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3b1e

Go back to Sodium Binding Sites List in 3b1e
Sodium binding site 1 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: Alpha-Aminoacrylate 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: Alpha-Aminoacrylate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:15.6
occ:1.00
 O A:HOH839 2.3 13.2 1.0
OG A:SER358 2.3 11.0 1.0
O A:HOH1218 2.5 21.2 1.0
O A:HOH1219 2.5 18.1 1.0
O A:HOH1142 2.6 22.8 1.0
CB A:SER358 3.4 9.7 1.0
N A:SER358 3.9 8.8 1.0
OE1 A:GLU359 4.3 11.9 1.0
CA A:SER358 4.3 9.3 1.0
O A:HOH970 4.4 22.1 1.0
OE2 A:GLU359 4.5 12.4 1.0
O A:HOH1124 4.5 26.0 1.0
O A:HOH888 4.5 9.3 1.0
O A:HOH915 4.5 15.1 1.0
CD A:GLU359 4.6 12.4 1.0
O A:HOH1033 4.7 19.4 1.0
O A:HOH1178 4.9 22.1 1.0
O A:HOH1248 4.9 26.6 1.0

Sodium binding site 2 out of 4 in 3b1e

Go back to Sodium Binding Sites List in 3b1e
Sodium binding site 2 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: Alpha-Aminoacrylate 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: Alpha-Aminoacrylate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:18.4
occ:1.00
 O B:HOH1227 2.4 22.0 1.0
O B:HOH958 2.4 17.6 1.0
O B:HOH943 2.4 12.1 1.0
OG B:SER358 2.5 12.2 1.0
O B:HOH1237 2.5 21.7 1.0
O B:HOH953 2.6 21.5 1.0
CB B:SER358 3.4 9.8 1.0
N B:SER358 4.0 9.3 1.0
O B:HOH1186 4.2 37.5 1.0
O B:HOH1038 4.3 17.9 1.0
CA B:SER358 4.3 9.4 1.0
OE2 B:GLU359 4.4 12.3 1.0
OE1 B:GLU359 4.4 11.2 1.0
O B:HOH816 4.5 7.5 1.0
CD B:GLU359 4.6 11.7 1.0
O B:HOH874 4.7 21.8 1.0
O B:HOH1024 4.7 20.3 1.0
CB B:SER135 4.9 9.0 1.0
O B:HOH987 4.9 20.0 1.0
O B:HOH1170 5.0 22.3 1.0

Sodium binding site 3 out of 4 in 3b1e

Go back to Sodium Binding Sites List in 3b1e
Sodium binding site 3 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: Alpha-Aminoacrylate 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: Alpha-Aminoacrylate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:20.4
occ:1.00
 O C:HOH1156 2.3 24.3 1.0
O C:HOH925 2.3 15.9 1.0
OG C:SER358 2.4 14.0 1.0
O C:HOH1076 2.5 23.3 1.0
O B:HOH1042 2.6 20.9 1.0
CB C:SER358 3.5 12.1 1.0
N C:SER358 4.0 11.1 1.0
OE1 C:GLU359 4.2 12.3 1.0
OE2 C:GLU359 4.2 15.3 1.0
O C:HOH824 4.2 20.5 1.0
CA C:SER358 4.3 11.7 1.0
O C:HOH842 4.4 12.0 1.0
CD C:GLU359 4.5 12.4 1.0
O C:HOH927 4.6 25.0 1.0
O C:HOH1114 4.7 28.1 1.0
CB C:SER135 4.8 11.5 1.0
OG C:SER116 4.9 11.7 1.0

Sodium binding site 4 out of 4 in 3b1e

Go back to Sodium Binding Sites List in 3b1e
Sodium binding site 4 out of 4 in the Crystal Structure of Betac-S Lyase From Streptococcus Anginosus in Complex with L-Serine: Alpha-Aminoacrylate 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: Alpha-Aminoacrylate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:16.6
occ:1.00
 O D:HOH1155 2.3 23.9 1.0
O D:HOH976 2.4 18.3 1.0
O D:HOH851 2.5 11.6 1.0
OG D:SER358 2.5 10.8 1.0
O D:HOH1003 2.5 18.1 1.0
O D:HOH1154 2.7 18.5 1.0
CB D:SER358 3.5 9.2 1.0
N D:SER358 4.0 8.2 1.0
O D:HOH1051 4.3 26.0 1.0
OE1 D:GLU359 4.3 11.9 1.0
O D:HOH931 4.4 15.5 1.0
O D:HOH1127 4.4 32.5 1.0
OE2 D:GLU359 4.4 11.8 1.0
CA D:SER358 4.4 9.2 1.0
O D:HOH978 4.4 16.5 1.0
O D:HOH813 4.5 9.0 1.0
CD D:GLU359 4.6 11.3 1.0
O D:HOH981 4.7 19.0 1.0
O D:HOH1122 4.9 25.4 1.0
O D:HOH990 4.9 18.4 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: Sun Aug 17 12:45:07 2025

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