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Sodium in PDB 5bph: Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis

Enzymatic activity of Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis

All present enzymatic activity of Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5bph was solved by H.T.Tran, L.W.Kang, M.K.Hong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.96 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.585, 106.071, 210.769, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis (pdb code 5bph). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5bph:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5bph

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Sodium binding site 1 out of 5 in the Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:17.3
occ:1.00
 OG1 A:THR273 2.3 18.1 1.0
OG1 A:THR94 2.3 16.9 1.0
O A:GLU68 2.3 19.8 1.0
O A:HOH575 2.3 18.3 1.0
O A:SER91 2.5 16.5 1.0
SD A:MET95 3.3 24.6 1.0
C A:SER91 3.4 16.0 1.0
CB A:THR273 3.5 15.6 1.0
C A:GLU68 3.6 20.1 1.0
CA A:SER91 3.6 14.3 1.0
CB A:THR94 3.6 17.7 1.0
CG2 A:THR273 3.8 18.2 1.0
CG A:MET95 3.9 22.2 1.0
CB A:GLU68 4.2 22.6 1.0
N A:THR273 4.2 16.4 1.0
CG A:GLU68 4.3 23.8 1.0
OE2 A:GLU68 4.3 30.4 1.0
O A:HOH576 4.3 18.1 1.0
O A:ALA90 4.3 15.8 1.0
N A:MET95 4.3 16.9 1.0
CB A:SER91 4.3 14.7 1.0
C A:THR94 4.4 17.0 1.0
CA A:THR94 4.4 16.7 1.0
CA A:THR273 4.4 15.2 1.0
CA A:GLU68 4.4 21.4 1.0
O A:HOH547 4.5 27.6 1.0
N A:ASP69 4.5 17.6 1.0
CA A:ASP69 4.6 17.5 1.0
N A:ALA92 4.7 15.1 1.0
CG2 A:THR94 4.7 20.4 1.0
N A:THR94 4.7 18.1 1.0
N A:SER91 4.8 15.8 1.0
CD A:GLU68 4.8 31.1 1.0
CE A:MET95 4.8 29.5 1.0
OG A:SER91 4.8 17.3 1.0
O A:VAL271 5.0 17.2 1.0
O A:THR94 5.0 18.3 1.0

Sodium binding site 2 out of 5 in 5bph

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Sodium binding site 2 out of 5 in the Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:29.2
occ:1.00
 NE2 A:HIS280 2.1 37.7 1.0
CE1 B:HIS265 2.1 39.8 1.0
NE2 B:HIS265 2.5 39.9 1.0
CD2 A:HIS280 2.8 34.2 1.0
O B:HOH687 3.1 48.5 1.0
CE1 A:HIS280 3.1 39.1 1.0
ND1 B:HIS265 3.3 44.4 1.0
O A:HOH615 3.4 27.4 1.0
CD2 B:HIS265 3.8 38.4 1.0
CG A:HIS280 4.0 32.8 1.0
ND1 A:HIS280 4.1 39.0 1.0
CG B:HIS265 4.2 31.6 1.0
CB A:SER279 4.7 33.7 1.0

Sodium binding site 3 out of 5 in 5bph

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Sodium binding site 3 out of 5 in the Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:18.1
occ:1.00
 OG1 B:THR94 2.3 17.7 1.0
O B:GLU68 2.3 18.1 1.0
O B:HOH566 2.3 18.4 1.0
OG1 B:THR273 2.4 17.5 1.0
O B:SER91 2.5 17.0 1.0
SD B:MET95 3.1 22.4 1.0
C B:SER91 3.4 17.5 1.0
C B:GLU68 3.5 18.8 1.0
CB B:THR273 3.6 15.3 1.0
CB B:THR94 3.6 17.7 1.0
CA B:SER91 3.7 15.7 1.0
CG2 B:THR273 3.8 18.2 1.0
CG B:MET95 4.0 19.3 1.0
CG B:GLU68 4.2 24.1 1.0
CB B:GLU68 4.2 21.2 1.0
N B:THR273 4.2 16.9 1.0
O B:ALA90 4.3 15.9 1.0
N B:MET95 4.3 18.6 1.0
O B:HOH583 4.4 17.7 1.0
OE2 B:GLU68 4.4 26.2 1.0
CB B:SER91 4.4 16.1 1.0
C B:THR94 4.4 20.0 1.0
CA B:GLU68 4.4 19.0 1.0
O B:HOH616 4.4 25.6 1.0
N B:ASP69 4.4 18.3 1.0
CA B:THR94 4.5 16.1 1.0
CA B:THR273 4.5 17.7 1.0
CA B:ASP69 4.5 17.0 1.0
N B:ALA92 4.7 15.0 1.0
CG2 B:THR94 4.7 17.9 1.0
N B:THR94 4.7 16.4 1.0
CE B:MET95 4.8 25.2 1.0
N B:SER91 4.8 16.3 1.0
CD B:GLU68 4.8 30.9 1.0
O B:VAL271 4.9 18.8 1.0
O B:THR94 4.9 20.5 1.0
OG B:SER91 5.0 17.2 1.0

Sodium binding site 4 out of 5 in 5bph

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Sodium binding site 4 out of 5 in the Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:18.5
occ:1.00
 O C:GLU68 2.3 19.4 1.0
OG1 C:THR94 2.3 18.1 1.0
O C:HOH551 2.3 19.0 1.0
OG1 C:THR273 2.3 18.8 1.0
O C:SER91 2.4 15.7 1.0
SD C:MET95 3.2 24.8 1.0
C C:SER91 3.4 17.0 1.0
C C:GLU68 3.5 18.6 1.0
CB C:THR273 3.6 16.0 1.0
CB C:THR94 3.6 17.8 1.0
CA C:SER91 3.7 16.9 1.0
CG2 C:THR273 3.8 17.6 1.0
CG C:MET95 4.0 19.4 1.0
CB C:GLU68 4.1 21.1 1.0
CG C:GLU68 4.1 22.9 1.0
N C:THR273 4.2 16.3 1.0
O C:ALA90 4.3 16.2 1.0
C C:THR94 4.3 18.8 1.0
O C:HOH572 4.4 18.9 1.0
N C:MET95 4.4 18.1 1.0
OE2 C:GLU68 4.4 25.9 1.0
CB C:SER91 4.4 14.9 1.0
CA C:GLU68 4.4 19.1 1.0
CA C:THR94 4.4 17.9 1.0
N C:ASP69 4.5 17.3 1.0
CA C:THR273 4.5 17.2 1.0
O C:HOH561 4.5 31.8 1.0
CA C:ASP69 4.5 17.6 1.0
N C:ALA92 4.7 16.0 1.0
CG2 C:THR94 4.7 17.2 1.0
N C:THR94 4.8 18.1 1.0
CD C:GLU68 4.8 29.6 1.0
N C:SER91 4.8 14.8 1.0
CE C:MET95 4.8 27.5 1.0
OG C:SER91 4.9 17.8 1.0
O C:VAL271 4.9 21.0 1.0
O C:THR94 4.9 20.8 1.0
C C:ALA90 5.0 16.5 1.0

Sodium binding site 5 out of 5 in 5bph

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Sodium binding site 5 out of 5 in the Crystal Structure of Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:20.3
occ:1.00
 O D:GLU68 2.3 21.5 1.0
OG1 D:THR273 2.3 20.8 1.0
O D:HOH558 2.3 21.2 1.0
OG1 D:THR94 2.4 20.3 1.0
O D:SER91 2.4 19.8 1.0
SD D:MET95 3.1 26.9 1.0
C D:SER91 3.4 20.8 1.0
C D:GLU68 3.5 19.5 1.0
CB D:THR273 3.6 20.9 1.0
CA D:SER91 3.6 17.5 1.0
CB D:THR94 3.7 20.5 1.0
CG2 D:THR273 3.8 23.4 1.0
CG D:MET95 3.9 26.5 1.0
CB D:GLU68 4.1 25.1 1.0
N D:THR273 4.2 21.2 1.0
CB D:SER91 4.3 16.3 1.0
CG D:GLU68 4.3 25.1 1.0
N D:MET95 4.3 21.9 1.0
C D:THR94 4.3 23.0 1.0
O D:ALA90 4.4 17.9 1.0
OE2 D:GLU68 4.4 34.6 1.0
O D:HOH579 4.4 19.9 1.0
CA D:GLU68 4.4 19.6 1.0
CA D:THR94 4.4 21.5 1.0
N D:ASP69 4.4 20.3 1.0
CA D:ASP69 4.5 19.8 1.0
CA D:THR273 4.5 20.4 1.0
O D:HOH522 4.5 34.3 1.0
N D:ALA92 4.6 18.9 1.0
CE D:MET95 4.7 27.4 1.0
N D:THR94 4.8 21.3 1.0
CG2 D:THR94 4.8 20.9 1.0
N D:SER91 4.8 17.6 1.0
CD D:GLU68 4.8 32.7 1.0
OG D:SER91 4.9 18.9 1.0
O D:THR94 4.9 22.5 1.0

Reference:

H.T.Tran, M.K.Hong, H.P.Ngo, K.H.Huynh, Y.J.Ahn, Z.Wang, L.W.Kang. Structure of D-Alanine-D-Alanine Ligase From Yersinia Pestis: Nucleotide Phosphate Recognition By the Serine Loop. Acta Crystallogr D Struct V. 72 12 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894530
DOI: 10.1107/S2059798315021671
Page generated: Sun Aug 17 23:07:05 2025

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