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

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

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

Protein crystallography data

The structure of Crystal Structure of Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5bpf 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) 37.51 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.872, 106.475, 211.462, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 25.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis (pdb code 5bpf). 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 Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5bpf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5bpf

Go back to Sodium Binding Sites List in 5bpf
Sodium binding site 1 out of 5 in the Crystal Structure of Adp 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 Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:19.5
occ:1.00
 O A:GLU68 2.3 20.6 1.0
O A:HOH551 2.3 20.9 1.0
OG1 A:THR273 2.3 19.4 1.0
OG1 A:THR94 2.3 21.2 1.0
O A:SER91 2.3 20.5 1.0
C A:SER91 3.3 18.6 1.0
SD A:MET95 3.3 28.6 1.0
C A:GLU68 3.5 22.9 1.0
CA A:SER91 3.5 17.6 1.0
CB A:THR273 3.5 19.4 1.0
CB A:THR94 3.7 20.2 1.0
CG2 A:THR273 3.8 21.6 1.0
N A:THR273 4.1 20.1 1.0
CG A:MET95 4.2 23.3 1.0
CB A:GLU68 4.2 25.7 1.0
CB A:SER91 4.2 18.0 1.0
O A:ALA90 4.3 16.7 1.0
O A:HOH527 4.3 31.4 1.0
O A:HOH532 4.3 20.3 1.0
CA A:THR273 4.4 20.4 1.0
C A:THR94 4.4 21.8 1.0
N A:ASP69 4.4 21.3 1.0
CA A:GLU68 4.4 24.5 1.0
N A:MET95 4.4 22.9 1.0
OE1 A:GLU68 4.4 36.4 1.0
CG A:GLU68 4.4 28.7 1.0
CA A:THR94 4.5 20.0 1.0
CA A:ASP69 4.5 20.7 1.0
N A:ALA92 4.5 18.5 1.0
CG2 A:THR94 4.6 20.7 1.0
N A:SER91 4.7 17.0 1.0
N A:THR94 4.8 19.0 1.0
O A:THR94 4.8 22.2 1.0
C A:ALA90 4.9 18.1 1.0
CE A:MET95 4.9 26.3 1.0
CD A:GLU68 5.0 32.8 1.0
OG A:SER91 5.0 17.6 1.0

Sodium binding site 2 out of 5 in 5bpf

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Sodium binding site 2 out of 5 in the Crystal Structure of Adp 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 Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:28.3
occ:1.00
 CE1 A:HIS265 2.3 41.4 1.0
NE2 A:HIS265 3.1 45.9 1.0
ND1 A:HIS265 3.3 41.2 1.0
CD2 A:HIS265 4.3 43.2 1.0
CG A:HIS265 4.5 38.0 1.0

Sodium binding site 3 out of 5 in 5bpf

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Sodium binding site 3 out of 5 in the Crystal Structure of Adp 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 Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:17.8
occ:1.00
 O B:HOH546 2.2 20.5 1.0
O B:GLU68 2.3 20.5 1.0
OG1 B:THR273 2.3 20.0 1.0
OG1 B:THR94 2.3 18.7 1.0
O B:SER91 2.3 16.1 1.0
SD B:MET95 3.2 31.0 1.0
C B:SER91 3.3 16.8 1.0
C B:GLU68 3.5 21.2 1.0
CA B:SER91 3.5 16.4 1.0
CB B:THR273 3.6 20.0 1.0
CB B:THR94 3.6 18.9 1.0
CG2 B:THR273 3.8 21.2 1.0
CG B:MET95 4.0 24.9 1.0
CB B:GLU68 4.1 23.5 1.0
CG B:GLU68 4.2 24.4 1.0
N B:THR273 4.2 20.2 1.0
O B:HOH547 4.3 34.3 1.0
O B:ALA90 4.3 17.3 1.0
CB B:SER91 4.3 15.6 1.0
C B:THR94 4.3 19.6 1.0
N B:MET95 4.3 20.2 1.0
OE2 B:GLU68 4.3 30.5 1.0
CA B:GLU68 4.4 21.9 1.0
CA B:THR94 4.4 18.4 1.0
O B:HOH534 4.4 21.6 1.0
CA B:THR273 4.4 22.1 1.0
N B:ASP69 4.5 19.6 1.0
CA B:ASP69 4.5 17.9 1.0
N B:ALA92 4.6 15.4 1.0
CG2 B:THR94 4.7 19.4 1.0
N B:THR94 4.7 18.5 1.0
N B:SER91 4.7 15.0 1.0
CD B:GLU68 4.8 28.2 1.0
O B:THR94 4.8 21.4 1.0
CE B:MET95 4.8 28.5 1.0
OG B:SER91 4.8 15.2 1.0
O B:VAL271 4.9 23.7 1.0
C B:ALA90 4.9 16.0 1.0

Sodium binding site 4 out of 5 in 5bpf

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Sodium binding site 4 out of 5 in the Crystal Structure of Adp 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 Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:21.7
occ:1.00
 O C:GLU68 2.2 20.9 1.0
OG1 C:THR94 2.3 21.9 1.0
O C:HOH591 2.3 25.4 1.0
OG1 C:THR273 2.3 19.3 1.0
O C:SER91 2.3 17.7 1.0
C C:SER91 3.2 18.8 1.0
SD C:MET95 3.3 28.1 1.0
CA C:SER91 3.5 17.4 1.0
C C:GLU68 3.5 23.1 1.0
CB C:THR94 3.6 22.3 1.0
CB C:THR273 3.6 19.7 1.0
CG2 C:THR273 3.8 19.5 1.0
CG C:MET95 4.0 25.1 1.0
CB C:SER91 4.1 18.0 1.0
O C:HOH539 4.1 19.7 1.0
CB C:GLU68 4.2 25.3 1.0
N C:THR273 4.2 20.1 1.0
O C:ALA90 4.2 17.8 1.0
N C:MET95 4.3 21.4 1.0
CA C:GLU68 4.4 23.8 1.0
C C:THR94 4.4 23.6 1.0
CG C:GLU68 4.4 28.6 1.0
CA C:THR94 4.4 21.2 1.0
OE1 C:GLU68 4.4 32.5 1.0
N C:ASP69 4.5 21.1 1.0
CA C:THR273 4.5 20.3 1.0
O C:HOH520 4.5 36.3 1.0
N C:ALA92 4.5 17.7 1.0
CG2 C:THR94 4.6 24.5 1.0
CA C:ASP69 4.6 23.1 1.0
N C:THR94 4.6 22.4 1.0
N C:SER91 4.7 17.2 1.0
CE C:MET95 4.8 28.1 1.0
OG C:SER91 4.8 19.6 1.0
C C:ALA90 4.9 18.3 1.0
O C:THR94 4.9 21.3 1.0
CD C:GLU68 5.0 32.7 1.0

Sodium binding site 5 out of 5 in 5bpf

Go back to Sodium Binding Sites List in 5bpf
Sodium binding site 5 out of 5 in the Crystal Structure of Adp 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 Adp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:23.7
occ:1.00
 O D:GLU68 2.2 24.9 1.0
OG1 D:THR273 2.3 26.5 1.0
O D:HOH546 2.3 24.6 1.0
OG1 D:THR94 2.3 25.5 1.0
O D:SER91 2.3 24.5 1.0
SD D:MET95 3.1 32.8 1.0
C D:SER91 3.3 21.2 1.0
C D:GLU68 3.4 24.9 1.0
CB D:THR273 3.5 26.5 1.0
CA D:SER91 3.6 21.2 1.0
CB D:THR94 3.6 25.4 1.0
CG2 D:THR273 3.8 27.6 1.0
CG D:MET95 4.0 28.6 1.0
CB D:GLU68 4.1 27.7 1.0
N D:THR273 4.2 26.4 1.0
CB D:SER91 4.2 20.8 1.0
CG D:GLU68 4.2 30.7 1.0
O D:HOH532 4.3 19.7 1.0
CA D:GLU68 4.3 26.5 1.0
OE2 D:GLU68 4.4 38.5 1.0
N D:MET95 4.4 28.7 1.0
C D:THR94 4.4 28.6 1.0
CA D:THR273 4.4 26.5 1.0
O D:ALA90 4.4 21.3 1.0
N D:ASP69 4.4 24.3 1.0
O D:HOH530 4.5 36.8 1.0
CA D:THR94 4.5 26.9 1.0
CA D:ASP69 4.5 25.6 1.0
N D:ALA92 4.5 22.5 1.0
CG2 D:THR94 4.6 28.4 1.0
CE D:MET95 4.7 32.5 1.0
N D:SER91 4.8 19.8 1.0
N D:THR94 4.8 24.8 1.0
CD D:GLU68 4.8 34.9 1.0
O D:THR94 4.8 29.1 1.0
OG D:SER91 4.9 19.5 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: Mon Oct 7 20:08:23 2024

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