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Sodium in PDB 5c1o: Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis

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

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

Protein crystallography data

The structure of Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5c1o 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) 47.69 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.029, 106.795, 212.012, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.3

Other elements in 5c1o:

The structure of Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis (pdb code 5c1o). 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-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5c1o:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5c1o

Go back to Sodium Binding Sites List in 5c1o
Sodium binding site 1 out of 5 in the Crystal Structure of Amp-Pnp 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-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:35.6
occ:1.00
 OG1 A:THR273 2.2 36.0 1.0
O A:GLU68 2.2 33.0 1.0
O A:SER91 2.3 29.2 1.0
O A:HOH504 2.3 29.4 1.0
OG1 A:THR94 2.3 35.1 1.0
SD A:MET95 3.2 47.4 1.0
C A:SER91 3.3 32.4 1.0
C A:GLU68 3.5 35.3 1.0
CA A:SER91 3.6 30.2 1.0
CB A:THR94 3.6 31.8 1.0
CB A:THR273 3.6 32.5 1.0
CG A:MET95 3.9 45.1 1.0
CG2 A:THR273 4.0 34.8 1.0
CB A:GLU68 4.1 39.1 1.0
CG A:GLU68 4.1 43.2 1.0
N A:MET95 4.2 34.3 1.0
N A:THR273 4.2 34.2 1.0
C A:THR94 4.3 33.2 1.0
O A:ALA90 4.3 25.9 1.0
CB A:SER91 4.3 29.6 1.0
CA A:THR94 4.4 34.2 1.0
CA A:GLU68 4.4 36.6 1.0
N A:ASP69 4.4 30.6 1.0
CA A:ASP69 4.5 30.8 1.0
CA A:THR273 4.5 34.7 1.0
N A:ALA92 4.5 28.4 1.0
OE2 A:GLU68 4.6 53.5 1.0
CG2 A:THR94 4.7 34.3 1.0
N A:THR94 4.7 36.5 1.0
N A:SER91 4.8 31.2 1.0
CD A:GLU68 4.9 53.0 1.0
CE A:MET95 4.9 46.7 1.0
O A:THR94 4.9 40.2 1.0
CA A:MET95 5.0 35.9 1.0
OG A:SER91 5.0 28.8 1.0

Sodium binding site 2 out of 5 in 5c1o

Go back to Sodium Binding Sites List in 5c1o
Sodium binding site 2 out of 5 in the Crystal Structure of Amp-Pnp 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-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:36.4
occ:1.00
 OG1 B:THR273 2.2 36.8 1.0
OG1 B:THR94 2.3 35.6 1.0
O B:GLU68 2.3 30.6 1.0
O B:HOH505 2.3 38.0 1.0
O B:SER91 2.3 31.9 1.0
C B:SER91 3.3 32.3 1.0
SD B:MET95 3.3 47.2 1.0
CA B:SER91 3.5 29.1 1.0
C B:GLU68 3.5 34.8 1.0
CB B:THR94 3.6 32.9 1.0
CB B:THR273 3.6 31.8 1.0
CG B:MET95 3.8 40.0 1.0
CG2 B:THR273 4.0 32.4 1.0
CB B:SER91 4.2 28.9 1.0
N B:THR273 4.2 35.4 1.0
O B:ALA90 4.2 31.5 1.0
N B:MET95 4.3 39.5 1.0
C B:THR94 4.3 36.0 1.0
CB B:GLU68 4.3 42.5 1.0
CA B:THR94 4.4 33.7 1.0
CA B:THR273 4.4 33.9 1.0
CG B:GLU68 4.5 51.2 1.0
N B:ASP69 4.5 31.8 1.0
CA B:GLU68 4.5 38.7 1.0
N B:ALA92 4.5 31.9 1.0
CA B:ASP69 4.6 33.8 1.0
CG2 B:THR94 4.6 33.5 1.0
N B:SER91 4.7 30.6 1.0
N B:THR94 4.7 34.3 1.0
OE2 B:GLU68 4.8 62.6 1.0
CE B:MET95 4.8 43.7 1.0
O B:THR94 4.8 38.7 1.0
C B:ALA90 4.9 32.7 1.0
CB B:MET95 5.0 36.9 1.0

Sodium binding site 3 out of 5 in 5c1o

Go back to Sodium Binding Sites List in 5c1o
Sodium binding site 3 out of 5 in the Crystal Structure of Amp-Pnp 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-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:39.5
occ:1.00
 CE1 B:HIS265 2.3 63.8 1.0
NE2 C:HIS280 2.5 65.1 1.0
NE2 B:HIS265 2.7 62.6 1.0
CD2 C:HIS280 3.1 54.2 1.0
ND1 B:HIS265 3.6 61.4 1.0
CE1 C:HIS280 3.6 64.2 1.0
CD2 B:HIS265 4.0 64.3 1.0
CG C:HIS280 4.4 57.9 1.0
CG B:HIS265 4.4 58.9 1.0
CB C:SER279 4.5 56.5 1.0
ND1 C:HIS280 4.6 62.7 1.0

Sodium binding site 4 out of 5 in 5c1o

Go back to Sodium Binding Sites List in 5c1o
Sodium binding site 4 out of 5 in the Crystal Structure of Amp-Pnp 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-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:38.4
occ:1.00
 OG1 C:THR94 2.3 36.5 1.0
O C:GLU68 2.3 36.8 1.0
OG1 C:THR273 2.3 39.4 1.0
O C:HOH507 2.3 41.8 1.0
O C:SER91 2.3 40.1 1.0
C C:SER91 3.3 32.5 1.0
SD C:MET95 3.4 49.2 1.0
CA C:SER91 3.5 29.9 1.0
C C:GLU68 3.5 37.7 1.0
CB C:THR94 3.5 31.8 1.0
CB C:THR273 3.6 35.2 1.0
CG2 C:THR273 3.8 38.1 1.0
CG C:MET95 3.9 42.2 1.0
O C:ALA90 4.1 30.4 1.0
CB C:SER91 4.2 29.0 1.0
N C:MET95 4.3 34.5 1.0
C C:THR94 4.3 35.9 1.0
N C:THR273 4.3 37.7 1.0
CA C:THR94 4.3 32.5 1.0
CB C:GLU68 4.3 40.2 1.0
N C:ASP69 4.5 34.8 1.0
CA C:GLU68 4.5 37.2 1.0
CA C:THR273 4.5 35.2 1.0
N C:ALA92 4.5 34.1 1.0
CG C:GLU68 4.5 46.4 1.0
OE2 C:GLU68 4.6 50.5 1.0
CG2 C:THR94 4.6 34.3 1.0
CA C:ASP69 4.6 35.1 1.0
N C:THR94 4.6 33.9 1.0
O C:HOH512 4.7 47.1 1.0
N C:SER91 4.7 29.1 1.0
OG C:SER91 4.8 28.0 1.0
C C:ALA90 4.8 30.4 1.0
O C:THR94 4.9 44.9 1.0

Sodium binding site 5 out of 5 in 5c1o

Go back to Sodium Binding Sites List in 5c1o
Sodium binding site 5 out of 5 in the Crystal Structure of Amp-Pnp 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-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:47.5
occ:1.00
 O D:GLU68 2.2 40.2 1.0
OG1 D:THR94 2.3 37.1 1.0
OG1 D:THR273 2.3 39.6 1.0
O D:SER91 2.3 37.8 1.0
SD D:MET95 3.1 60.3 1.0
C D:SER91 3.3 33.8 1.0
C D:GLU68 3.4 41.1 1.0
CB D:THR273 3.6 37.4 1.0
CB D:THR94 3.6 41.2 1.0
CA D:SER91 3.6 31.8 1.0
CG2 D:THR273 3.8 35.7 1.0
CB D:GLU68 3.9 48.4 1.0
CG D:MET95 4.0 51.7 1.0
N D:MET95 4.2 46.0 1.0
CA D:GLU68 4.2 42.1 1.0
CB D:SER91 4.3 32.0 1.0
N D:THR273 4.3 40.8 1.0
CG D:GLU68 4.3 55.4 1.0
O D:ALA90 4.4 31.0 1.0
C D:THR94 4.4 42.9 1.0
N D:ASP69 4.4 44.3 1.0
CA D:THR273 4.5 39.3 1.0
CA D:THR94 4.5 42.3 1.0
N D:ALA92 4.6 37.9 1.0
OE2 D:GLU68 4.6 68.6 1.0
CG2 D:THR94 4.6 41.7 1.0
CA D:ASP69 4.6 45.5 1.0
CE D:MET95 4.7 60.2 1.0
N D:THR94 4.8 42.0 1.0
N D:SER91 4.8 32.1 1.0
CD D:GLU68 5.0 64.5 1.0
CA D:MET95 5.0 43.3 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 20:11:58 2024

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