Atomistry » Sodium » PDB 5bpl-5ccx » 5c1o
Atomistry »
  Sodium »
    PDB 5bpl-5ccx »
      5c1o »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy