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Sodium in PDB 5c1p: Crystal Structure of Adp and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis

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

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

Protein crystallography data

The structure of Crystal Structure of Adp and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5c1p was solved by H.T.Tran, L.W.Kang, M.K.Hong, H.P.T.Ngo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.02 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.670, 106.545, 211.103, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Adp and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis (pdb code 5c1p). 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 and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5c1p:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5c1p

Go back to Sodium Binding Sites List in 5c1p
Sodium binding site 1 out of 5 in the Crystal Structure of Adp and D-Alanyl-D-Alanine 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 and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:26.7
occ:1.00
 O A:HOH517 2.3 27.6 1.0
OG1 A:THR94 2.3 26.9 1.0
O A:GLU68 2.3 23.8 1.0
OG1 A:THR273 2.3 25.9 1.0
O A:SER91 2.3 28.3 1.0
SD A:MET95 3.2 37.5 1.0
C A:SER91 3.3 25.3 1.0
C A:GLU68 3.5 27.7 1.0
CB A:THR273 3.6 23.7 1.0
CB A:THR94 3.6 24.2 1.0
CA A:SER91 3.6 22.6 1.0
CG2 A:THR273 3.8 25.4 1.0
CG A:MET95 4.0 30.6 1.0
N A:THR273 4.2 25.9 1.0
CB A:GLU68 4.2 32.2 1.0
CG A:GLU68 4.3 36.9 1.0
O A:ALA90 4.3 18.2 1.0
O A:HOH525 4.3 34.4 1.0
CB A:SER91 4.3 22.0 1.0
C A:THR94 4.3 27.2 1.0
N A:MET95 4.4 29.3 1.0
OE1 A:GLU68 4.4 44.2 1.0
CA A:GLU68 4.4 30.4 1.0
CA A:THR94 4.4 26.2 1.0
N A:ASP69 4.4 23.6 1.0
CA A:THR273 4.4 24.2 1.0
O A:HOH520 4.4 23.2 1.0
CA A:ASP69 4.5 25.3 1.0
N A:ALA92 4.6 26.3 1.0
CG2 A:THR94 4.6 24.5 1.0
O A:THR94 4.7 33.7 1.0
N A:THR94 4.7 26.8 1.0
N A:SER91 4.8 22.8 1.0
CD A:GLU68 4.9 42.4 1.0
CE A:MET95 4.9 34.6 1.0
OG A:SER91 5.0 21.9 1.0
C A:ALA90 5.0 24.4 1.0

Sodium binding site 2 out of 5 in 5c1p

Go back to Sodium Binding Sites List in 5c1p
Sodium binding site 2 out of 5 in the Crystal Structure of Adp and D-Alanyl-D-Alanine 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 and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:27.5
occ:1.00
 O B:GLU68 2.2 26.6 1.0
OG1 B:THR273 2.2 27.7 1.0
O B:SER91 2.2 23.7 1.0
O B:HOH512 2.2 25.1 1.0
OG1 B:THR94 2.3 27.9 1.0
C B:SER91 3.2 24.2 1.0
SD B:MET95 3.4 38.6 1.0
C B:GLU68 3.4 26.2 1.0
CA B:SER91 3.4 22.7 1.0
CB B:THR273 3.5 26.7 1.0
CB B:THR94 3.6 25.5 1.0
CG2 B:THR273 3.7 27.5 1.0
CG B:MET95 4.1 33.1 1.0
CB B:GLU68 4.1 30.5 1.0
N B:THR273 4.2 24.9 1.0
CB B:SER91 4.2 21.0 1.0
CG B:GLU68 4.2 34.8 1.0
O B:ALA90 4.2 23.2 1.0
CA B:GLU68 4.3 27.1 1.0
O B:HOH515 4.3 29.4 1.0
C B:THR94 4.3 25.8 1.0
N B:MET95 4.4 27.2 1.0
N B:ASP69 4.4 24.5 1.0
CA B:THR273 4.4 25.9 1.0
OE2 B:GLU68 4.4 47.0 1.0
CA B:THR94 4.4 26.1 1.0
N B:ALA92 4.5 22.2 1.0
CA B:ASP69 4.5 25.0 1.0
CG2 B:THR94 4.6 24.2 1.0
N B:SER91 4.6 23.6 1.0
N B:THR94 4.7 27.5 1.0
O B:HOH523 4.7 41.6 1.0
OG B:SER91 4.8 20.5 1.0
O B:THR94 4.8 30.9 1.0
CD B:GLU68 4.8 39.3 1.0
C B:ALA90 4.9 24.6 1.0

Sodium binding site 3 out of 5 in 5c1p

Go back to Sodium Binding Sites List in 5c1p
Sodium binding site 3 out of 5 in the Crystal Structure of Adp and D-Alanyl-D-Alanine 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 and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:28.8
occ:1.00
 OG1 C:THR273 2.2 23.6 1.0
O C:GLU68 2.2 31.9 1.0
OG1 C:THR94 2.3 29.1 1.0
O C:SER91 2.3 26.4 1.0
O C:HOH543 2.3 32.2 1.0
C C:SER91 3.2 24.0 1.0
SD C:MET95 3.3 37.6 1.0
C C:GLU68 3.4 32.2 1.0
CA C:SER91 3.5 21.9 1.0
CB C:THR273 3.5 26.2 1.0
CB C:THR94 3.6 28.9 1.0
CG2 C:THR273 3.7 28.4 1.0
CG C:MET95 4.1 30.1 1.0
N C:THR273 4.1 24.4 1.0
CB C:GLU68 4.2 33.4 1.0
CB C:SER91 4.2 20.1 1.0
CG C:GLU68 4.2 40.1 1.0
O C:ALA90 4.3 21.9 1.0
O C:HOH535 4.3 24.7 1.0
CA C:GLU68 4.3 30.5 1.0
N C:MET95 4.3 26.4 1.0
OE2 C:GLU68 4.3 49.9 1.0
C C:THR94 4.4 28.7 1.0
CA C:THR273 4.4 26.1 1.0
N C:ASP69 4.4 27.1 1.0
CA C:THR94 4.4 27.9 1.0
N C:ALA92 4.5 24.8 1.0
CA C:ASP69 4.6 27.1 1.0
CG2 C:THR94 4.6 30.0 1.0
N C:SER91 4.7 20.8 1.0
O C:HOH517 4.8 37.6 1.0
N C:THR94 4.8 29.1 1.0
CD C:GLU68 4.8 41.6 1.0
OG C:SER91 4.8 20.7 1.0
O C:THR94 4.9 26.4 1.0
C C:ALA90 4.9 22.7 1.0
CE C:MET95 5.0 36.4 1.0

Sodium binding site 4 out of 5 in 5c1p

Go back to Sodium Binding Sites List in 5c1p
Sodium binding site 4 out of 5 in the Crystal Structure of Adp and D-Alanyl-D-Alanine 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 and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na408

b:23.2
occ:1.00
 NE2 C:HIS280 2.2 38.4 1.0
O C:HOH575 2.2 38.5 1.0
CD2 C:HIS280 3.0 34.9 1.0
CE1 C:HIS280 3.3 44.5 1.0
CG C:HIS280 4.2 39.2 1.0
ND1 C:HIS280 4.3 45.6 1.0
CB C:SER279 4.8 42.4 1.0

Sodium binding site 5 out of 5 in 5c1p

Go back to Sodium Binding Sites List in 5c1p
Sodium binding site 5 out of 5 in the Crystal Structure of Adp and D-Alanyl-D-Alanine 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 and D-Alanyl-D-Alanine Complexed D-Alanine-D- Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:33.3
occ:1.00
 O D:GLU68 2.3 29.4 1.0
OG1 D:THR94 2.3 30.6 1.0
OG1 D:THR273 2.3 34.2 1.0
O D:HOH508 2.3 26.4 1.0
O D:SER91 2.3 31.5 1.0
SD D:MET95 3.2 41.4 1.0
C D:SER91 3.3 30.6 1.0
C D:GLU68 3.5 33.0 1.0
CB D:THR273 3.6 32.3 1.0
CB D:THR94 3.6 32.2 1.0
CA D:SER91 3.6 28.7 1.0
CG2 D:THR273 3.8 34.7 1.0
CG D:MET95 4.0 38.2 1.0
N D:THR273 4.1 29.9 1.0
CB D:GLU68 4.2 37.7 1.0
CG D:GLU68 4.2 38.5 1.0
N D:MET95 4.3 36.1 1.0
C D:THR94 4.3 34.6 1.0
OE2 D:GLU68 4.3 50.6 1.0
CB D:SER91 4.3 25.7 1.0
O D:ALA90 4.3 28.6 1.0
O D:HOH521 4.4 28.4 1.0
CA D:GLU68 4.4 32.3 1.0
CA D:THR273 4.4 34.3 1.0
CA D:THR94 4.4 33.4 1.0
N D:ASP69 4.5 30.0 1.0
N D:ALA92 4.6 31.7 1.0
CA D:ASP69 4.6 30.4 1.0
CG2 D:THR94 4.6 34.2 1.0
N D:THR94 4.7 32.8 1.0
O D:THR94 4.8 32.0 1.0
CD D:GLU68 4.8 48.0 1.0
N D:SER91 4.8 27.8 1.0
CE D:MET95 4.8 39.3 1.0
OG D:SER91 4.9 26.2 1.0
CA D:MET95 5.0 34.6 1.0
C D:ALA90 5.0 26.0 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 20:12:05 2024

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