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Sodium in PDB 4zqi: Crystal Structure of Apo D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis

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

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

Protein crystallography data

The structure of Crystal Structure of Apo D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 4zqi was solved by H.-T.Tran, L.-W.Kang, M.-K.Hong, H.P.T.Ngo, K.H.Huynh, Y.J.Ahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.41 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.993, 107.027, 211.003, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.8

Sodium Binding Sites:

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

Sodium binding site 1 out of 5 in 4zqi

Go back to Sodium Binding Sites List in 4zqi
Sodium binding site 1 out of 5 in the Crystal Structure of Apo 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 Apo D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:27.2
occ:1.00
 O A:GLU68 2.3 25.5 1.0
OG1 A:THR273 2.3 31.2 1.0
OG1 A:THR94 2.3 23.8 1.0
O A:SER91 2.3 24.7 1.0
SD A:MET95 3.2 38.4 1.0
C A:SER91 3.3 21.7 1.0
C A:GLU68 3.5 26.6 1.0
CB A:THR273 3.6 29.4 1.0
CB A:THR94 3.6 21.0 1.0
CA A:SER91 3.6 20.8 1.0
CG2 A:THR273 3.9 31.7 1.0
CG A:MET95 4.1 28.4 1.0
CB A:GLU68 4.1 31.7 1.0
N A:THR273 4.1 28.5 1.0
OE2 A:GLU68 4.2 50.7 1.0
CG A:GLU68 4.2 35.5 1.0
C A:THR94 4.3 25.9 1.0
N A:MET95 4.3 27.5 1.0
CB A:SER91 4.4 20.9 1.0
CA A:GLU68 4.4 27.7 1.0
CA A:THR94 4.4 23.2 1.0
CA A:THR273 4.4 30.6 1.0
O A:ALA90 4.4 22.8 1.0
N A:ASP69 4.4 25.3 1.0
CA A:ASP69 4.6 25.2 1.0
N A:ALA92 4.6 19.3 1.0
CG2 A:THR94 4.7 20.1 1.0
N A:THR94 4.7 22.7 1.0
CD A:GLU68 4.8 42.2 1.0
O A:THR94 4.8 29.2 1.0
CE A:MET95 4.9 38.8 1.0
O A:VAL271 4.9 25.1 1.0
N A:SER91 4.9 22.8 1.0

Sodium binding site 2 out of 5 in 4zqi

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Sodium binding site 2 out of 5 in the Crystal Structure of Apo 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 Apo D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:27.1
occ:1.00
 O B:GLU68 2.2 28.4 1.0
O B:SER91 2.3 27.4 1.0
OG1 B:THR94 2.3 30.2 1.0
OG1 B:THR273 2.3 28.0 1.0
SD B:MET95 3.2 38.4 1.0
C B:SER91 3.2 23.7 1.0
C B:GLU68 3.5 28.8 1.0
CA B:SER91 3.5 21.5 1.0
CB B:THR94 3.6 24.1 1.0
CB B:THR273 3.6 27.6 1.0
CG2 B:THR273 3.9 30.1 1.0
CG B:MET95 4.0 31.3 1.0
O B:HOH504 4.2 38.5 1.0
CB B:GLU68 4.2 33.0 1.0
N B:THR273 4.2 26.0 1.0
CB B:SER91 4.2 21.4 1.0
O B:ALA90 4.3 23.1 1.0
OE2 B:GLU68 4.3 61.4 1.0
C B:THR94 4.4 28.1 1.0
CG B:GLU68 4.4 41.2 1.0
N B:MET95 4.4 27.0 1.0
CA B:GLU68 4.4 32.8 1.0
CA B:THR94 4.4 25.8 1.0
N B:ASP69 4.4 25.6 1.0
O B:HOH507 4.4 23.9 1.0
CA B:THR273 4.5 27.9 1.0
CA B:ASP69 4.5 29.4 1.0
N B:ALA92 4.5 19.6 1.0
CG2 B:THR94 4.6 23.5 1.0
N B:SER91 4.7 24.0 1.0
N B:THR94 4.7 25.8 1.0
O B:THR94 4.8 32.7 1.0
CE B:MET95 4.9 36.5 1.0
CD B:GLU68 4.9 51.9 1.0
C B:ALA90 4.9 26.6 1.0
OG B:SER91 5.0 19.9 1.0
O B:VAL271 5.0 29.4 1.0

Sodium binding site 3 out of 5 in 4zqi

Go back to Sodium Binding Sites List in 4zqi
Sodium binding site 3 out of 5 in the Crystal Structure of Apo 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 Apo D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:32.2
occ:1.00
 CE1 B:HIS265 2.3 43.9 1.0
NE2 C:HIS280 2.4 51.5 1.0
NE2 B:HIS265 2.7 42.1 1.0
CD2 C:HIS280 3.0 42.5 1.0
ND1 B:HIS265 3.5 44.0 1.0
CE1 C:HIS280 3.6 50.5 1.0
CD2 B:HIS265 4.0 43.5 1.0
CG C:HIS280 4.3 47.5 1.0
CG B:HIS265 4.4 39.1 1.0
CB C:SER279 4.4 45.5 1.0
ND1 C:HIS280 4.6 49.4 1.0

Sodium binding site 4 out of 5 in 4zqi

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Sodium binding site 4 out of 5 in the Crystal Structure of Apo 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 Apo D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:30.0
occ:1.00
 O C:SER91 2.2 28.7 1.0
O C:GLU68 2.2 29.0 1.0
OG1 C:THR94 2.3 28.6 1.0
OG1 C:THR273 2.3 24.2 1.0
C C:SER91 3.2 26.2 1.0
SD C:MET95 3.3 41.1 1.0
CA C:SER91 3.4 25.1 1.0
C C:GLU68 3.5 35.0 1.0
CB C:THR273 3.6 23.4 1.0
CB C:THR94 3.6 25.8 1.0
CG2 C:THR273 3.8 25.6 1.0
CG C:MET95 4.0 32.6 1.0
CB C:SER91 4.2 23.2 1.0
O C:HOH521 4.2 26.4 1.0
O C:ALA90 4.2 23.7 1.0
N C:THR273 4.2 27.2 1.0
O C:HOH515 4.2 41.6 1.0
CB C:GLU68 4.3 34.4 1.0
N C:MET95 4.3 26.7 1.0
C C:THR94 4.4 30.0 1.0
CA C:THR94 4.4 24.9 1.0
CG C:GLU68 4.4 43.9 1.0
N C:ASP69 4.4 27.8 1.0
OE2 C:GLU68 4.4 48.7 1.0
CA C:GLU68 4.4 32.4 1.0
N C:ALA92 4.4 26.2 1.0
CA C:THR273 4.5 29.1 1.0
CA C:ASP69 4.5 31.8 1.0
CG2 C:THR94 4.6 27.0 1.0
N C:SER91 4.6 22.1 1.0
N C:THR94 4.6 29.0 1.0
C C:ALA90 4.9 26.1 1.0
OG C:SER91 4.9 25.3 1.0
O C:THR94 4.9 31.6 1.0
CD C:GLU68 5.0 46.2 1.0
CE C:MET95 5.0 38.3 1.0

Sodium binding site 5 out of 5 in 4zqi

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Sodium binding site 5 out of 5 in the Crystal Structure of Apo 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 Apo D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:31.7
occ:1.00
 O D:GLU68 2.3 34.9 1.0
O D:SER91 2.3 30.5 1.0
OG1 D:THR94 2.3 32.9 1.0
OG1 D:THR273 2.3 34.6 1.0
O D:HOH508 2.3 32.2 1.0
SD D:MET95 3.2 46.0 1.0
C D:SER91 3.2 26.8 1.0
C D:GLU68 3.5 34.3 1.0
CA D:SER91 3.5 26.5 1.0
CB D:THR273 3.6 31.2 1.0
CB D:THR94 3.6 31.1 1.0
CG2 D:THR273 3.9 31.5 1.0
CG D:MET95 4.0 32.9 1.0
N D:THR273 4.2 32.5 1.0
CB D:GLU68 4.2 43.6 1.0
CB D:SER91 4.3 26.9 1.0
N D:MET95 4.3 37.2 1.0
OE2 D:GLU68 4.3 68.7 1.0
O D:ALA90 4.3 27.0 1.0
C D:THR94 4.3 37.9 1.0
CG D:GLU68 4.3 48.9 1.0
O D:HOH507 4.4 31.5 1.0
CA D:GLU68 4.4 41.1 1.0
CA D:THR94 4.4 33.5 1.0
N D:ASP69 4.4 34.9 1.0
CA D:THR273 4.4 32.1 1.0
N D:ALA92 4.5 25.9 1.0
CA D:ASP69 4.5 37.6 1.0
CG2 D:THR94 4.7 29.3 1.0
N D:THR94 4.7 34.6 1.0
N D:SER91 4.7 27.5 1.0
O D:THR94 4.9 39.9 1.0
CD D:GLU68 4.9 64.0 1.0
CE D:MET95 4.9 42.2 1.0
C D:ALA90 5.0 27.7 1.0
CA D:MET95 5.0 36.5 1.0

Reference:

H.-T.Tran, M.-K.Hong, H.-P.-T.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.,Sect.D V. 72 12 2016.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798315021671
Page generated: Mon Oct 7 19:45:05 2024

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