Atomistry » Sodium » PDB 2uzz-2vrp » 2v5h
Atomistry »
  Sodium »
    PDB 2uzz-2vrp »
      2v5h »

Sodium in PDB 2v5h: Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942

Enzymatic activity of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942

All present enzymatic activity of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942:
2.7.2.8;

Protein crystallography data

The structure of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942, PDB code: 2v5h was solved by J.L.Llacer, C.Marco-Marin, F.Gil-Ortiz, I.Fita, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.379, 161.027, 91.562, 90.00, 106.53, 90.00
R / Rfree (%) 20 / 23.6

Other elements in 2v5h:

The structure of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 (pdb code 2v5h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942, PDB code: 2v5h:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2v5h

Go back to Sodium Binding Sites List in 2v5h
Sodium binding site 1 out of 6 in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1293

b:57.8
occ:1.00
 O A:HOH2028 2.7 26.6 1.0
O A:THR280 2.8 40.8 1.0
O A:GLU277 3.0 37.4 1.0
O A:HOH2027 3.0 27.3 1.0
OE1 A:GLU277 3.3 40.0 1.0
C A:THR280 4.0 40.7 1.0
C A:GLU277 4.1 37.1 1.0
CD A:GLU277 4.1 40.0 1.0
CA A:ASP281 4.3 41.5 1.0
OD1 A:ASP281 4.4 46.0 1.0
N A:ASP281 4.6 41.1 1.0
OE2 A:GLU277 4.6 40.5 1.0
CA A:GLU277 4.7 36.6 1.0
O A:LEU276 4.9 36.3 1.0
C A:ASP281 5.0 41.0 1.0

Sodium binding site 2 out of 6 in 2v5h

Go back to Sodium Binding Sites List in 2v5h
Sodium binding site 2 out of 6 in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1298

b:37.2
occ:1.00
 O B:THR280 2.5 40.6 1.0
O B:GLU277 2.8 37.2 1.0
O B:HOH2022 2.9 35.6 1.0
OE1 B:GLU277 3.1 39.9 1.0
C B:THR280 3.7 40.6 1.0
CD B:GLU277 3.7 39.8 1.0
C B:GLU277 3.8 37.0 1.0
OE2 B:GLU277 4.0 40.1 1.0
CA B:GLU277 4.0 36.6 1.0
CA B:ASP281 4.0 41.6 1.0
O B:ALA282 4.1 40.0 1.0
O B:LEU276 4.1 36.4 1.0
N B:ASP281 4.3 41.1 1.0
C B:ASP281 4.4 41.0 1.0
N B:ALA282 4.6 40.4 1.0
CG B:GLU277 4.7 37.2 1.0
CD1 B:ILE284 4.8 41.2 1.0
CA B:THR280 4.8 40.4 1.0
N B:THR280 4.8 40.0 1.0
OD1 B:ASP281 4.8 46.1 1.0
CB B:GLU277 4.9 36.7 1.0
C B:LEU276 4.9 36.0 1.0
N B:GLU277 5.0 36.1 1.0

Sodium binding site 3 out of 6 in 2v5h

Go back to Sodium Binding Sites List in 2v5h
Sodium binding site 3 out of 6 in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1293

b:37.0
occ:1.00
 O C:HOH2015 2.6 32.6 1.0
O C:THR280 2.7 40.7 1.0
O C:GLU277 2.8 37.2 1.0
O C:HOH2014 3.0 36.8 1.0
OE1 C:GLU277 3.1 39.8 1.0
C C:THR280 3.8 40.6 1.0
C C:GLU277 3.9 37.0 1.0
CD C:GLU277 3.9 39.9 1.0
CA C:ASP281 4.2 41.5 1.0
CA C:GLU277 4.3 36.7 1.0
OE2 C:GLU277 4.4 40.0 1.0
O C:LEU276 4.5 36.3 1.0
N C:ASP281 4.5 41.0 1.0
OD1 C:ASP281 4.5 46.1 1.0
O C:ALA282 4.7 40.0 1.0
C C:ASP281 4.8 41.0 1.0
N C:THR280 4.9 40.1 1.0
CG C:GLU277 4.9 37.3 1.0
CA C:THR280 5.0 40.4 1.0

Sodium binding site 4 out of 6 in 2v5h

Go back to Sodium Binding Sites List in 2v5h
Sodium binding site 4 out of 6 in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1295

b:50.3
occ:1.00
 O D:THR280 2.4 40.6 1.0
O D:GLU277 2.6 37.3 1.0
OE1 D:GLU277 3.2 40.0 1.0
O D:HOH2016 3.5 29.1 1.0
C D:THR280 3.6 40.6 1.0
C D:GLU277 3.7 37.1 1.0
CD D:GLU277 4.0 39.9 1.0
CA D:GLU277 4.2 36.7 1.0
CA D:ASP281 4.2 41.5 1.0
O D:LEU276 4.3 36.2 1.0
N D:ASP281 4.4 41.0 1.0
OD1 D:ASP281 4.4 46.1 1.0
OE2 D:GLU277 4.5 40.3 1.0
N D:THR280 4.6 40.2 1.0
CA D:THR280 4.7 40.5 1.0
O D:ALA282 4.8 40.0 1.0
N D:ILE278 4.8 37.5 1.0
C D:ASP281 4.8 41.0 1.0
O D:ILE278 4.9 38.9 1.0
CG D:GLU277 4.9 37.3 1.0
C D:ILE278 5.0 38.5 1.0

Sodium binding site 5 out of 6 in 2v5h

Go back to Sodium Binding Sites List in 2v5h
Sodium binding site 5 out of 6 in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1296

b:46.1
occ:1.00
 O E:THR280 2.2 40.8 1.0
O E:GLU277 2.3 37.1 1.0
C E:THR280 3.4 40.7 1.0
OE1 E:GLU277 3.4 40.2 1.0
C E:GLU277 3.5 37.1 1.0
O E:LEU276 4.1 36.4 1.0
CA E:GLU277 4.1 36.7 1.0
CD E:GLU277 4.1 40.0 1.0
CA E:ASP281 4.1 41.6 1.0
N E:ASP281 4.2 41.1 1.0
N E:THR280 4.3 40.1 1.0
OD1 E:ASP281 4.4 46.2 1.0
CA E:THR280 4.4 40.4 1.0
N E:ILE278 4.6 37.5 1.0
O E:ILE278 4.6 38.7 1.0
OE2 E:GLU277 4.7 40.3 1.0
C E:ILE278 4.7 38.5 1.0
C E:ASP281 4.8 41.0 1.0
CA E:ILE278 4.9 38.1 1.0
O E:ALA282 4.9 40.0 1.0
CG E:GLU277 4.9 37.3 1.0
C E:LEU276 5.0 36.0 1.0
N E:ALA282 5.0 40.4 1.0

Sodium binding site 6 out of 6 in 2v5h

Go back to Sodium Binding Sites List in 2v5h
Sodium binding site 6 out of 6 in the Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Controlling the Storage of Nitrogen As Arginine: the Complex of Pii and Acetylglutamate Kinase From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1294

b:47.5
occ:1.00
 O F:HOH2022 2.5 37.2 1.0
O F:HOH2023 2.6 46.5 1.0
O F:GLU277 2.7 37.4 1.0
O F:THR280 2.7 40.8 1.0
OE1 F:GLU277 3.1 40.0 1.0
C F:GLU277 3.8 37.1 1.0
C F:THR280 3.9 40.7 1.0
CD F:GLU277 3.9 39.8 1.0
CA F:GLU277 4.4 36.7 1.0
CA F:ASP281 4.4 41.5 1.0
OE2 F:GLU277 4.4 40.2 1.0
OD1 F:ASP281 4.5 46.1 1.0
N F:ASP281 4.6 41.0 1.0
O F:LEU276 4.6 36.5 1.0
CG F:GLU277 4.9 37.2 1.0
N F:THR280 4.9 40.2 1.0
N F:ILE278 4.9 37.5 1.0
O F:ILE278 5.0 38.7 1.0

Reference:

J.L.Llacer, A.Contreras, K.Forchhammer, C.Marco-Marin, F.Gil-Ortiz, R.Maldonado, I.Fita, V.Rubio. The Crystal Structure of the Complex of Pii and Acetylglutamate Kinase Reveals How Pii Controls the Storage of Nitrogen As Arginine. Proc.Natl.Acad.Sci.Usa V. 104 17644 2007.
ISSN: ISSN 0027-8424
PubMed: 17959776
DOI: 10.1073/PNAS.0705987104
Page generated: Mon Oct 7 04:26:22 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy