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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

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