Sodium in PDB 8s3a: Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad, PDB code: 8s3a was solved by M.Grzechowiak, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.52 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.794, 157.031, 94.882, 90, 99.59, 90
R / Rfree (%) 15.7 / 19.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad (pdb code 8s3a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad, PDB code: 8s3a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8s3a

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Sodium binding site 1 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


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 Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na609

b:35.5
occ:1.00
 O A:HOH740 2.2 38.2 1.0
O A:SER27 2.4 41.2 1.0
O A:ILE30 2.4 38.0 1.0
OE2 E:GLU38 2.4 41.2 1.0
O A:HOH738 2.5 33.4 1.0
C A:SER27 3.4 40.3 1.0
CD E:GLU38 3.4 44.1 1.0
C A:ILE30 3.6 38.8 1.0
OG A:SER27 3.8 42.9 1.0
OE1 E:GLU38 3.8 44.6 1.0
CA A:LEU28 4.0 40.6 1.0
O A:LEU28 4.1 39.9 1.0
C A:LEU28 4.1 41.5 1.0
N A:LEU28 4.1 39.1 1.0
N A:ILE30 4.2 41.6 1.0
CA A:ILE30 4.3 39.1 1.0
CA A:SER27 4.3 41.8 1.0
OD1 A:ASP59 4.4 42.9 1.0
CB A:ILE30 4.4 38.8 1.0
O A:HIS58 4.4 30.0 1.0
N A:TYR32 4.5 30.1 1.0
C A:PRO31 4.5 31.0 1.0
N A:PRO31 4.6 31.4 1.0
O A:HOH710 4.6 34.6 1.0
CG E:GLU38 4.6 37.9 1.0
CB A:SER27 4.7 43.6 1.0
CA A:PRO31 4.7 31.4 1.0
N A:LEU29 4.8 45.5 1.0
O A:HOH837 4.8 40.6 1.0
CB E:GLU38 4.9 34.0 1.0
O A:PRO31 4.9 31.8 1.0

Sodium binding site 2 out of 8 in 8s3a

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Sodium binding site 2 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


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 Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na610

b:58.1
occ:1.00
 O A:ASP44 2.3 37.4 1.0
O B:ASP44 2.4 37.5 1.0
O B:HOH721 2.7 43.7 1.0
O4 A:PEG603 3.0 53.1 1.0
C A:ASP44 3.4 37.5 1.0
C B:ASP44 3.6 39.9 1.0
C4 A:PEG603 3.8 58.0 1.0
O A:HOH866 3.8 51.6 1.0
CA A:ASP44 3.9 37.0 1.0
CB A:ASP44 4.2 36.6 1.0
CA B:ASP44 4.2 35.1 1.0
N A:ASP45 4.5 36.7 1.0
C3 A:PEG603 4.6 64.3 1.0
CB B:ASP44 4.6 40.4 1.0
O A:HOH821 4.6 33.7 1.0
N B:ASP45 4.6 42.2 1.0
O B:HOH675 4.7 31.1 1.0
CA A:ASP45 4.8 36.9 1.0
CA B:ASP45 4.9 41.1 1.0
O A:HOH703 5.0 49.8 1.0
CG A:ASP44 5.0 39.4 1.0

Sodium binding site 3 out of 8 in 8s3a

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Sodium binding site 3 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


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 Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:32.5
occ:1.00
 O B:ILE30 2.3 36.3 1.0
OE2 F:GLU38 2.3 38.6 1.0
O B:HOH620 2.3 35.9 1.0
O B:SER27 2.4 38.9 1.0
O B:HOH692 2.6 32.7 1.0
CD F:GLU38 3.3 39.0 1.0
C B:ILE30 3.5 33.9 1.0
C B:SER27 3.5 36.6 1.0
OE1 F:GLU38 3.8 38.8 1.0
OG B:SER27 4.0 36.7 1.0
N B:ILE30 4.1 36.4 1.0
CA B:LEU28 4.1 35.8 1.0
C B:LEU28 4.1 36.7 1.0
CA B:ILE30 4.2 35.3 1.0
O B:LEU28 4.2 34.1 1.0
N B:LEU28 4.2 37.0 1.0
CB B:ILE30 4.3 33.8 1.0
O B:HIS58 4.3 29.0 1.0
N B:TYR32 4.5 30.6 1.0
OD2 B:ASP59 4.5 39.3 1.0
CA B:SER27 4.5 39.7 1.0
N B:PRO31 4.5 29.0 1.0
C B:PRO31 4.5 29.1 1.0
CG F:GLU38 4.5 30.2 1.0
O F:HOH875 4.6 50.7 1.0
CA B:PRO31 4.6 28.4 1.0
O B:HOH608 4.7 36.0 1.0
N B:LEU29 4.7 39.1 1.0
CB F:GLU38 4.8 32.4 1.0
CB B:SER27 4.9 37.3 1.0
C B:LEU29 4.9 43.3 1.0
O B:PRO31 4.9 27.8 1.0

Sodium binding site 4 out of 8 in 8s3a

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Sodium binding site 4 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


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 Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:35.5
occ:1.00
 O C:HOH615 2.3 42.0 1.0
O C:ILE30 2.3 35.1 1.0
O C:SER27 2.3 33.6 1.0
OE1 D:GLU38 2.4 43.0 1.0
O C:HOH673 2.5 35.9 1.0
CD D:GLU38 3.3 43.3 1.0
C C:SER27 3.4 36.1 1.0
C C:ILE30 3.4 34.4 1.0
OE2 D:GLU38 3.8 45.2 1.0
OG C:SER27 4.0 42.3 1.0
CA C:LEU28 4.0 35.3 1.0
N C:ILE30 4.0 39.9 1.0
C C:LEU28 4.1 36.8 1.0
CA C:ILE30 4.1 36.2 1.0
N C:LEU28 4.1 38.4 1.0
O C:LEU28 4.2 38.2 1.0
CB C:ILE30 4.3 36.4 1.0
O C:HIS58 4.3 31.4 1.0
N C:TYR32 4.4 28.8 1.0
CA C:SER27 4.4 34.8 1.0
C C:PRO31 4.5 32.5 1.0
OD2 C:ASP59 4.5 40.5 1.0
N C:PRO31 4.5 34.0 1.0
CG D:GLU38 4.6 34.2 1.0
CA C:PRO31 4.7 36.0 1.0
O C:HOH608 4.7 36.5 1.0
N C:LEU29 4.8 36.2 1.0
CB D:GLU38 4.8 32.7 1.0
CB C:SER27 4.8 36.5 1.0
O C:PRO31 4.9 32.6 1.0
C C:LEU29 4.9 41.1 1.0
CG2 C:ILE30 5.0 38.1 1.0

Sodium binding site 5 out of 8 in 8s3a

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Sodium binding site 5 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


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 Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na505

b:57.4
occ:1.00
 O C:ASP44 2.0 45.3 1.0
O E:ASP44 2.6 49.4 1.0
O C:HOH725 2.7 46.0 1.0
O C:HOH709 2.8 57.3 1.0
C C:ASP44 3.1 42.4 1.0
O E:HOH1410 3.5 53.9 1.0
C E:ASP44 3.7 47.9 1.0
CA C:ASP44 3.7 42.4 1.0
CB C:ASP44 3.9 41.4 1.0
N C:ASP45 4.1 44.8 1.0
CA E:ASP44 4.3 46.2 1.0
CA C:ASP45 4.5 51.5 1.0
O C:HOH650 4.5 39.3 1.0
O E:HOH1259 4.5 39.9 1.0
CB E:ASP44 4.7 47.8 1.0
N E:ASP45 4.8 48.5 1.0
CG C:ASP44 5.0 44.1 1.0
CA E:ASP45 5.0 50.2 1.0

Sodium binding site 6 out of 8 in 8s3a

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Sodium binding site 6 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na505

b:34.9
occ:1.00
 O D:HOH620 2.2 42.1 1.0
OE2 C:GLU38 2.2 41.2 1.0
O D:SER27 2.3 35.1 1.0
O D:ILE30 2.4 37.0 1.0
O D:HOH679 2.4 37.5 1.0
CD C:GLU38 3.2 42.5 1.0
C D:SER27 3.4 39.6 1.0
C D:ILE30 3.5 38.2 1.0
OE1 C:GLU38 3.6 40.8 1.0
OG D:SER27 3.9 43.7 1.0
CA D:LEU28 4.1 38.7 1.0
N D:ILE30 4.1 38.9 1.0
C D:LEU28 4.1 39.1 1.0
N D:LEU28 4.1 39.4 1.0
O D:LEU28 4.2 40.3 1.0
CA D:ILE30 4.2 36.0 1.0
CB D:ILE30 4.3 36.6 1.0
CA D:SER27 4.4 37.1 1.0
O D:HIS58 4.4 32.0 1.0
OD1 D:ASP59 4.4 41.6 1.0
CG C:GLU38 4.4 33.3 1.0
N D:TYR32 4.5 30.4 1.0
C D:PRO31 4.5 31.8 1.0
N D:PRO31 4.6 34.6 1.0
O D:HOH602 4.7 35.8 1.0
CB C:GLU38 4.7 32.3 1.0
CA D:PRO31 4.7 33.1 1.0
CB D:SER27 4.7 37.6 1.0
N D:LEU29 4.8 38.6 1.0
O D:PRO31 4.9 34.5 1.0
C D:LEU29 5.0 41.4 1.0

Sodium binding site 7 out of 8 in 8s3a

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Sodium binding site 7 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1109

b:31.9
occ:1.00
 OE1 A:GLU38 2.2 36.0 1.0
O E:HOH1324 2.2 38.9 1.0
O E:SER27 2.3 30.6 1.0
O E:ILE30 2.3 31.3 1.0
O E:HOH1279 2.6 36.8 1.0
CD A:GLU38 3.2 38.6 1.0
O A:HOH705 3.4 49.4 1.0
C E:SER27 3.4 33.0 1.0
C E:ILE30 3.5 33.6 1.0
OE2 A:GLU38 3.7 42.7 1.0
O E:LEU28 3.9 37.8 1.0
CA E:LEU28 3.9 31.8 1.0
C E:LEU28 4.0 34.1 1.0
N E:ILE30 4.1 32.2 1.0
OG E:SER27 4.1 38.9 1.0
N E:LEU28 4.1 30.1 1.0
CA E:ILE30 4.2 30.1 1.0
O E:HIS58 4.3 28.5 1.0
CG A:GLU38 4.3 29.7 1.0
CB E:ILE30 4.3 36.8 1.0
OD2 E:ASP59 4.4 42.4 1.0
CA E:SER27 4.4 35.2 1.0
N E:TYR32 4.5 27.1 1.0
C E:PRO31 4.5 26.7 1.0
N E:PRO31 4.5 30.2 1.0
CB A:GLU38 4.6 30.6 1.0
CA E:PRO31 4.6 28.7 1.0
C E:LEU29 4.7 38.8 1.0
N E:LEU29 4.7 34.4 1.0
CB E:SER27 4.9 35.2 1.0
O E:HOH1205 4.9 32.9 1.0
O E:HOH1366 5.0 38.1 1.0
O E:PRO31 5.0 26.4 1.0

Sodium binding site 8 out of 8 in 8s3a

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Sodium binding site 8 out of 8 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2,6-Pyridinedicarboxylic Acid and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na607

b:30.9
occ:1.00
 OE1 B:GLU38 2.2 36.3 1.0
O F:HOH862 2.2 37.5 1.0
O F:SER27 2.3 31.9 1.0
O F:ILE30 2.4 32.0 1.0
O F:HOH815 2.5 37.1 1.0
CD B:GLU38 3.2 38.8 1.0
C F:SER27 3.3 32.1 1.0
C F:ILE30 3.6 31.3 1.0
OE2 B:GLU38 3.7 42.0 1.0
OG F:SER27 4.0 38.3 1.0
CA F:LEU28 4.0 31.7 1.0
C F:LEU28 4.1 35.0 1.0
O F:LEU28 4.1 34.3 1.0
N F:LEU28 4.1 30.3 1.0
N F:ILE30 4.2 29.1 1.0
O B:HOH696 4.3 47.3 1.0
CA F:ILE30 4.3 28.1 1.0
O F:HIS58 4.3 25.9 1.0
CG B:GLU38 4.4 29.3 1.0
CA F:SER27 4.4 34.1 1.0
N F:TYR32 4.4 28.1 1.0
CB F:ILE30 4.4 28.9 1.0
OD2 F:ASP59 4.4 38.5 1.0
C F:PRO31 4.5 28.0 1.0
CB B:GLU38 4.5 28.2 1.0
N F:PRO31 4.6 27.8 1.0
CA F:PRO31 4.7 27.7 1.0
N F:LEU29 4.7 34.4 1.0
CB F:SER27 4.8 34.8 1.0
C F:LEU29 4.8 40.2 1.0
O F:HOH706 4.9 31.2 1.0
O F:HOH884 4.9 35.9 1.0
O F:PRO31 4.9 29.1 1.0
C1 B:EDO505 5.0 49.0 1.0

Reference:

M.Grzechowiak, J.Sliwiak, A.Link, M.Ruszkowski. Legume-Type Glutamate Dehydrogenase: Structure, Activity, and Inhibition Studies. Int.J.Biol.Macromol. V. 278 34648 2024.
ISSN: ISSN 0141-8130
PubMed: 39142482
DOI: 10.1016/J.IJBIOMAC.2024.134648
Page generated: Wed Oct 9 13:25:37 2024

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