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Sodium in PDB 4gbj: Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans

Protein crystallography data

The structure of Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans, PDB code: 4gbj was solved by K.Michalska, J.Holowicki, S.Clancy, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.01 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.633, 89.645, 151.506, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans (pdb code 4gbj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans, PDB code: 4gbj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4gbj

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Sodium binding site 1 out of 4 in the Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans


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 Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:62.1
occ:1.00
 O B:GLU151 2.2 51.2 1.0
O B:VAL154 2.4 49.4 1.0
O B:HOH524 2.5 50.4 1.0
O B:HOH510 2.7 48.2 1.0
C B:GLU151 3.4 49.7 1.0
C B:VAL154 3.5 48.8 1.0
CA B:GLU151 4.1 41.6 1.0
CA B:LYS155 4.2 46.2 1.0
O B:LYS155 4.2 50.0 1.0
N B:LYS155 4.3 45.5 1.0
N B:VAL154 4.4 41.6 1.0
CB B:GLU151 4.4 45.3 1.0
N B:ASN152 4.5 48.4 1.0
CA B:VAL154 4.6 41.3 1.0
C B:LYS155 4.7 48.0 1.0
C B:ASN152 4.7 50.8 1.0
CA B:ASN152 4.7 49.5 1.0
O B:ASN152 4.8 51.1 1.0

Sodium binding site 2 out of 4 in 4gbj

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Sodium binding site 2 out of 4 in the Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans


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 Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:39.8
occ:1.00
 O C:HOH499 2.2 50.0 1.0
O C:HOH498 2.2 55.3 1.0
O C:HOH454 2.3 35.1 1.0
O C:VAL154 2.3 40.1 1.0
O C:GLU151 2.4 38.6 1.0
C C:VAL154 3.5 40.3 1.0
C C:GLU151 3.6 38.8 1.0
CA C:LYS155 4.2 41.6 1.0
N C:LYS155 4.3 39.9 1.0
N C:VAL154 4.3 34.6 1.0
CA C:GLU151 4.3 33.8 1.0
O C:LYS155 4.4 45.7 1.0
CA C:VAL154 4.5 34.6 1.0
N C:ASN152 4.7 34.8 1.0
C C:ASN152 4.7 39.2 1.0
CB C:GLU151 4.7 36.2 1.0
C C:LYS155 4.8 45.0 1.0
CA C:ASN152 4.8 37.5 1.0
N C:PHE153 4.9 34.0 1.0
O C:LYS130 5.0 51.0 1.0
O C:ASN152 5.0 41.3 1.0

Sodium binding site 3 out of 4 in 4gbj

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Sodium binding site 3 out of 4 in the Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans


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 Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:36.5
occ:1.00
 O C:HOH481 2.2 49.1 1.0
OE1 C:GLU50 2.3 66.7 1.0
O D:HOH451 2.4 38.8 1.0
O C:HOH463 2.5 44.0 1.0
O C:ARG33 2.8 70.8 1.0
O D:LEU44 3.1 59.7 1.0
CD C:GLU50 3.5 70.2 1.0
C C:ARG33 4.0 70.8 1.0
OE2 C:GLU50 4.1 74.2 1.0
C D:LEU44 4.2 58.3 1.0
CA D:GLY45 4.3 55.0 1.0
O D:LEU22 4.4 55.8 1.0
O C:ASN32 4.5 54.5 1.0
O C:GLU50 4.5 44.8 1.0
O D:TYR26 4.6 49.1 1.0
CG C:GLU50 4.7 60.0 1.0
N D:GLY45 4.7 54.2 1.0
CA C:ARG33 4.7 61.3 1.0
CD2 D:LEU22 4.8 49.3 1.0
CB C:GLU50 4.8 48.2 1.0
C D:GLY45 4.9 56.9 1.0
CA C:GLU50 4.9 45.5 1.0
O D:GLY45 4.9 58.3 1.0

Sodium binding site 4 out of 4 in 4gbj

Go back to Sodium Binding Sites List in 4gbj
Sodium binding site 4 out of 4 in the Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans


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 Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:35.6
occ:1.00
 O D:HOH514 2.2 50.5 1.0
O D:HOH518 2.2 42.3 1.0
O D:VAL154 2.3 37.9 1.0
O D:GLU151 2.4 42.1 1.0
O D:HOH519 2.4 59.1 1.0
O B:HOH492 2.4 55.4 1.0
C D:VAL154 3.5 37.9 1.0
C D:GLU151 3.6 43.3 1.0
CA D:LYS155 4.2 37.6 1.0
N D:LYS155 4.3 36.8 1.0
CA D:GLU151 4.3 38.2 1.0
N D:VAL154 4.4 32.8 1.0
O D:LYS155 4.5 43.8 1.0
O B:HOH478 4.5 51.2 1.0
CA D:VAL154 4.6 31.2 1.0
N D:ASN152 4.6 39.6 1.0
C D:ASN152 4.6 39.3 1.0
CB D:GLU151 4.7 40.4 1.0
O D:ASN152 4.7 38.5 1.0
CA D:ASN152 4.7 39.5 1.0
C D:LYS155 4.8 41.7 1.0
O D:LYS130 4.8 44.3 1.0

Reference:

K.Michalska, J.Holowicki, S.Clancy, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of Nad-Binding 6-Phosphogluconate Dehydrogenase From Dyadobacter Fermentans To Be Published.
Page generated: Mon Oct 7 15:32:23 2024

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