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Sodium in PDB 3h2z: The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri

Enzymatic activity of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri

All present enzymatic activity of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri:
1.1.1.17;

Protein crystallography data

The structure of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri, PDB code: 3h2z was solved by R.Wu, S.Clancy, A.Joachimiak, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 151.092, 151.092, 92.179, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri (pdb code 3h2z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri, PDB code: 3h2z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3h2z

Go back to Sodium Binding Sites List in 3h2z
Sodium binding site 1 out of 5 in the The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na387

b:49.1
occ:1.00
 OD2 A:ASP266 2.1 24.7 1.0
O A:HOH651 2.3 46.2 1.0
CG A:ASP266 3.2 20.8 1.0
CB A:ASP266 3.8 19.1 1.0
O A:HOH440 4.2 29.8 1.0
OD1 A:ASP266 4.3 21.0 1.0
O A:HOH566 4.3 28.0 1.0
CA A:ASP266 4.4 17.9 1.0

Sodium binding site 2 out of 5 in 3h2z

Go back to Sodium Binding Sites List in 3h2z
Sodium binding site 2 out of 5 in the The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na389

b:69.1
occ:1.00
 O A:HOH497 2.2 44.4 1.0
O A:HOH498 2.3 34.0 1.0
O A:HOH508 3.6 43.1 1.0
OD2 A:ASP365 4.1 23.9 0.7
CA A:SER368 4.3 21.0 1.0
CB A:SER368 4.7 19.6 1.0
O A:ASN367 4.8 22.7 1.0
N A:SER368 4.9 20.8 1.0
C A:ASN367 5.0 22.2 1.0

Sodium binding site 3 out of 5 in 3h2z

Go back to Sodium Binding Sites List in 3h2z
Sodium binding site 3 out of 5 in the The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na390

b:53.8
occ:1.00
 O A:HOH503 2.3 31.6 1.0
O A:HOH633 2.4 43.8 1.0
O A:HOH477 2.4 28.5 1.0
OD1 A:ASP81 3.9 22.6 1.0
OG A:SER113 4.0 18.1 0.5
O A:HOH433 4.2 34.3 1.0
O A:HOH536 4.2 20.0 1.0
SE A:MSE1 4.3 36.6 0.4
CG A:ASP81 4.4 20.8 1.0
O A:HOH574 4.6 28.6 1.0
O A:HOH478 4.6 42.6 1.0
O A:PRO114 4.6 16.7 1.0
CB A:ASP81 4.6 14.8 1.0

Sodium binding site 4 out of 5 in 3h2z

Go back to Sodium Binding Sites List in 3h2z
Sodium binding site 4 out of 5 in the The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na391

b:25.1
occ:1.00
 NZ A:LYS18 3.1 17.2 1.0
NH2 A:ARG159 3.3 14.9 1.0
NH1 A:ARG159 3.4 15.7 1.0
O A:HOH447 3.6 34.0 1.0
CD A:LYS18 3.8 16.9 1.0
CZ A:ARG159 3.8 15.7 1.0
CE A:LYS18 3.9 17.3 1.0
CD2 A:LEU19 4.1 20.0 1.0
CG A:LYS18 4.4 15.8 1.0
O A:HOH471 4.5 43.8 1.0
OD2 A:ASP22 4.6 22.9 1.0
OD2 A:ASP58 4.7 22.0 1.0
CG A:LEU19 4.9 18.5 1.0
CG2 A:VAL50 4.9 15.9 1.0

Sodium binding site 5 out of 5 in 3h2z

Go back to Sodium Binding Sites List in 3h2z
Sodium binding site 5 out of 5 in the The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na392

b:37.5
occ:1.00
 O A:HOH508 2.1 43.1 1.0
O A:HOH638 2.6 36.8 1.0
N A:VAL370 3.4 19.9 1.0
N A:GLU369 3.5 22.5 1.0
CB A:SER368 3.8 19.6 1.0
CB A:GLU369 3.9 22.6 1.0
CA A:GLU369 4.0 21.9 1.0
CG2 A:VAL370 4.0 19.0 1.0
O A:HOH497 4.1 44.4 1.0
CG1 A:VAL370 4.1 20.7 1.0
C A:GLU369 4.2 21.1 1.0
C A:SER368 4.3 21.4 1.0
CB A:VAL370 4.4 18.9 1.0
CA A:SER368 4.4 21.0 1.0
OG A:SER368 4.4 18.5 1.0
CA A:VAL370 4.4 18.9 1.0
CD2 A:LEU315 4.4 19.3 1.0
CG A:GLU369 4.5 26.1 1.0
CD1 A:LEU315 4.8 20.2 1.0

Reference:

R.Wu, S.Clancy, A.Joachimiak. The Crystal Structure of Mannitol-1-Phosphate Dehydrogenase From Shigella Flexneri To Be Published.
Page generated: Sun Aug 17 15:17:48 2025

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