Atomistry » Sodium » PDB 3h0n-3hwd » 3h2z
Atomistry »
  Sodium »
    PDB 3h0n-3hwd »
      3h2z »

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: Mon Oct 7 10:21:43 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