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Sodium in PDB 4e6p: Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021

Enzymatic activity of Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021

All present enzymatic activity of Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021:
1.1.1.14;

Protein crystallography data

The structure of Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021, PDB code: 4e6p was solved by P.R.Kumar, S.C.Almo, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.30 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.190, 90.407, 87.228, 90.00, 118.08, 90.00
R / Rfree (%) 16.1 / 20.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021 (pdb code 4e6p). 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 A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021, PDB code: 4e6p:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4e6p

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Sodium binding site 1 out of 4 in the Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021


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 A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:33.5
occ:1.00
 O A:GLY51 2.3 29.2 1.0
O A:ALA54 2.4 29.1 1.0
O A:ALA47 2.4 31.4 1.0
O A:HOH457 2.5 45.8 1.0
O A:HOH468 2.5 45.5 1.0
O A:HOH444 2.5 39.3 1.0
C A:GLY51 3.2 30.4 1.0
C A:ALA47 3.2 35.8 1.0
C A:ALA54 3.5 30.6 1.0
N A:PRO52 3.9 31.5 1.0
CA A:PRO52 3.9 39.0 1.0
N A:ALA48 3.9 34.4 1.0
CA A:ALA48 4.0 38.3 1.0
CB A:ALA47 4.0 34.7 1.0
CA A:ALA47 4.1 39.1 1.0
CA A:GLY51 4.1 35.7 1.0
N A:ALA54 4.1 32.6 1.0
N A:GLY51 4.1 31.7 1.0
CA A:ALA54 4.2 30.3 1.0
C A:PRO52 4.2 34.0 1.0
CB A:ALA54 4.3 24.3 1.0
O A:PRO52 4.5 35.1 1.0
N A:TYR55 4.5 29.1 1.0
O A:ALA48 4.6 43.1 1.0
C A:ALA48 4.6 42.2 1.0
O A:HOH496 4.7 35.2 1.0
CA A:TYR55 4.8 33.1 1.0
N A:ALA53 4.8 31.3 1.0
O A:HOH483 4.8 37.6 1.0

Sodium binding site 2 out of 4 in 4e6p

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Sodium binding site 2 out of 4 in the Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021


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 A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:30.7
occ:1.00
 O B:GLY51 2.3 23.2 1.0
O B:HOH479 2.4 34.0 1.0
O B:ALA54 2.4 21.9 1.0
O B:HOH421 2.4 28.0 1.0
O B:ALA47 2.4 27.3 1.0
O B:HOH495 2.5 39.1 1.0
C B:ALA47 3.2 26.9 1.0
C B:GLY51 3.2 28.7 1.0
C B:ALA54 3.5 21.3 1.0
N B:ALA48 3.9 25.4 1.0
CB B:ALA47 3.9 21.0 1.0
CA B:PRO52 3.9 28.1 1.0
N B:PRO52 4.0 26.4 1.0
CA B:ALA47 4.0 25.4 1.0
CA B:ALA48 4.0 29.0 1.0
N B:ALA54 4.1 23.4 1.0
CA B:GLY51 4.1 30.3 1.0
CA B:ALA54 4.1 25.6 1.0
N B:GLY51 4.1 26.9 1.0
CB B:ALA54 4.2 30.7 1.0
C B:PRO52 4.2 24.8 1.0
O B:PRO52 4.4 25.3 1.0
N B:TYR55 4.5 19.4 1.0
C B:ALA48 4.7 31.4 1.0
O B:HOH435 4.7 27.2 1.0
CA B:TYR55 4.8 23.1 1.0
O B:ALA48 4.9 28.6 1.0
N B:ALA53 4.9 20.6 1.0

Sodium binding site 3 out of 4 in 4e6p

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Sodium binding site 3 out of 4 in the Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021


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 A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:31.9
occ:1.00
 O C:GLY51 2.3 28.4 1.0
O C:HOH512 2.3 24.2 1.0
O C:HOH492 2.4 40.3 1.0
O C:ALA47 2.4 35.1 1.0
O C:ALA54 2.4 26.0 1.0
O C:HOH497 2.4 40.7 1.0
C C:GLY51 3.1 31.1 1.0
C C:ALA47 3.2 35.0 1.0
C C:ALA54 3.5 25.6 1.0
N C:PRO52 3.9 29.6 1.0
N C:ALA48 3.9 34.9 1.0
CA C:PRO52 3.9 28.8 1.0
CA C:ALA47 4.0 29.0 1.0
CA C:ALA48 4.0 31.6 1.0
CB C:ALA47 4.0 25.0 1.0
N C:ALA54 4.1 22.9 1.0
CA C:GLY51 4.1 35.0 1.0
N C:GLY51 4.1 34.2 1.0
CA C:ALA54 4.2 24.3 1.0
C C:PRO52 4.3 28.3 1.0
CB C:ALA54 4.4 24.9 1.0
O C:PRO52 4.6 29.6 1.0
N C:TYR55 4.6 25.1 1.0
C C:ALA48 4.6 34.4 1.0
O C:ALA48 4.8 36.8 1.0
N C:ALA53 4.8 27.0 1.0
CA C:TYR55 4.8 27.6 1.0
O C:HOH468 4.9 36.5 1.0

Sodium binding site 4 out of 4 in 4e6p

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Sodium binding site 4 out of 4 in the Crystal Structure of A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021


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 A Probable Sorbitol Dehydrogenase (Target Psi- 012078) From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:19.3
occ:1.00
 O D:ALA54 2.3 17.8 1.0
O D:GLY51 2.3 22.4 1.0
O2 D:EDO304 2.3 29.6 1.0
O D:HOH415 2.5 33.2 1.0
O D:ALA47 2.5 23.4 1.0
O1 D:EDO304 2.5 29.2 1.0
C1 D:EDO304 3.1 33.0 1.0
C D:GLY51 3.1 21.5 1.0
C2 D:EDO304 3.2 34.0 1.0
C D:ALA47 3.2 21.2 1.0
C D:ALA54 3.4 18.8 1.0
N D:PRO52 3.8 18.5 1.0
CA D:PRO52 3.9 25.2 1.0
CB D:ALA47 4.0 25.5 1.0
N D:ALA54 4.0 22.5 1.0
N D:ALA48 4.0 19.3 1.0
C D:PRO52 4.0 23.0 1.0
CA D:ALA47 4.0 24.9 1.0
O D:PRO52 4.1 21.1 1.0
CA D:ALA54 4.1 19.3 1.0
CA D:GLY51 4.1 20.4 1.0
N D:GLY51 4.1 19.2 1.0
CA D:ALA48 4.1 20.8 1.0
CB D:ALA54 4.3 19.2 1.0
N D:TYR55 4.5 21.1 1.0
N D:ALA53 4.7 25.0 1.0
CA D:TYR55 4.7 23.0 1.0
O D:HOH444 4.8 24.8 1.0
C D:ALA48 4.8 27.9 1.0

Reference:

P.R.Kumar, N.Banu, R.Bhosle, J.Bonanno, S.Chamala, S.Chowdhury, A.Gizzi, S.Glen, J.Hammonds, B.Hillerich, J.D.Love, B.Matikainen, R.Seidel, R.Toro, W.Zencheck, S.C.Almo. Crystal Structure of A Probable Sorbitol Dehydrogenase From Sinorhizobium Meliloti 1021 To Be Published.
Page generated: Mon Oct 7 15:06:22 2024

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