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Sodium in PDB 7krg: Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na

Enzymatic activity of Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na

All present enzymatic activity of Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na:
1.1.1.138;

Protein crystallography data

The structure of Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na, PDB code: 7krg was solved by S.G.Lee, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.40 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.867, 119.322, 111.211, 90, 94.88, 90
R / Rfree (%) 15.4 / 18.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na (pdb code 7krg). 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 Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na, PDB code: 7krg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7krg

Go back to Sodium Binding Sites List in 7krg
Sodium binding site 1 out of 4 in the Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na


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 Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:26.2
occ:1.00
 O A:ARG267 2.2 32.8 1.0
OXT C:ARG267 2.3 34.3 1.0
O A:HOH418 2.4 33.5 1.0
O C:HOH422 2.4 25.0 1.0
O C:HOH407 2.5 36.6 1.0
O A:HOH416 2.5 27.0 1.0
C A:ARG267 3.2 31.2 1.0
C C:ARG267 3.3 34.0 1.0
OXT A:ARG267 3.5 33.8 1.0
O C:ARG267 3.6 28.7 1.0
CG2 C:ILE165 3.8 22.8 1.0
CG2 A:ILE165 3.9 25.7 1.0
O A:THR265 4.0 24.7 1.0
O C:THR265 4.1 23.9 1.0
C A:THR265 4.6 23.0 1.0
CA A:ARG267 4.6 25.8 1.0
C C:THR265 4.6 25.8 1.0
CA C:ARG267 4.6 31.7 1.0
CA A:THR265 4.7 23.2 1.0
CA C:THR265 4.7 20.3 1.0
N A:ARG267 4.8 24.0 1.0
O A:TYR264 4.8 22.6 1.0
N C:ARG267 4.8 26.8 1.0
CB C:ILE165 4.9 20.9 1.0
O C:TYR264 4.9 21.3 1.0
CB A:ILE165 4.9 25.1 1.0

Sodium binding site 2 out of 4 in 7krg

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Sodium binding site 2 out of 4 in the Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na


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 Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:27.3
occ:1.00
 O B:ARG267 2.2 31.1 1.0
O D:ARG267 2.2 30.7 1.0
O D:HOH405 2.4 40.5 1.0
O D:HOH423 2.4 24.3 1.0
O B:HOH431 2.5 37.3 1.0
O B:HOH425 2.6 25.2 1.0
C B:ARG267 3.2 32.6 1.0
C D:ARG267 3.3 28.6 1.0
OXT B:ARG267 3.6 30.3 1.0
OXT D:ARG267 3.7 27.3 1.0
CG2 D:ILE165 3.9 25.5 1.0
CG2 B:ILE165 3.9 29.3 1.0
O B:THR265 4.2 23.9 1.0
O D:THR265 4.2 25.8 1.0
CA B:ARG267 4.6 29.7 1.0
CA D:ARG267 4.6 27.1 1.0
C B:THR265 4.7 26.1 1.0
C D:THR265 4.7 25.6 1.0
CA B:THR265 4.7 23.1 1.0
N B:ARG267 4.8 25.9 1.0
CA D:THR265 4.8 23.0 1.0
O B:TYR264 4.8 24.0 1.0
N D:ARG267 4.8 21.3 1.0
O D:HOH553 4.9 52.6 1.0
O B:HOH607 4.9 44.6 1.0
O D:TYR264 5.0 22.9 1.0
CB B:ILE165 5.0 24.3 1.0
CB D:ILE165 5.0 25.7 1.0

Sodium binding site 3 out of 4 in 7krg

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Sodium binding site 3 out of 4 in the Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na


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 Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:35.5
occ:1.00
 O E:ARG267 2.3 36.1 1.0
O E:HOH430 2.4 29.2 1.0
O E:HOH413 2.5 45.5 1.0
C E:ARG267 3.3 34.6 1.0
O E:HOH511 3.5 51.0 1.0
OXT E:ARG267 3.6 34.3 1.0
CG2 E:ILE165 3.8 31.9 1.0
O E:THR265 4.0 27.6 1.0
CA E:ARG267 4.6 29.9 1.0
C E:THR265 4.6 24.8 1.0
CA E:THR265 4.7 25.1 1.0
N E:ARG267 4.8 29.6 1.0
O E:TYR264 4.8 22.8 1.0
O E:HOH520 4.9 49.4 1.0
CB E:ILE165 5.0 29.6 1.0

Sodium binding site 4 out of 4 in 7krg

Go back to Sodium Binding Sites List in 7krg
Sodium binding site 4 out of 4 in the Crystal Structure of Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na


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 Mannitol Dehydrogenase (Chmdh) From Cladosporium Herbarum in Complex with Nadp+ and Na within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na301

b:31.4
occ:1.00
 O G:ARG267 2.3 34.1 1.0
O G:HOH408 2.7 28.8 1.0
C G:ARG267 3.4 33.8 1.0
CG2 G:ILE165 3.7 31.2 1.0
OXT G:ARG267 3.7 31.9 1.0
O G:THR265 3.9 26.3 1.0
C G:THR265 4.5 27.0 1.0
CA G:THR265 4.6 24.6 1.0
O G:HOH578 4.6 50.1 1.0
CA G:ARG267 4.7 30.8 1.0
N G:ARG267 4.8 30.1 1.0
CB G:ILE165 4.9 28.2 1.0
O G:TYR264 5.0 20.5 1.0

Reference:

S.G.Lee, J.M.Jez. Assessing the Structural and Clinical Biology of Singlet Putative Allergens in Non-Allergenic Protein Families To Be Published.
Page generated: Tue Oct 8 17:25:58 2024

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