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Sodium in PDB 5tej: Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh

Enzymatic activity of Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh

All present enzymatic activity of Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh:
1.17.1.8;

Protein crystallography data

The structure of Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh, PDB code: 5tej was solved by N.Mank, K.Arnette, V.Klapper, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.059, 91.039, 125.922, 90.00, 120.07, 90.00
R / Rfree (%) 18.2 / 21.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh (pdb code 5tej). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh, PDB code: 5tej:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5tej

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Sodium binding site 1 out of 4 in the Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:35.6
occ:1.00
 O B:ALA27 2.1 35.7 1.0
O B:ASN24 2.3 31.6 1.0
O B:HIS22 2.5 36.4 1.0
O B:ALA21 2.7 31.4 1.0
C B:HIS22 3.2 36.3 1.0
C B:ALA27 3.3 36.1 1.0
C B:ASN24 3.4 32.1 1.0
CA B:HIS22 3.7 35.6 1.0
C B:ALA21 3.8 31.3 1.0
N B:ASN24 4.0 32.9 1.0
N B:ALA27 4.2 35.7 1.0
N B:HIS23 4.2 37.0 1.0
CA B:ALA27 4.2 34.9 1.0
N B:HIS22 4.2 32.8 1.0
N B:LYS28 4.2 37.8 1.0
N B:PRO25 4.3 33.5 1.0
CA B:PRO25 4.3 34.6 1.0
CA B:ASN24 4.3 31.6 1.0
C B:HIS23 4.4 35.3 1.0
CA B:LYS28 4.4 40.0 1.0
CA B:HIS23 4.6 38.0 1.0
CB B:ALA27 4.7 34.4 1.0
C B:PRO25 4.7 35.3 1.0
CE B:MET1 4.8 51.1 1.0
CB B:ASN24 4.9 30.0 1.0
O B:HIS23 5.0 35.3 1.0

Sodium binding site 2 out of 4 in 5tej

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Sodium binding site 2 out of 4 in the Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:32.3
occ:1.00
 O C:ASN24 2.2 24.5 1.0
O C:ALA27 2.2 30.3 1.0
O C:ALA21 2.4 29.2 1.0
O C:HIS22 2.4 32.3 1.0
C C:HIS22 3.0 30.3 1.0
C C:ASN24 3.3 25.7 1.0
C C:ALA27 3.3 30.2 1.0
CA C:HIS22 3.5 29.8 1.0
C C:ALA21 3.5 27.7 1.0
N C:ASN24 3.7 25.9 1.0
N C:HIS22 3.9 27.9 1.0
N C:HIS23 3.9 30.1 1.0
CA C:ASN24 4.1 25.1 1.0
N C:ALA27 4.1 29.1 1.0
CA C:ALA27 4.1 29.0 1.0
C C:HIS23 4.2 28.8 1.0
N C:PRO25 4.2 27.2 1.0
CA C:PRO25 4.3 28.7 1.0
N C:LYS28 4.3 32.0 1.0
CB C:ALA27 4.4 27.5 1.0
CA C:HIS23 4.5 30.7 1.0
CA C:LYS28 4.6 33.8 1.0
CB C:ASN24 4.7 23.6 1.0
C C:PRO25 4.7 29.3 1.0
CA C:ALA21 4.8 26.9 1.0
O C:HIS23 4.8 30.5 1.0
CB C:HIS22 4.9 30.2 1.0

Sodium binding site 3 out of 4 in 5tej

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Sodium binding site 3 out of 4 in the Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:36.8
occ:1.00
 O D:HOH474 2.2 41.4 1.0
O D:ALA27 2.2 35.7 1.0
O D:ASN24 2.4 34.3 1.0
O D:HIS22 2.5 42.8 1.0
O D:HOH472 2.6 36.3 1.0
O D:ALA21 2.8 31.6 1.0
C D:HIS22 3.2 41.0 1.0
C D:ALA27 3.4 34.7 1.0
C D:ASN24 3.5 36.2 1.0
CA D:HIS22 3.7 38.9 1.0
C D:ALA21 3.9 32.8 1.0
N D:ASN24 4.1 37.6 1.0
N D:HIS22 4.2 35.2 1.0
N D:HIS23 4.2 43.0 1.0
CA D:LYS28 4.3 38.4 1.0
CA D:PRO25 4.3 37.7 1.0
N D:ALA27 4.3 34.6 1.0
N D:PRO25 4.3 37.1 1.0
CA D:ALA27 4.3 33.5 1.0
N D:LYS28 4.3 35.7 1.0
CA D:ASN24 4.4 36.2 1.0
C D:HIS23 4.4 42.3 1.0
CE D:MET1 4.6 53.8 1.0
C D:PRO25 4.6 37.3 1.0
CA D:HIS23 4.7 45.6 1.0
CB D:LYS28 4.8 42.6 1.0
CB D:ALA27 4.8 32.0 1.0

Sodium binding site 4 out of 4 in 5tej

Go back to Sodium Binding Sites List in 5tej
Sodium binding site 4 out of 4 in the Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:39.9
occ:1.00
 O D:HOH457 2.4 39.1 1.0
OD1 D:ASN180 2.5 30.8 1.0
O D:HOH444 2.5 31.3 1.0
O D:HOH449 2.6 33.0 1.0
O D:GLY179 2.7 33.4 1.0
O D:HOH403 3.2 33.6 1.0
C D:GLY179 3.6 32.5 1.0
CG D:ASN180 3.7 29.8 1.0
CA D:ASN180 4.1 30.2 1.0
O D:HOH426 4.2 36.8 1.0
N D:ASN180 4.2 31.3 1.0
CB D:ASN180 4.4 29.4 1.0
ND2 D:ASN180 4.7 29.3 1.0
O D:MET178 4.7 29.8 1.0
CA D:GLY179 4.7 32.3 1.0

Reference:

N.Mank, K.Arnette, V.Klapper, M.Chruszcz. Structure of 4-Hydroxy-Tetrahydrodipicolinate Reductase From Vibrio Vulnificus with 2,5 Furan Dicarboxylic and Nadh To Be Published.
Page generated: Tue Dec 15 11:36:43 2020

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