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Sodium in PDB 7nea: Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant).

Enzymatic activity of Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant).

All present enzymatic activity of Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant).:
2.6.1.42;

Protein crystallography data

The structure of Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant)., PDB code: 7nea was solved by K.M.Boyko, T.Petrova, A.Y.Nikolaeva, Y.S.Zeifman, T.V.Rakitina, D.A.Suplatov, V.O.Popov, E.Y.Bezsudnova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.13 / 2.00
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 146.497, 146.497, 143.776, 90, 90, 120
R / Rfree (%) 16.1 / 20.1

Other elements in 7nea:

The structure of Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant). also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant). (pdb code 7nea). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant)., PDB code: 7nea:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7nea

Go back to Sodium Binding Sites List in 7nea
Sodium binding site 1 out of 3 in the Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant).


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 Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:33.8
occ:1.00
 O A:HIS15 2.3 27.2 1.0
O A:HOH721 2.3 34.6 1.0
O A:HOH564 2.3 41.5 1.0
O A:HOH717 2.3 41.8 1.0
O A:HOH645 2.4 29.6 1.0
C A:HIS15 3.2 26.9 1.0
CA A:HIS15 4.0 25.9 1.0
N A:ARG16 4.2 25.6 1.0
O A:HOH522 4.2 33.1 1.0
CB A:HIS15 4.2 28.5 1.0
NE1 A:TRP12 4.3 23.5 1.0
O A:HOH643 4.4 29.6 1.0
CA A:ARG16 4.4 29.0 1.0
OE1 A:GLU82 4.6 33.0 1.0
O A:HOH740 5.0 51.1 1.0

Sodium binding site 2 out of 3 in 7nea

Go back to Sodium Binding Sites List in 7nea
Sodium binding site 2 out of 3 in the Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant).


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 Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:38.6
occ:1.00
 O A:HOH642 2.3 44.0 1.0
O A:HOH716 2.3 39.1 1.0
O A:HOH725 2.3 37.6 1.0
O A:HOH589 2.4 40.4 1.0
O A:ARG303 2.4 32.1 1.0
O A:LEU306 2.5 31.6 1.0
C A:ARG303 3.4 31.8 1.0
C A:LEU306 3.6 28.4 1.0
CA A:ASN304 3.9 34.5 1.0
N A:LEU306 4.0 27.7 1.0
N A:ASN304 4.1 31.8 1.0
O A:HOH668 4.2 42.6 1.0
C A:ASN304 4.2 32.6 1.0
CA A:LEU306 4.2 27.4 1.0
O A:ASN304 4.3 29.6 1.0
CB A:LEU306 4.3 29.2 1.0
O A:HOH741 4.4 50.3 1.0
CD A:PRO308 4.4 30.4 1.0
CA A:ARG303 4.5 32.7 1.0
OD1 A:ASN304 4.6 49.7 1.0
CB A:ARG303 4.7 36.3 1.0
N A:THR307 4.7 26.8 1.0
O A:HOH749 4.7 49.5 1.0
N A:TRP305 4.8 30.4 1.0
CA A:THR307 5.0 26.8 1.0

Sodium binding site 3 out of 3 in 7nea

Go back to Sodium Binding Sites List in 7nea
Sodium binding site 3 out of 3 in the Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant).


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 Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:36.2
occ:1.00
 O A:HOH715 2.3 40.4 1.0
O A:HOH758 2.3 40.4 1.0
O A:HOH639 2.3 33.8 1.0
O A:ARG272 2.3 34.9 1.0
O A:HOH695 2.4 39.5 1.0
O A:HOH656 3.5 37.8 1.0
C A:ARG272 3.6 32.3 1.0
N A:HIS273 4.3 29.0 1.0
CA A:HIS273 4.3 29.3 1.0
CB A:ARG272 4.5 33.1 1.0
ND1 A:HIS273 4.6 29.7 1.0
CA A:ARG272 4.6 30.9 1.0
O A:HOH752 4.7 45.9 1.0
O A:HOH728 4.7 25.6 1.0

Reference:

E.Y.Bezsudnova, K.M.Boyko, T.Petrova, A.Y.Nikolaeva, Y.S.Zeifman, T.V.Rakitina, D.A.Suplatov, V.O.Popov. Crystal Structure of Branched-Chain Amino Acid Aminotransferase From Thermobaculum Terrenum (M3 Mutant). To Be Published.
Page generated: Tue Oct 8 18:09:04 2024

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