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Sodium in PDB 7ug3: Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae

Enzymatic activity of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae

All present enzymatic activity of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae:
2.6.1.62;

Protein crystallography data

The structure of Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae, PDB code: 7ug3 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.42 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.07, 90.83, 103.86, 90, 93.87, 90
R / Rfree (%) 22.5 / 26

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae (pdb code 7ug3). 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 Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae, PDB code: 7ug3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7ug3

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Sodium binding site 1 out of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae


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 Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:35.7
occ:1.00
 O A:VAL96 2.3 35.9 1.0
OG1 A:THR99 2.3 34.5 1.0
O A:LEU103 2.4 36.1 1.0
O A:PRO100 2.4 39.9 1.0
O A:HOH762 2.6 37.2 1.0
O A:THR99 2.7 36.5 1.0
C A:THR99 3.1 35.8 1.0
C A:VAL96 3.4 35.0 1.0
C A:PRO100 3.4 41.1 1.0
CB A:THR99 3.4 34.5 1.0
C A:LEU103 3.5 36.2 1.0
CA A:THR99 3.7 35.1 1.0
CA A:VAL96 3.7 34.6 1.0
N A:PRO100 3.9 40.1 1.0
N A:THR99 3.9 35.2 1.0
CB A:LEU103 4.1 36.1 1.0
CG1 A:VAL96 4.1 35.6 1.0
CA A:LEU103 4.1 36.6 1.0
N A:ALA101 4.2 43.0 1.0
N A:LEU103 4.2 36.6 1.0
CA A:PRO100 4.2 42.1 1.0
CA A:ALA101 4.2 44.5 1.0
O A:LEU95 4.3 33.2 1.0
C A:ALA101 4.4 44.4 1.0
O A:ALA101 4.5 44.3 1.0
CB A:VAL96 4.6 34.9 1.0
N A:ALA97 4.6 32.5 1.0
N A:GLU104 4.6 37.9 1.0
CG2 A:THR99 4.7 33.2 1.0
CA A:GLU104 4.8 37.8 1.0
N A:VAL96 4.9 33.7 1.0
C A:ALA97 4.9 34.6 1.0

Sodium binding site 2 out of 4 in 7ug3

Go back to Sodium Binding Sites List in 7ug3
Sodium binding site 2 out of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae


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 Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:35.7
occ:1.00
 O B:LEU103 2.3 37.4 1.0
O B:VAL96 2.4 33.5 1.0
OG1 B:THR99 2.5 33.0 1.0
O B:HOH805 2.5 36.1 1.0
O B:PRO100 2.5 42.8 1.0
O B:THR99 2.7 34.4 1.0
C B:THR99 3.2 35.0 1.0
C B:PRO100 3.4 43.5 1.0
C B:VAL96 3.4 32.9 1.0
C B:LEU103 3.4 37.6 1.0
CB B:THR99 3.4 34.0 1.0
CA B:THR99 3.7 34.6 1.0
CA B:VAL96 3.7 32.4 1.0
N B:PRO100 3.9 42.6 1.0
N B:THR99 4.0 33.7 1.0
CG1 B:VAL96 4.1 33.5 1.0
CB B:LEU103 4.1 37.1 1.0
CA B:LEU103 4.1 37.8 1.0
N B:LEU103 4.1 38.0 1.0
N B:ALA101 4.2 37.6 1.0
CA B:PRO100 4.2 43.5 1.0
CA B:ALA101 4.3 38.4 1.0
O B:ALA101 4.3 37.7 1.0
C B:ALA101 4.4 38.7 1.0
O B:HOH838 4.4 47.8 1.0
O B:LEU95 4.4 30.4 1.0
N B:GLU104 4.5 37.0 1.0
CB B:VAL96 4.5 32.7 1.0
N B:ALA97 4.6 33.4 1.0
CA B:GLU104 4.7 37.0 1.0
CG2 B:THR99 4.8 33.4 1.0
N B:VAL96 4.9 31.8 1.0
C B:ALA97 5.0 35.4 1.0

Sodium binding site 3 out of 4 in 7ug3

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Sodium binding site 3 out of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae


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 Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:35.7
occ:1.00
 O C:LEU103 2.2 40.9 1.0
O C:PRO100 2.3 47.5 1.0
O C:HOH721 2.3 40.2 1.0
O C:VAL96 2.4 41.9 1.0
OG1 C:THR99 2.6 41.4 1.0
O C:THR99 2.7 44.0 1.0
C C:THR99 3.2 42.7 1.0
C C:PRO100 3.2 48.2 1.0
C C:LEU103 3.4 41.2 1.0
C C:VAL96 3.4 41.0 1.0
CB C:THR99 3.6 41.7 1.0
CA C:THR99 3.8 42.1 1.0
CA C:VAL96 3.9 40.5 1.0
N C:PRO100 3.9 47.2 1.0
N C:ALA101 4.0 47.7 1.0
CA C:ALA101 4.0 47.2 1.0
CB C:LEU103 4.0 40.1 1.0
O C:HOH695 4.0 35.7 1.0
CA C:LEU103 4.0 41.3 1.0
O C:ALA101 4.0 47.3 1.0
N C:LEU103 4.1 42.5 1.0
N C:THR99 4.1 42.5 1.0
C C:ALA101 4.1 47.6 1.0
CA C:PRO100 4.1 47.8 1.0
CG1 C:VAL96 4.2 42.1 1.0
O C:LEU95 4.5 41.5 1.0
N C:GLU104 4.5 45.1 1.0
N C:ALA97 4.6 42.1 1.0
CB C:VAL96 4.6 41.3 1.0
CA C:GLU104 4.7 46.0 1.0
N C:SER102 4.9 46.8 1.0
C C:ALA97 4.9 44.2 1.0
CG2 C:THR99 4.9 40.2 1.0
CA C:ALA97 5.0 44.1 1.0

Sodium binding site 4 out of 4 in 7ug3

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Sodium binding site 4 out of 4 in the Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae


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 Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:35.7
occ:1.00
 O D:LEU103 2.2 34.7 1.0
O D:PRO100 2.3 43.7 1.0
OG1 D:THR99 2.3 37.3 1.0
O D:VAL96 2.3 37.2 1.0
O D:HOH721 2.4 37.2 1.0
O D:THR99 2.8 39.6 1.0
C D:THR99 3.2 40.3 1.0
C D:PRO100 3.3 45.9 1.0
C D:LEU103 3.4 35.3 1.0
C D:VAL96 3.4 37.0 1.0
CB D:THR99 3.4 38.8 1.0
CA D:THR99 3.7 39.4 1.0
CA D:VAL96 3.8 36.0 1.0
N D:PRO100 3.9 45.8 1.0
N D:THR99 3.9 38.0 1.0
CA D:LEU103 4.0 36.0 1.0
N D:LEU103 4.1 37.6 1.0
CB D:LEU103 4.1 36.7 1.0
CA D:ALA101 4.1 47.9 1.0
N D:ALA101 4.2 48.7 1.0
CG1 D:VAL96 4.2 36.8 1.0
CA D:PRO100 4.2 46.6 1.0
C D:ALA101 4.3 47.8 1.0
O D:LEU95 4.3 39.2 1.0
O D:ALA101 4.3 47.2 1.0
N D:GLU104 4.4 43.4 1.0
N D:ALA97 4.6 37.7 1.0
CB D:VAL96 4.6 37.0 1.0
CA D:GLU104 4.7 42.2 1.0
CG2 D:THR99 4.7 38.9 1.0
C D:ALA97 4.9 39.6 1.0
N D:VAL96 5.0 34.7 1.0
N D:SER102 5.0 40.6 1.0
CA D:ALA97 5.0 39.3 1.0

Reference:

M.Yang, T.E.Edwards, P.S.Horanyi, D.D.Lorimer. Crystal Structure of Adenosylmethionie-8-Amino-7-Oxononanoate Aminotransferase From Klebsiella Pneumoniae To Be Published.
Page generated: Mon Aug 18 12:08:07 2025

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