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Sodium in PDB 5yr6: Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470

Enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470

All present enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470:
3.4.11.18;

Protein crystallography data

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470, PDB code: 5yr6 was solved by V.Pillalamarri, T.Arya, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.61 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.439, 77.325, 47.759, 90.00, 91.70, 90.00
R / Rfree (%) 18 / 21.1

Other elements in 5yr6:

The structure of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470 also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470 (pdb code 5yr6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470, PDB code: 5yr6:

Sodium binding site 1 out of 1 in 5yr6

Go back to Sodium Binding Sites List in 5yr6
Sodium binding site 1 out of 1 in the Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Methionine Aminopeptidase Type 1B (F309L Mutant) in Complex with TNP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.5
occ:1.00
 O A:VAL209 2.2 21.3 1.0
O A:HOH441 2.3 24.3 1.0
O A:SER363 2.3 22.9 1.0
O A:ASN207 2.4 23.8 1.0
C A:ASN207 3.3 22.3 1.0
O A:HOH435 3.3 23.7 1.0
C A:SER363 3.3 22.9 1.0
C A:VAL209 3.3 21.0 1.0
N A:ASN207 3.6 23.7 1.0
CA A:ASN207 3.9 24.6 1.0
C A:VAL206 3.9 20.3 1.0
N A:SER363 3.9 23.9 1.0
N A:VAL209 3.9 21.6 1.0
CA A:SER363 4.0 22.8 1.0
O A:SER205 4.0 20.9 1.0
O A:VAL206 4.1 23.4 1.0
O A:HOH422 4.1 20.6 1.0
CB A:SER363 4.1 23.9 1.0
CA A:VAL209 4.2 20.9 1.0
N A:GLU208 4.3 24.2 1.0
C A:GLU208 4.3 23.6 1.0
C A:SER205 4.4 20.5 1.0
N A:ALA364 4.4 22.4 1.0
N A:ILE210 4.4 21.2 1.0
N A:VAL206 4.6 21.2 1.0
CB A:SER205 4.6 19.6 1.0
CA A:VAL206 4.7 21.5 1.0
CA A:ALA364 4.7 23.0 1.0
CD1 A:ILE225 4.7 29.0 1.0
CA A:ILE210 4.7 21.6 1.0
CA A:GLU208 4.7 24.2 1.0
CB A:VAL209 4.7 19.8 1.0
CG1 A:ILE225 4.7 24.6 1.0
OG A:SER363 4.9 23.8 1.0
O A:GLU208 4.9 21.8 1.0

Reference:

V.Pillalamarri, T.Arya, N.Haque, S.C.Bala, A.K.Marapaka, A.Addlagatta. Discovery of Natural Product Ovalicin Sensitive Type 1 Methionine Aminopeptidases: Molecular and Structural Basis. Biochem. J. V. 476 991 2019.
ISSN: ESSN 1470-8728
PubMed: 30837307
DOI: 10.1042/BCJ20180874
Page generated: Tue Oct 8 01:25:10 2024

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