Sodium in PDB 6xfr: Metallo-Beta-Lactamase From Pontibacter Korlensis

Protein crystallography data

The structure of Metallo-Beta-Lactamase From Pontibacter Korlensis, PDB code: 6xfr was solved by G.Schenk, M.A.Schembri, S.Prombhul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.25 / 2.61
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.941, 97.941, 103.237, 90, 90, 90
R / Rfree (%) 17.6 / 23.6

Other elements in 6xfr:

The structure of Metallo-Beta-Lactamase From Pontibacter Korlensis also contains other interesting chemical elements:

Zinc (Zn) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Metallo-Beta-Lactamase From Pontibacter Korlensis (pdb code 6xfr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Metallo-Beta-Lactamase From Pontibacter Korlensis, PDB code: 6xfr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6xfr

Go back to Sodium Binding Sites List in 6xfr
Sodium binding site 1 out of 2 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:55.6
occ:1.00
CZ2 A:TRP205 2.7 65.3 1.0
NE1 A:TRP205 3.0 32.1 1.0
O B:TRP205 3.1 29.4 1.0
CE2 A:TRP205 3.1 48.5 1.0
CB B:PRO204 3.5 34.9 1.0
N B:TRP205 3.7 27.7 1.0
CG2 A:ILE13 3.8 32.1 1.0
CH2 A:TRP205 3.9 66.9 1.0
C B:TRP205 4.0 33.5 1.0
CA B:PRO204 4.1 31.7 1.0
C B:PRO204 4.2 28.5 1.0
CD1 B:TRP205 4.2 28.6 1.0
NE1 B:TRP205 4.2 31.2 1.0
CG B:TRP205 4.3 34.4 1.0
CD1 A:TRP205 4.4 27.9 1.0
CA B:TRP205 4.4 25.4 1.0
CE2 B:TRP205 4.4 40.4 1.0
CD2 B:TRP205 4.5 46.3 1.0
CD2 A:TRP205 4.5 48.0 1.0
CG B:PRO204 4.8 42.0 1.0
O A:LYS12 4.9 25.1 1.0
CB B:TRP205 5.0 24.5 1.0

Sodium binding site 2 out of 2 in 6xfr

Go back to Sodium Binding Sites List in 6xfr
Sodium binding site 2 out of 2 in the Metallo-Beta-Lactamase From Pontibacter Korlensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Metallo-Beta-Lactamase From Pontibacter Korlensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na313

b:135.0
occ:1.00
CB B:LEU102 2.4 58.5 1.0
CG B:LEU102 3.1 70.9 1.0
CD2 B:LEU102 3.2 73.7 1.0
CA B:LEU102 3.5 54.6 1.0
CB B:ASP144 3.5 38.8 1.0
CA B:ASP144 3.7 41.4 1.0
N B:LEU102 3.8 47.5 1.0
OG B:SER100 3.8 38.7 1.0
C B:LEU102 4.0 48.8 1.0
N B:THR103 4.1 33.6 1.0
O B:ALA143 4.4 39.8 1.0
O B:ASP144 4.5 30.6 1.0
CD1 B:LEU102 4.6 81.6 1.0
CE1 B:PHE136 4.6 38.4 1.0
C B:ASP144 4.6 39.2 1.0
CB B:SER100 4.6 33.1 1.0
N B:ASP144 4.7 37.3 1.0
O B:LEU102 4.8 45.2 1.0
C B:ALA143 4.9 39.6 1.0
CZ B:PHE136 4.9 42.8 1.0
CD1 B:PHE136 5.0 33.7 1.0
CG B:ASP144 5.0 42.5 1.0

Reference:

G.Schenk, M.A.Schembri, S.Prombhul. Metallo-Beta-Lactamase From Pontibacter Korlensis To Be Published.
Page generated: Mon Jul 12 15:50:18 2021

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