Atomistry » Sodium » PDB 6s08-6sez » 6scd
Atomistry »
  Sodium »
    PDB 6s08-6sez »
      6scd »

Sodium in PDB 6scd: Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri

Protein crystallography data

The structure of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri, PDB code: 6scd was solved by A.Bollinger, S.Thies, S.Kobus, A.Hoeppner, S.H.J.Smits, K.-E.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.34 / 1.35
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.526, 98.268, 121.233, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 15.2

Other elements in 6scd:

The structure of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri (pdb code 6scd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri, PDB code: 6scd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6scd

Go back to Sodium Binding Sites List in 6scd
Sodium binding site 1 out of 3 in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:15.6
occ:1.00
O A:ILE295 2.2 14.4 1.0
O A:THR290 2.4 16.2 1.0
O A:HOH714 2.4 22.6 1.0
O A:HOH693 2.4 23.0 1.0
O A:ASP292 2.5 13.2 1.0
O A:HOH607 2.5 17.8 1.0
C A:ILE295 3.4 12.4 1.0
C A:ASP292 3.5 12.7 1.0
C A:THR290 3.5 15.0 1.0
C A:SER291 3.9 14.7 1.0
O A:SER291 4.0 15.7 1.0
N A:ASP292 4.1 13.9 1.0
N A:ILE295 4.1 12.9 1.0
O A:HOH779 4.2 40.6 1.0
CA A:SER293 4.2 13.3 1.0
CA A:ILE295 4.2 12.6 1.0
N A:SER293 4.2 13.2 1.0
CA A:SER291 4.3 14.8 0.7
CA A:SER291 4.3 15.6 0.3
C A:SER293 4.3 13.1 1.0
N A:SER296 4.4 11.9 1.0
N A:SER291 4.4 14.1 1.0
CA A:ASP292 4.4 13.6 1.0
O A:SER293 4.5 15.2 1.0
CA A:SER296 4.5 13.6 1.0
CA A:THR290 4.5 14.7 1.0
O A:HOH763 4.5 22.1 1.0
CB A:ILE295 4.6 13.2 1.0
CG2 A:THR290 4.8 19.6 1.0
N A:GLN294 5.0 12.7 1.0

Sodium binding site 2 out of 3 in 6scd

Go back to Sodium Binding Sites List in 6scd
Sodium binding site 2 out of 3 in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:17.2
occ:1.00
OG B:SER171 2.9 17.8 1.0
N B:PHE98 3.1 26.1 1.0
N B:MET172 3.2 14.3 1.0
O B:HOH606 3.2 23.8 1.0
CG B:MET172 3.3 17.0 0.7
CG B:MET172 3.3 14.8 0.3
CB B:SER171 3.4 15.1 1.0
SD B:MET172 3.5 16.3 0.3
CB B:PHE98 3.5 36.4 1.0
CB B:MET172 3.5 17.6 0.7
CB B:MET172 3.6 15.1 0.3
CA B:GLY97 3.8 21.2 1.0
CA B:PHE98 3.9 30.7 1.0
SD B:MET172 3.9 24.9 0.7
CA B:MET172 3.9 15.6 0.7
CE B:MET172 3.9 20.9 0.7
CA B:MET172 4.0 15.0 0.3
C B:GLY97 4.0 27.9 1.0
C B:SER171 4.1 13.5 1.0
O B:HOH519 4.2 39.6 1.0
CA B:SER171 4.3 13.6 1.0
NE2 B:HIS249 4.8 16.4 1.0
O B:TRP170 5.0 15.1 1.0
C B:PHE98 5.0 25.9 1.0

Sodium binding site 3 out of 3 in 6scd

Go back to Sodium Binding Sites List in 6scd
Sodium binding site 3 out of 3 in the Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Polyester Hydrolase Pe-H Y250S Mutant of Pseudomonas Aestusnigri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:20.1
occ:1.00
O B:ALA220 2.8 13.6 1.0
O B:PRO194 2.9 13.9 1.0
O B:HOH607 3.0 13.6 1.0
N B:ALA226 3.1 13.3 1.0
CB B:ALA226 3.3 13.7 1.0
CB B:HIS225 3.4 14.4 1.0
CB B:ALA220 3.6 14.4 1.0
C B:ALA193 3.7 13.9 1.0
C B:ALA220 3.7 12.4 1.0
N B:PRO194 3.7 13.4 1.0
CA B:ALA226 3.8 13.6 1.0
CD B:PRO194 4.0 13.2 1.0
C B:PRO194 4.0 13.2 1.0
CA B:ALA193 4.0 13.5 1.0
O B:ALA193 4.0 13.8 1.0
C B:HIS225 4.1 13.3 1.0
O B:PRO221 4.2 13.7 1.0
CG B:PRO194 4.3 15.0 1.0
CA B:ALA220 4.3 12.9 1.0
CA B:HIS225 4.3 13.8 1.0
C B:PRO221 4.3 12.2 1.0
CA B:VAL222 4.3 12.4 1.0
N B:VAL222 4.4 12.6 1.0
CA B:PRO194 4.4 12.9 1.0
OD2 B:ASP217 4.4 12.6 1.0
CG B:HIS225 4.4 14.9 1.0
CB B:ALA193 4.7 13.7 1.0
N B:PRO221 4.8 13.1 1.0
CG2 B:VAL222 4.8 14.6 1.0
N B:HIS225 5.0 13.9 1.0
CD2 B:HIS225 5.0 14.1 1.0

Reference:

A.Bollinger, S.Thies, S.Kobus, A.Hoeppner, S.H.J.Smits, C.Coscolin, M.Ferrer, K.-E.Jaeger. A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas Aestusnigri - Structural and Functional Insights Front Microbiol 2020.
ISSN: ESSN 1664-302X
DOI: 10.3389/FMICB.2020.00114
Page generated: Tue Oct 8 13:25:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy