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Sodium in PDB 7pw1: Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba

Enzymatic activity of Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba

All present enzymatic activity of Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba:
3.8.1.5;

Protein crystallography data

The structure of Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba, PDB code: 7pw1 was solved by A.Mazur, P.Grinkevich, T.Prudnikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.04 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.897, 68.897, 156.259, 90, 90, 90
R / Rfree (%) 13.8 / 17.4

Other elements in 7pw1:

The structure of Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba (pdb code 7pw1). 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 Ancestral Haloalkane Dehalogenase Anclinb-Dmba, PDB code: 7pw1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7pw1

Go back to Sodium Binding Sites List in 7pw1
Sodium binding site 1 out of 4 in the Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba


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 Ancestral Haloalkane Dehalogenase Anclinb-Dmba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:21.5
occ:1.00
 OE1 A:GLN36 2.7 14.1 1.0
N A:CYS62 2.9 13.2 1.0
O A:PHE35 2.9 15.3 1.0
CB A:CYS62 3.4 12.7 1.0
SG A:CYS62 3.4 15.2 1.0
CG1 A:VAL34 3.5 16.1 1.0
CA A:CYS62 3.7 12.9 1.0
NE1 A:TRP94 3.7 15.6 1.0
CA A:ALA61 3.7 13.2 1.0
CD A:GLN36 3.7 13.3 1.0
C A:PHE35 3.7 15.0 1.0
C A:ALA61 3.7 13.4 1.0
CZ2 A:TRP94 4.0 14.9 1.0
O A:ILE60 4.1 15.2 1.0
NA A:NA403 4.2 20.6 1.0
N A:PHE35 4.2 12.8 1.0
CE2 A:TRP94 4.2 14.1 1.0
CA A:GLN36 4.2 13.5 1.0
N A:ALA61 4.3 13.2 1.0
CG2 A:ILE60 4.3 16.8 1.0
CB A:GLN36 4.3 13.9 1.0
O A:CYS62 4.3 14.9 1.0
N A:GLN36 4.3 13.1 1.0
C A:ILE60 4.4 14.3 1.0
C A:CYS62 4.5 12.8 1.0
NE2 A:GLN36 4.5 14.0 1.0
CG A:GLN36 4.5 14.3 1.0
CA A:PHE35 4.6 13.5 1.0
C A:VAL34 4.6 14.5 1.0
CB A:VAL34 4.8 13.8 1.0
CB A:ALA61 4.9 14.6 1.0
CD1 A:TRP94 4.9 15.6 1.0
CA A:VAL34 4.9 13.5 1.0
O A:ALA61 5.0 14.4 1.0

Sodium binding site 2 out of 4 in 7pw1

Go back to Sodium Binding Sites List in 7pw1
Sodium binding site 2 out of 4 in the Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba


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 Ancestral Haloalkane Dehalogenase Anclinb-Dmba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:20.6
occ:1.00
 O A:PHE35 2.8 15.3 1.0
O A:CYS62 2.9 14.9 1.0
N A:HIS37 3.1 11.8 1.0
CD2 A:HIS37 3.3 13.4 1.0
CA A:GLN36 3.5 13.5 1.0
N A:CYS62 3.5 13.2 1.0
NE2 A:GLN36 3.6 14.0 1.0
C A:PHE35 3.7 15.0 1.0
NE1 A:TRP46 3.7 14.6 1.0
CD1 A:TRP46 3.8 14.0 1.0
C A:GLN36 3.8 12.5 1.0
CA A:SER43 3.8 12.6 1.0
C A:CYS62 3.8 12.8 1.0
CB A:HIS37 3.8 13.2 1.0
C A:ALA61 3.9 13.4 1.0
CB A:ALA61 3.9 14.6 1.0
CG A:HIS37 3.9 12.7 1.0
CD A:GLN36 4.0 13.3 1.0
CA A:ALA61 4.0 13.2 1.0
N A:GLN36 4.0 13.1 1.0
CA A:HIS37 4.1 12.9 1.0
N A:SER43 4.1 13.0 1.0
NA A:NA402 4.2 21.5 1.0
OE1 A:GLN36 4.2 14.1 1.0
CB A:SER43 4.2 13.1 1.0
CA A:CYS62 4.2 12.9 1.0
NE2 A:HIS37 4.5 12.7 1.0
C A:SER42 4.5 14.0 1.0
O A:SER42 4.6 13.8 1.0
O A:ALA61 4.7 14.4 1.0
CB A:GLN36 4.7 13.9 1.0
CG A:GLN36 4.8 14.3 1.0
CA A:PHE35 4.9 13.5 1.0
CB A:PHE35 4.9 15.3 1.0
N A:ASP63 4.9 13.3 1.0
CE2 A:TRP46 5.0 13.7 1.0
O A:GLN36 5.0 13.3 1.0
C A:SER43 5.0 13.4 1.0

Sodium binding site 3 out of 4 in 7pw1

Go back to Sodium Binding Sites List in 7pw1
Sodium binding site 3 out of 4 in the Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba


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 Ancestral Haloalkane Dehalogenase Anclinb-Dmba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:21.8
occ:1.00
 ND1 A:HIS86 2.9 14.7 1.0
N A:ILE65 3.0 13.2 1.0
O A:HIS86 3.0 15.1 1.0
CA A:HIS86 3.5 13.9 1.0
CA A:LEU64 3.6 13.2 1.0
CD2 A:LEU64 3.6 15.9 1.0
CG2 A:ILE65 3.6 13.6 1.0
CB A:LEU64 3.6 13.0 1.0
C A:HIS86 3.7 14.1 1.0
CB A:HIS86 3.7 12.8 1.0
CG A:HIS86 3.7 12.8 1.0
CB A:ILE65 3.8 14.0 1.0
C A:LEU64 3.8 13.0 1.0
CE1 A:HIS86 3.9 14.5 1.0
CB A:TYR89 4.0 13.8 1.0
CA A:ILE65 4.0 14.1 1.0
N A:LEU90 4.0 13.8 1.0
CG A:LEU64 4.1 15.1 1.0
CB A:LEU90 4.1 15.0 1.0
CE A:MET22 4.2 12.5 0.5
CE A:MET22 4.5 30.4 0.5
CA A:LEU90 4.5 14.4 1.0
C A:TYR89 4.7 14.1 1.0
CA A:TYR89 4.8 15.2 1.0
O A:ILE65 4.8 13.8 1.0
N A:HIS86 4.9 15.2 1.0
CD2 A:HIS86 4.9 13.0 1.0
C A:ILE65 4.9 13.5 1.0
N A:ARG87 4.9 13.5 0.5
N A:LEU64 5.0 12.5 1.0
CD1 A:LEU64 5.0 15.8 1.0
O A:LEU64 5.0 13.6 1.0
SD A:MET22 5.0 28.0 0.5
N A:ARG87 5.0 14.5 0.5

Sodium binding site 4 out of 4 in 7pw1

Go back to Sodium Binding Sites List in 7pw1
Sodium binding site 4 out of 4 in the Crystal Structure of Ancestral Haloalkane Dehalogenase Anclinb-Dmba


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 Ancestral Haloalkane Dehalogenase Anclinb-Dmba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:22.6
occ:1.00
 NE2 A:HIS86 2.8 14.3 1.0
O A:PRO204 2.9 15.4 1.0
O A:TYR81 3.0 16.4 1.0
CB A:TYR81 3.2 16.9 1.0
CA A:PRO204 3.3 17.2 1.0
CD1 A:TRP208 3.3 14.4 1.0
CG A:TRP208 3.4 12.9 1.0
CD2 A:HIS86 3.4 13.0 1.0
C A:PRO204 3.5 15.8 1.0
NE1 A:TRP208 3.5 14.9 1.0
CB A:PRO204 3.6 16.8 1.0
CD2 A:TRP208 3.6 13.7 1.0
CE2 A:TRP208 3.6 13.3 1.0
N A:TRP208 3.7 15.5 1.0
CB A:SER207 3.7 17.4 1.0
C A:TYR81 3.9 16.3 1.0
CE1 A:HIS86 4.0 14.5 1.0
CA A:TYR81 4.1 15.8 1.0
CG A:TYR81 4.1 14.3 1.0
CB A:TRP208 4.1 15.0 1.0
CA A:TRP208 4.2 14.5 1.0
C A:SER207 4.2 15.2 1.0
CA A:SER207 4.4 15.4 1.0
CE3 A:TRP208 4.4 15.3 1.0
CD1 A:TYR81 4.5 15.3 1.0
CZ2 A:TRP208 4.5 12.9 1.0
N A:PRO204 4.6 16.3 1.0
CG A:HIS86 4.7 12.8 1.0
OG A:SER207 4.7 18.3 1.0
N A:SER207 4.7 16.7 1.0
O A:ARG203 4.7 17.3 1.0
CG A:PRO204 4.8 19.7 1.0
N A:THR205 4.8 15.8 1.0
ND1 A:HIS86 5.0 14.7 1.0

Reference:

A.Mazur, P.Grinkevich, R.Chaloupkova, P.Havlickova, B.Kascakova, M.Kuty, J.Damborsky, I.Kuta Smatanova, T.Prudnikova. Structural Analysis of the Ancestral Haloalkane Dehalogenase Anclinb-Dmba. Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34769421
DOI: 10.3390/IJMS222111992
Page generated: Fri Apr 7 15:38:42 2023

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