Atomistry » Sodium » PDB 7p8p-7q1k » 7pw1
Atomistry »
  Sodium »
    PDB 7p8p-7q1k »
      7pw1 »

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

Last articles

Cl in 6COG
Cl in 6CST
Cl in 6CTW
Cl in 6CTZ
Cl in 6CTT
Cl in 6CSP
Cl in 6CU9
Cl in 6CTX
Cl in 6CTU
Cl in 6CTP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy