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Sodium in PDB 5mxp: Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue

Enzymatic activity of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue

All present enzymatic activity of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue:
3.8.1.5;

Protein crystallography data

The structure of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue, PDB code: 5mxp was solved by K.Tratsiak, P.Rezacova, T.Prudnikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.26 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.371, 78.343, 150.514, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue (pdb code 5mxp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue, PDB code: 5mxp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 5mxp

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Sodium binding site 1 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.5
occ:1.00
 O A:LEU19 2.5 19.4 1.0
OG A:SER21 2.7 20.3 1.0
OH A:TYR86 2.7 14.6 1.0
O A:HOH796 2.7 25.4 1.0
C A:LEU19 3.5 17.8 1.0
CB A:SER21 3.6 18.0 1.0
CZ A:TYR86 3.6 11.8 1.0
N A:SER21 3.6 16.0 1.0
CE2 A:TYR86 3.7 11.4 1.0
C A:GLY20 3.8 18.6 1.0
CB A:PRO74 3.9 14.5 1.0
CG A:PRO74 4.1 14.4 1.0
CA A:SER21 4.1 17.0 1.0
CA A:GLY20 4.2 18.1 1.0
N A:GLY20 4.2 17.4 1.0
O A:HOH695 4.3 35.8 1.0
O A:VAL18 4.3 13.8 1.0
CB A:LEU19 4.3 16.4 1.0
O A:GLY20 4.3 23.3 1.0
CA A:LEU19 4.6 15.8 1.0
O A:HOH509 4.7 18.7 0.5
O A:HOH633 4.8 25.7 1.0
CE1 A:TYR86 4.9 12.1 1.0
O A:HOH687 5.0 19.1 1.0
CD2 A:TYR86 5.0 12.1 1.0

Sodium binding site 2 out of 9 in 5mxp

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Sodium binding site 2 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:31.8
occ:1.00
 O A:HOH720 2.5 23.6 1.0
O A:HOH799 2.6 24.3 1.0
OD2 A:ASP142 2.7 26.6 1.0
O A:PHE246 2.8 16.3 1.0
CG A:ASP142 3.4 27.0 1.0
C A:PHE246 3.7 17.5 1.0
CB A:ASP142 3.7 22.0 1.0
CA A:PHE246 3.7 17.0 1.0
CG A:PRO249 3.8 23.7 1.0
CB A:PRO249 4.0 25.4 1.0
O A:GLY245 4.2 16.8 1.0
N A:PHE246 4.3 15.5 1.0
CD A:PRO249 4.4 20.9 1.0
O A:HOH611 4.4 33.5 1.0
OD1 A:ASP142 4.5 22.4 1.0
C A:GLY245 4.5 13.4 1.0
CA A:ASP142 4.7 27.7 1.0
CD1 A:PHE246 4.7 23.7 1.0
N A:PRO249 4.8 20.5 1.0
CA A:PRO249 4.8 20.7 1.0
CB A:PHE246 4.9 17.3 1.0
N A:LEU247 4.9 12.6 1.0

Sodium binding site 3 out of 9 in 5mxp

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Sodium binding site 3 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:38.8
occ:1.00
 O B:HOH678 2.5 22.6 1.0
OG1 B:THR145 2.7 19.5 1.0
OD2 B:ASP142 2.8 33.4 1.0
CG B:ASP142 3.4 36.5 1.0
OD1 B:ASP142 3.5 26.2 1.0
CB B:THR145 3.6 17.4 1.0
CE B:MET177 3.7 26.9 0.5
O B:HOH642 3.8 22.1 1.0
O B:HOH776 3.8 34.8 1.0
CE B:MET177 4.0 11.5 0.5
CE1 B:PHE246 4.1 17.1 1.0
CD1 B:PHE246 4.1 17.0 1.0
CG2 B:THR145 4.2 17.9 1.0
O B:HOH700 4.2 31.5 1.0
O B:HOH757 4.2 24.7 1.0
SD B:MET177 4.5 25.4 0.5
CB B:ASP142 4.5 29.6 1.0
CA B:THR145 4.9 17.7 1.0
N B:ASP142 4.9 24.3 1.0
N B:THR145 4.9 19.0 1.0
O B:HOH791 4.9 32.8 1.0
SD B:MET177 5.0 10.8 0.5

Sodium binding site 4 out of 9 in 5mxp

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Sodium binding site 4 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:24.8
occ:0.49
 NA B:NA403 0.0 24.8 0.5
NA B:NA403 1.7 22.8 0.5
O B:HOH703 2.5 32.3 1.0
O B:HOH759 2.5 36.3 1.0
O B:ARG257 2.5 21.4 1.0
O B:LEU260 2.8 16.5 1.0
C B:LEU260 3.5 17.1 1.0
C B:ARG257 3.6 20.7 1.0
O B:HOH730 3.8 30.1 1.0
C B:GLN258 3.9 17.3 1.0
CA B:GLN258 3.9 18.2 1.0
O B:GLN258 3.9 17.4 1.0
CA B:PRO261 3.9 16.4 1.0
N B:PRO261 4.0 16.2 1.0
O B:HOH673 4.2 35.5 1.0
N B:GLN258 4.2 18.0 1.0
N B:LEU260 4.3 15.4 1.0
N B:ASN262 4.3 15.3 1.0
O B:HOH577 4.4 30.3 1.0
C B:PRO261 4.4 15.6 1.0
CA B:LEU260 4.5 15.5 1.0
N B:GLN259 4.6 16.1 1.0
O B:HOH544 4.7 23.4 1.0
O B:HOH790 4.7 33.6 1.0
N B:LEU263 4.7 14.8 1.0
O B:TYR256 4.7 19.1 1.0
NA B:NA405 4.8 37.5 1.0
OE1 B:GLN258 4.8 21.9 1.0
CB B:LEU263 4.8 15.6 1.0
CA B:ARG257 4.8 20.9 1.0
C B:GLN259 4.9 16.5 1.0
O B:HOH683 5.0 23.5 1.0

Sodium binding site 5 out of 9 in 5mxp

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Sodium binding site 5 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:22.8
occ:0.51
 NA B:NA403 0.0 22.8 0.5
NA B:NA403 1.7 24.8 0.5
O B:HOH759 2.4 36.3 1.0
O B:LEU260 2.8 16.5 1.0
O B:ARG257 2.9 21.4 1.0
N B:LEU263 3.3 14.8 1.0
O B:HOH730 3.3 30.1 1.0
N B:ASN262 3.5 15.3 1.0
O B:HOH567 3.6 25.8 1.0
CB B:LEU263 3.7 15.6 1.0
NA B:NA405 3.8 37.5 1.0
C B:PRO261 3.8 15.6 1.0
C B:LEU260 3.9 17.1 1.0
O B:LEU263 3.9 17.9 1.0
O B:HOH703 4.0 32.3 1.0
CA B:LEU263 4.0 14.8 1.0
CA B:PRO261 4.0 16.4 1.0
C B:ARG257 4.1 20.7 1.0
CA B:ASN262 4.2 15.2 1.0
C B:ASN262 4.2 14.9 1.0
O B:HOH544 4.4 23.4 1.0
N B:PRO261 4.4 16.2 1.0
C B:LEU263 4.4 14.8 1.0
O B:HOH673 4.5 35.5 1.0
O B:PRO261 4.6 13.5 1.0
CA B:ARG257 4.9 20.9 1.0

Sodium binding site 6 out of 9 in 5mxp

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Sodium binding site 6 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:45.7
occ:1.00
 OH B:TYR114 2.8 19.4 1.0
O B:HOH595 2.9 31.8 1.0
O B:HOH529 2.9 38.0 1.0
NH1 B:ARG121 3.5 22.5 1.0
CE1 B:TYR114 3.5 16.4 1.0
CG B:GLU92 3.6 29.4 1.0
CZ B:TYR114 3.7 15.3 1.0
NE2 B:HIS118 3.9 26.9 1.0
CD2 B:HIS118 4.1 26.1 1.0
CE1 B:HIS118 4.1 29.8 1.0
CD B:GLU92 4.1 44.8 1.0
O B:HOH762 4.1 36.6 1.0
OE2 B:GLU92 4.2 59.2 1.0
CZ B:ARG121 4.2 26.6 1.0
CG B:HIS118 4.2 23.9 1.0
ND1 B:HIS118 4.3 32.4 1.0
NH2 B:ARG121 4.3 22.6 1.0
O B:HOH505 4.8 38.5 1.0
CD1 B:TYR114 4.8 13.7 1.0
OE1 B:GLU92 4.9 60.6 1.0
CB B:GLU92 5.0 25.6 1.0

Sodium binding site 7 out of 9 in 5mxp

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Sodium binding site 7 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:37.5
occ:1.00
 O B:LEU263 2.8 17.9 1.0
O B:HOH730 2.8 30.1 1.0
O B:HOH567 3.3 25.8 1.0
O B:ARG257 3.3 21.4 1.0
CA B:ARG257 3.5 20.9 1.0
CB B:ARG257 3.5 27.6 1.0
NE2 A:GLN289 3.7 15.2 1.0
NA B:NA403 3.8 22.8 0.5
CG B:ARG257 3.8 30.8 1.0
C B:ARG257 3.8 20.7 1.0
C B:LEU263 3.9 14.8 1.0
OE1 A:GLN285 4.0 22.2 1.0
CD A:GLN289 4.2 14.9 1.0
CB B:LEU263 4.3 15.6 1.0
CD2 B:LEU263 4.4 22.1 1.0
CG A:GLN289 4.4 13.7 1.0
CA B:LEU263 4.6 14.8 1.0
O A:HOH568 4.6 28.2 1.0
CG B:LEU263 4.6 18.5 1.0
O A:HOH705 4.8 35.5 1.0
NA B:NA403 4.8 24.8 0.5
N B:GLU264 4.8 14.0 1.0
CG2 B:THR265 4.8 15.6 1.0
CD B:ARG257 4.8 31.1 1.0
N B:ARG257 4.8 20.2 1.0
NH1 B:ARG257 4.8 38.3 1.0
O B:HOH759 4.9 36.3 1.0
N B:LEU263 4.9 14.8 1.0
CA B:GLU264 4.9 15.5 1.0
CD A:GLN285 5.0 17.8 1.0
O B:HOH673 5.0 35.5 1.0

Sodium binding site 8 out of 9 in 5mxp

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Sodium binding site 8 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:35.0
occ:1.00
 O A:HOH606 2.1 25.6 1.0
O A:HOH589 2.7 22.1 1.0
O A:HOH592 2.8 16.0 1.0
O B:THR265 3.3 16.7 1.0
O B:HOH619 3.4 21.2 1.0
O A:HOH738 3.5 32.3 1.0
CB A:ALA286 3.8 12.1 1.0
O A:ACT402 3.8 25.8 0.8
OG1 B:THR265 3.9 16.8 1.0
CA A:ALA286 4.0 11.9 1.0
CB A:ALA266 4.1 10.8 1.0
O B:HOH515 4.2 31.3 1.0
C B:THR265 4.3 13.1 1.0
OE1 A:GLN289 4.3 16.8 1.0
N A:ALA286 4.4 11.5 1.0
O A:LYS282 4.5 13.1 1.0
NE2 A:GLN289 4.8 15.2 1.0
CD A:GLN289 4.8 14.9 1.0
CA B:ALA266 4.8 12.5 1.0
O A:PHE267 4.8 13.0 1.0
O A:HOH629 4.8 15.6 1.0
CA A:ALA266 4.9 11.1 1.0
N B:ALA266 4.9 12.5 1.0
CB B:THR265 5.0 14.9 1.0
C A:ACT402 5.0 28.3 1.0

Sodium binding site 9 out of 9 in 5mxp

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Sodium binding site 9 out of 9 in the Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Haloalkane Dehalogenase Dmxa From Marinobacter Sp. ELB17 Possessing A Unique Catalytic Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:22.9
occ:1.00
 O B:LEU19 2.5 19.7 1.0
OH B:TYR86 2.7 14.4 1.0
O B:HOH778 2.7 23.4 1.0
OG B:SER21 2.8 17.3 1.0
C B:LEU19 3.6 18.3 1.0
CZ B:TYR86 3.6 13.3 1.0
CB B:SER21 3.6 17.3 1.0
N B:SER21 3.7 19.0 1.0
CE2 B:TYR86 3.7 13.2 1.0
O B:HOH513 3.8 33.7 1.0
CB B:PRO74 3.9 12.9 1.0
C B:GLY20 3.9 20.4 1.0
CG B:PRO74 4.0 12.2 1.0
CA B:SER21 4.2 18.2 1.0
N B:GLY20 4.2 19.5 1.0
CA B:GLY20 4.3 22.2 1.0
O B:VAL18 4.3 17.2 1.0
CB B:LEU19 4.4 17.7 1.0
O B:GLY20 4.4 21.5 1.0
CA B:LEU19 4.6 17.9 1.0
O B:HOH533 4.7 24.0 1.0
CE1 B:TYR86 4.9 12.5 1.0

Reference:

L.Chrast, K.Tratsiak, J.Planas-Iglesias, L.Daniel, T.Prudnikova, J.Brezovsky, D.Bednar, I.Kuta Smatanova, R.Chaloupkova, J.Damborsky. Deciphering the Structural Basis of High Thermostability of Dehalogenase From Psychrophilic Bacteriummarinobactersp. ELB17. Microorganisms V. 7 2019.
ISSN: ISSN 2076-2607
PubMed: 31661858
DOI: 10.3390/MICROORGANISMS7110498
Page generated: Tue Dec 15 11:19:36 2020

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