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Sodium in PDB 6hze: BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II

Protein crystallography data

The structure of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II, PDB code: 6hze was solved by A.Basle, A.Cartmell, A.Labourel, H.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.498, 107.376, 139.211, 90.00, 98.68, 90.00
R / Rfree (%) 21.3 / 28.2

Sodium Binding Sites:

The binding sites of Sodium atom in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II (pdb code 6hze). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II, PDB code: 6hze:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 6hze

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Sodium binding site 1 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:53.6
occ:1.00
 NE2 A:HIS836 3.9 39.9 1.0
CE1 A:HIS836 4.0 40.6 1.0
N A:GLY839 4.2 41.7 1.0
CA A:GLY839 4.5 41.6 1.0
N A:VAL840 5.0 39.6 1.0

Sodium binding site 2 out of 10 in 6hze

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Sodium binding site 2 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:11.5
occ:1.00
 NE A:ARG332 3.3 26.5 1.0
NH2 A:ARG332 3.4 26.1 1.0
ND2 A:ASN389 3.5 27.2 1.0
CG A:MET355 3.6 27.2 1.0
CA A:HIS356 3.7 28.0 1.0
N A:LYS357 3.7 27.4 1.0
CZ A:ARG332 3.8 26.2 1.0
C A:HIS356 3.8 27.7 1.0
N A:HIS356 3.9 28.1 1.0
SD A:MET355 3.9 26.6 1.0
CB A:ASN389 3.9 27.7 1.0
C A:MET355 4.0 28.2 1.0
CB A:ARG332 4.1 27.6 1.0
CG A:LYS357 4.1 26.9 1.0
CB A:MET355 4.1 27.8 1.0
CG A:ASN389 4.2 27.3 1.0
O A:MET355 4.2 28.4 1.0
CG A:ARG332 4.4 27.4 1.0
CD A:ARG332 4.4 26.8 1.0
O A:HIS356 4.6 27.9 1.0
CA A:LYS357 4.6 27.2 1.0
CA A:ARG332 4.7 28.3 1.0
CB A:HIS334 4.7 27.8 1.0
CE A:LYS357 4.7 26.6 1.0
CA A:MET355 4.7 28.4 1.0
N A:ALA333 4.8 28.7 1.0
N A:HIS334 4.8 28.4 1.0
ND1 A:HIS391 4.8 27.0 1.0
ND1 A:HIS356 4.9 28.0 1.0
CB A:LYS357 5.0 27.0 1.0

Sodium binding site 3 out of 10 in 6hze

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Sodium binding site 3 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:18.9
occ:1.00
 OG A:SER696 2.8 33.6 1.0
OG1 A:THR666 3.0 33.1 1.0
N A:SER696 3.2 32.5 1.0
CA A:LYS667 3.6 34.3 1.0
N A:LYS667 3.7 33.9 1.0
N A:TRP695 3.8 30.7 1.0
CB A:TRP695 3.8 31.3 1.0
CB A:SER696 3.8 33.6 1.0
CE3 A:TRP695 4.0 30.0 1.0
CB A:THR666 4.0 32.6 1.0
CB A:LYS667 4.0 35.2 1.0
C A:THR666 4.0 33.2 1.0
C A:TRP695 4.0 32.1 1.0
CA A:TRP695 4.0 31.2 1.0
CA A:SER696 4.0 33.3 1.0
CB A:THR694 4.2 30.8 1.0
O A:THR666 4.3 32.7 1.0
O A:VAL663 4.4 35.6 1.0
C A:THR694 4.5 30.6 1.0
CG1 A:VAL663 4.6 36.3 1.0
CD2 A:TRP695 4.6 30.1 1.0
CG A:TRP695 4.6 30.6 1.0
CA A:THR666 4.6 33.1 1.0
CA A:VAL663 4.7 35.3 1.0
CA A:THR694 4.7 30.2 1.0
OG1 A:THR694 4.8 31.3 1.0
CG2 A:VAL663 4.9 35.4 1.0
CG2 A:THR694 4.9 30.5 1.0
C A:LYS667 4.9 34.4 1.0
CB A:VAL663 5.0 35.9 1.0
CZ3 A:TRP695 5.0 29.5 1.0

Sodium binding site 4 out of 10 in 6hze

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Sodium binding site 4 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:17.7
occ:1.00
 N A:ASP689 3.3 30.6 1.0
N A:ALA679 3.5 29.2 1.0
CA A:THR678 3.7 28.8 1.0
CB A:THR678 3.9 28.6 1.0
CA A:ASP689 4.0 30.8 1.0
C A:THR678 4.0 29.0 1.0
OD1 A:ASP689 4.1 31.4 1.0
CB A:ALA679 4.1 29.9 1.0
CA A:ASP688 4.2 30.3 1.0
C A:ASP688 4.2 30.6 1.0
CA A:ALA679 4.4 29.6 1.0
CG2 A:THR678 4.5 28.6 1.0
O A:GLN677 4.8 28.6 1.0
O A:GLY687 4.9 29.5 1.0
CG A:ASP689 4.9 31.8 1.0
N A:THR678 4.9 28.5 1.0

Sodium binding site 5 out of 10 in 6hze

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Sodium binding site 5 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:26.6
occ:1.00
 N A:LYS851 3.2 34.6 1.0
CE1 A:HIS855 3.7 33.4 1.0
CB A:LYS851 3.7 35.7 1.0
CA A:PHE850 4.0 33.4 1.0
CA A:LYS851 4.1 35.5 1.0
C A:PHE850 4.1 34.3 1.0
CD A:LYS851 4.2 35.6 1.0
CG A:LYS851 4.4 36.0 1.0
ND1 A:HIS855 4.5 33.0 1.0
NE2 A:HIS855 4.6 34.0 1.0
CB A:PHE850 4.7 33.4 1.0
O A:LYS851 4.7 35.8 1.0
C A:LYS851 4.9 36.0 1.0
CD2 A:PHE850 5.0 32.4 1.0

Sodium binding site 6 out of 10 in 6hze

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Sodium binding site 6 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:30.5
occ:1.00
 NZ A:LYS743 3.6 40.2 1.0
N A:ILE737 3.7 37.7 1.0
CA A:LYS736 3.9 38.7 1.0
CE A:LYS743 3.9 40.4 1.0
CB A:LYS736 4.3 39.2 1.0
C A:LYS736 4.3 37.7 1.0
O A:VAL735 4.4 39.5 1.0
CB A:ILE737 4.6 37.0 1.0
O A:ILE737 4.6 37.8 1.0
CA A:ILE737 4.7 36.9 1.0
CG1 A:ILE737 4.7 37.0 1.0
N A:LYS736 5.0 38.5 1.0

Sodium binding site 7 out of 10 in 6hze

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Sodium binding site 7 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:30.7
occ:1.00
 NE2 A:HIS151 3.2 32.1 1.0
CE1 A:HIS151 3.9 31.8 1.0
CG A:GLU209 3.9 32.7 1.0
CD A:LYS247 4.2 32.6 1.0
O A:GLU209 4.3 33.3 1.0
CD2 A:HIS151 4.4 31.8 1.0
CE A:LYS247 4.4 33.5 1.0
CG A:PRO157 4.4 29.6 1.0
CD A:PRO248 4.5 32.6 1.0
CB A:GLU209 4.6 32.8 1.0
CB A:LYS247 4.6 31.8 1.0
CD A:GLU209 4.7 32.3 1.0
OE2 A:GLU209 4.7 32.4 1.0
CA A:GLU209 4.7 33.4 1.0
CG A:PRO248 4.8 33.3 1.0
CG A:LYS247 4.9 32.4 1.0
C A:GLU209 4.9 33.5 1.0

Sodium binding site 8 out of 10 in 6hze

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Sodium binding site 8 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:49.5
occ:1.00
 O A:ASP123 2.5 44.4 1.0
OG1 A:THR121 2.6 47.7 1.0
OG A:SER119 2.6 45.8 1.0
CB A:SER119 3.7 45.5 1.0
OE1 A:GLN115 3.7 42.0 1.0
C A:ASP123 3.7 45.5 1.0
O A:GLN115 3.9 41.2 1.0
CB A:THR121 4.0 48.3 1.0
O A:THR121 4.2 46.7 1.0
C A:THR121 4.4 47.4 1.0
C A:GLN115 4.4 40.8 1.0
CB A:GLN115 4.4 40.5 1.0
N A:ASP123 4.5 47.1 1.0
CA A:THR121 4.6 47.8 1.0
N A:PHE124 4.6 45.3 1.0
CA A:PHE124 4.6 44.1 1.0
N A:THR121 4.6 47.2 1.0
CA A:ASP123 4.7 47.0 1.0
CD A:GLN115 4.7 41.4 1.0
N A:MET122 4.9 47.8 1.0
CG2 A:THR121 4.9 48.4 1.0
CG A:GLN115 4.9 40.4 1.0
CA A:GLN115 4.9 39.8 1.0
CD1 A:PHE124 5.0 42.5 1.0
CA A:SER119 5.0 45.0 1.0

Sodium binding site 9 out of 10 in 6hze

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Sodium binding site 9 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na902

b:25.0
occ:1.00
 NE B:ARG332 3.2 53.8 1.0
NH2 B:ARG332 3.4 53.1 1.0
CA B:HIS356 3.6 53.4 1.0
CZ B:ARG332 3.7 53.4 1.0
N B:LYS357 3.7 52.8 1.0
CG B:MET355 3.8 53.6 1.0
C B:HIS356 3.8 53.2 1.0
N B:HIS356 3.9 53.8 1.0
SD B:MET355 4.0 53.3 1.0
ND2 B:ASN389 4.0 51.9 1.0
CG B:LYS357 4.0 52.1 1.0
C B:MET355 4.0 54.0 1.0
CB B:ARG332 4.0 54.5 1.0
O B:MET355 4.1 53.9 1.0
CG B:ARG332 4.2 54.7 1.0
CB B:ASN389 4.2 52.5 1.0
CB B:MET355 4.3 54.1 1.0
CD B:ARG332 4.3 54.2 1.0
CA B:ARG332 4.4 55.0 1.0
N B:ALA333 4.5 54.8 1.0
N B:HIS334 4.6 54.0 1.0
CB B:HIS334 4.6 53.6 1.0
CA B:LYS357 4.6 52.5 1.0
O B:HIS356 4.6 53.6 1.0
ND1 B:HIS356 4.6 52.6 1.0
CG B:ASN389 4.6 52.3 1.0
CA B:MET355 4.8 54.4 1.0
CB B:LYS357 4.9 52.1 1.0
CB B:HIS356 4.9 53.5 1.0
NH1 B:ARG332 4.9 53.4 1.0
CE B:LYS357 5.0 51.7 1.0

Sodium binding site 10 out of 10 in 6hze

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Sodium binding site 10 out of 10 in the BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of BP0997, GH138 Enzyme Targeting Pectin Rhamnogalacturonan II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na903

b:31.4
occ:1.00
 CE1 B:HIS356 3.9 52.2 1.0
CA B:GLY360 4.1 50.8 1.0
CD B:LYS357 4.2 51.7 1.0
NE2 B:HIS356 4.2 52.4 1.0
CH2 B:TRP372 4.2 52.7 1.0
CZ3 B:TRP372 4.2 53.0 1.0
CZ2 B:TRP372 4.3 52.9 1.0
CB B:LYS357 4.3 52.1 1.0
CE3 B:TRP372 4.4 53.5 1.0
CE2 B:TRP372 4.5 53.4 1.0
CD2 B:TRP372 4.5 53.6 1.0
CG B:LYS357 4.7 52.1 1.0
N B:GLY360 4.7 51.2 1.0
ND1 B:HIS356 5.0 52.6 1.0

Reference:

A.Labourel, A.Basle, J.Munoz-Munoz, D.Ndeh, S.Booth, S.A.Nepogodiev, R.A.Field, A.Cartmell. Structural and Functional Analyses of Glycoside Hydrolase 138 Enzymes Targeting Chain A Galacturonic Acid in the Complex Pectin Rhamnogalacturonan II. J.Biol.Chem. V. 294 7711 2019.
ISSN: ESSN 1083-351X
PubMed: 30877196
DOI: 10.1074/JBC.RA118.006626
Page generated: Tue Oct 8 09:29:34 2024

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