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Sodium in PDB 3b8x: Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine

Protein crystallography data

The structure of Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine, PDB code: 3b8x was solved by P.D.Cook, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.411, 98.123, 119.940, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine (pdb code 3b8x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine, PDB code: 3b8x:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3b8x

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Sodium binding site 1 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


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 Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na669

b:27.3
occ:1.00
 O A:HOH688 2.4 12.4 1.0
O A:THR175 2.4 6.7 1.0
O A:HOH751 2.5 14.2 1.0
OD2 A:ASP201 2.7 18.2 1.0
C A:THR175 3.4 14.9 1.0
CG A:ASP201 3.5 13.8 1.0
O A:HOH978 3.7 22.6 1.0
CB A:THR175 3.7 1.2 1.0
CA A:THR175 3.8 12.5 1.0
NZ A:LYS171 3.9 19.3 1.0
O A:HOH683 3.9 7.2 1.0
OD1 A:ASP201 4.0 14.2 1.0
O A:GLY177 4.3 6.9 1.0
O A:HOH705 4.4 10.1 1.0
O A:HOH979 4.4 28.3 1.0
OG1 A:THR175 4.4 7.2 1.0
CB A:ASP201 4.5 9.1 1.0
N A:PHE176 4.5 12.9 1.0
CE A:LYS171 4.8 10.4 1.0
CG2 A:THR175 4.9 17.8 1.0
CA A:PHE176 4.9 6.0 1.0

Sodium binding site 2 out of 8 in 3b8x

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Sodium binding site 2 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


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 Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na671

b:32.0
occ:1.00
 O A:HOH872 2.4 32.6 1.0
O A:HOH744 2.4 18.3 1.0
O A:LEU6 2.5 27.6 1.0
O A:ASN371 2.6 12.5 1.0
O A:HOH743 2.6 28.0 1.0
O A:HOH836 3.2 24.7 1.0
C A:LEU6 3.6 29.0 1.0
C A:ASN371 3.7 17.1 1.0
N A:ASN371 3.8 6.4 1.0
O A:PHE302 3.8 11.4 1.0
NH2 A:ARG273 3.9 12.2 1.0
O A:SER187 4.0 16.6 1.0
CA A:ALA7 4.2 35.8 1.0
N A:ALA7 4.3 22.3 1.0
CB A:ALA7 4.4 15.8 1.0
CA A:GLY370 4.4 16.9 1.0
CA A:ASN371 4.4 4.9 1.0
CD2 A:HIS372 4.5 59.3 1.0
NH1 A:ARG273 4.5 10.3 1.0
NE2 A:HIS372 4.6 17.7 1.0
C A:GLY370 4.6 3.2 1.0
CZ A:ARG273 4.6 21.1 1.0
CA A:LEU6 4.7 30.4 1.0
CG A:HIS372 4.7 19.9 1.0
O A:HOH853 4.7 24.7 1.0
N A:HIS372 4.7 7.8 1.0
CA A:HIS372 4.8 8.4 1.0
CE1 A:HIS372 4.8 96.5 1.0
ND1 A:HIS372 4.9 63.3 1.0

Sodium binding site 3 out of 8 in 3b8x

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Sodium binding site 3 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


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 Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na672

b:42.6
occ:1.00
 OE2 A:GLU80 2.4 14.2 1.0
OG1 A:THR124 2.5 26.7 1.0
NZ A:LYS103 2.7 40.4 1.0
O A:ALA122 2.8 15.9 1.0
OG1 A:THR127 3.1 13.9 1.0
N A:THR124 3.1 21.8 1.0
OG A:SER126 3.2 41.3 1.0
CD A:GLU80 3.2 22.7 1.0
CB A:THR124 3.2 25.1 1.0
CG2 A:THR124 3.3 99.9 1.0
OE1 A:GLU80 3.3 25.0 1.0
CE A:LYS103 3.6 23.0 1.0
CA A:THR124 3.6 20.1 1.0
C A:VAL123 4.0 66.9 1.0
C A:ALA122 4.0 10.1 1.0
CD A:LYS103 4.1 45.1 1.0
N A:THR127 4.2 14.1 1.0
C A:THR124 4.3 21.6 1.0
CA A:VAL123 4.4 11.9 1.0
CB A:THR127 4.4 13.2 1.0
CB A:SER126 4.5 31.2 1.0
CA A:THR127 4.6 15.9 1.0
CG A:GLU80 4.6 5.3 1.0
O A:THR124 4.7 27.6 1.0
N A:VAL123 4.7 18.8 1.0
C A:SER126 4.7 8.1 1.0
N A:SER126 4.8 18.7 1.0
CD1 A:ILE82 4.8 14.5 1.0
O A:VAL123 4.9 22.8 1.0
CA A:SER126 5.0 14.3 1.0

Sodium binding site 4 out of 8 in 3b8x

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Sodium binding site 4 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


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 Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na673

b:50.7
occ:1.00
 O A:HOH831 2.4 18.1 1.0
NH2 A:ARG273 2.9 12.2 1.0
OE1 A:GLN373 2.9 28.7 1.0
O A:HOH853 3.0 24.7 1.0
O A:HOH755 3.1 20.0 1.0
CG2 A:THR10 3.3 14.5 1.0
O A:ASN188 3.3 19.5 1.0
O A:HOH872 3.7 32.6 1.0
CD A:GLN373 3.7 19.7 1.0
CZ A:ARG273 3.8 21.1 1.0
NE A:ARG273 3.8 7.2 1.0
O A:HIS189 3.9 14.1 1.0
CB A:GLN373 4.0 12.2 1.0
N A:GLN373 4.1 11.6 1.0
CG A:GLN373 4.2 15.3 1.0
C A:ASN188 4.3 7.9 1.0
CA A:HIS189 4.3 9.2 1.0
C A:HIS189 4.3 15.6 1.0
NE2 A:GLN373 4.6 28.0 1.0
CB A:THR10 4.7 17.0 1.0
CA A:GLN373 4.7 13.6 1.0
N A:HIS189 4.7 11.0 1.0
CA A:HIS372 4.8 8.4 1.0
C A:HIS372 4.9 8.9 1.0
O A:HOH743 4.9 28.0 1.0
NH1 A:ARG273 5.0 10.3 1.0

Sodium binding site 5 out of 8 in 3b8x

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Sodium binding site 5 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na666

b:17.8
occ:1.00
 O B:HOH751 2.3 15.1 1.0
O B:HOH694 2.4 12.1 1.0
O B:LEU6 2.4 9.0 1.0
O B:HOH722 2.5 11.8 1.0
O B:ASN371 2.6 13.2 1.0
O B:HOH745 2.9 22.7 1.0
C B:LEU6 3.6 24.9 1.0
O B:SER187 3.8 13.5 1.0
C B:ASN371 3.8 18.3 1.0
CA B:ALA7 3.8 11.4 1.0
N B:ASN371 3.9 3.4 1.0
O B:PHE302 3.9 10.5 1.0
CB B:ALA7 4.0 14.0 1.0
NH2 B:ARG273 4.1 1.0 1.0
N B:ALA7 4.2 14.5 1.0
O B:HOH819 4.4 26.2 1.0
CD2 B:HIS372 4.5 17.0 1.0
CA B:ASN371 4.5 4.5 1.0
CA B:GLY370 4.6 2.0 1.0
NH1 B:ARG273 4.6 14.9 1.0
CA B:LEU6 4.7 13.2 1.0
C B:GLY370 4.7 10.2 1.0
C B:SER187 4.7 21.4 1.0
N B:HIS372 4.8 13.2 1.0
NE2 B:HIS372 4.8 14.5 1.0
CZ B:ARG273 4.8 16.6 1.0
CA B:HIS372 4.8 13.1 1.0
CG B:HIS372 4.9 14.2 1.0
O B:HOH783 4.9 19.3 1.0
CG B:LEU6 5.0 28.8 1.0

Sodium binding site 6 out of 8 in 3b8x

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Sodium binding site 6 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na667

b:43.5
occ:1.00
 O B:HOH995 2.4 35.5 1.0
O B:HOH847 2.4 13.7 1.0
O B:HOH997 2.5 46.6 1.0
O B:HOH912 2.6 54.8 1.0
O B:HOH1000 2.8 48.1 1.0
OD2 B:ASP378 2.9 29.4 1.0
OE2 B:GLU375 3.1 26.4 1.0
CG B:ASP378 3.8 24.0 1.0
CD B:GLU375 4.1 23.9 1.0
O B:HOH885 4.2 43.9 1.0
CB B:ASP378 4.3 14.2 1.0
OE1 B:GLU379 4.3 18.1 1.0
OE1 B:GLU375 4.3 35.1 1.0
OE2 B:GLU379 4.4 17.1 1.0
CD B:GLU379 4.8 16.0 1.0
OD1 B:ASP378 4.8 21.3 1.0
N B:ASP378 4.9 10.4 1.0

Sodium binding site 7 out of 8 in 3b8x

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Sodium binding site 7 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na668

b:14.6
occ:1.00
 OD1 B:ASN341 2.3 16.8 1.0
O B:HOH959 2.3 23.7 1.0
OD2 B:ASP343 2.4 12.3 1.0
O A:PHE242 2.4 16.8 1.0
O B:HOH895 2.5 33.6 1.0
OD1 B:ASP343 2.5 16.6 1.0
CG B:ASP343 2.8 16.7 1.0
CG B:ASN341 3.2 11.7 1.0
C A:PHE242 3.5 5.0 1.0
CB B:ASN341 3.6 21.8 1.0
CA B:ASN341 3.9 14.7 1.0
CG1 A:VAL243 3.9 14.3 1.0
O B:HOH712 4.0 13.3 1.0
CA A:VAL243 4.1 6.8 1.0
CB B:ASP343 4.3 4.5 1.0
N A:VAL243 4.3 10.8 1.0
O B:HOH947 4.3 21.8 1.0
ND2 B:ASN341 4.5 19.2 1.0
N A:PHE242 4.5 8.0 1.0
CA A:PHE242 4.6 9.8 1.0
CB A:VAL243 4.6 10.1 1.0
O B:HOH980 4.6 19.9 1.0
C B:ASN341 4.6 22.8 1.0
N B:ASP343 4.8 10.1 1.0
CG2 B:VAL344 4.8 15.2 1.0
N B:ASN341 4.9 23.8 1.0

Sodium binding site 8 out of 8 in 3b8x

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Sodium binding site 8 out of 8 in the Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188N Mutant with Bound Gdp-Perosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na670

b:27.2
occ:1.00
 O B:THR175 2.5 26.8 1.0
O B:HOH859 2.5 27.8 1.0
O B:HOH798 2.5 42.2 1.0
O B:HOH892 2.6 30.0 1.0
OD2 B:ASP201 2.7 22.4 1.0
O B:HOH765 2.7 17.9 1.0
C B:THR175 3.6 13.9 1.0
CG B:ASP201 3.6 18.0 1.0
NZ B:LYS171 3.9 26.4 1.0
CB B:THR175 4.0 12.2 1.0
CA B:THR175 4.1 12.8 1.0
OD1 B:ASP201 4.1 21.8 1.0
O B:GLY177 4.3 20.6 1.0
O B:HOH723 4.3 13.4 1.0
O B:HOH755 4.4 11.6 1.0
O B:HOH981 4.4 43.3 1.0
CE B:LYS171 4.4 20.3 1.0
CB B:ASP201 4.6 13.6 1.0
N B:PHE176 4.7 14.6 1.0
OG1 B:THR175 4.7 14.6 1.0
O B:HOH887 4.9 33.1 1.0
CA B:PHE176 5.0 20.6 1.0
C B:PHE176 5.0 27.4 1.0

Reference:

P.D.Cook, H.M.Holden. Gdp-4-Keto-6-Deoxy-D-Mannose 3-Dehydratase, Accommodating A Sugar Substrate in the Active Site. J.Biol.Chem. V. 283 4295 2008.
ISSN: ISSN 0021-9258
PubMed: 18045869
DOI: 10.1074/JBC.M708893200
Page generated: Tue Dec 15 06:03:17 2020

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