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Sodium in PDB 3hb7: The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A

Protein crystallography data

The structure of The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A, PDB code: 3hb7 was solved by A.J.Stein, X.Xu, H.Cui, J.Ng, A.Edwards, A.Savchenko, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.32 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.651, 105.425, 106.267, 90.00, 103.90, 90.00
R / Rfree (%) 19.6 / 23.8

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A (pdb code 3hb7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A, PDB code: 3hb7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3hb7

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Sodium binding site 1 out of 5 in the The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:27.3
occ:1.00
 O A:HOH268 2.9 29.4 1.0
OG1 A:THR135 3.1 20.3 0.5
OG1 C:THR135 3.4 17.9 1.0
OG A:SER132 3.6 22.8 1.0
CB C:THR135 3.8 17.1 1.0
OG1 A:THR135 3.8 19.6 0.5
CA C:SER132 3.8 18.3 1.0
CA A:SER132 3.8 19.5 1.0
NE A:ARG131 3.8 24.7 1.0
CG2 A:THR135 3.8 20.2 0.5
CB A:THR135 3.9 19.1 0.5
CB A:THR135 3.9 19.7 0.5
CG C:ARG131 4.0 17.7 1.0
CG2 C:THR135 4.0 16.3 1.0
CG2 A:THR135 4.1 16.4 0.5
CB A:SER132 4.2 19.4 1.0
OG C:SER132 4.3 22.3 1.0
N C:SER132 4.3 17.7 1.0
O C:ARG131 4.3 17.2 1.0
CD C:ARG131 4.3 19.1 1.0
CG A:ARG131 4.3 22.6 1.0
CB C:SER132 4.4 18.6 1.0
NH1 C:ARG131 4.4 21.8 1.0
N A:SER132 4.4 18.8 1.0
CD A:ARG131 4.5 25.2 1.0
NH2 A:ARG131 4.5 21.8 1.0
CZ A:ARG131 4.5 21.2 1.0
C C:ARG131 4.5 17.0 1.0
O A:ARG131 4.5 20.1 1.0
O C:SER132 4.7 17.5 1.0
C A:ARG131 4.7 19.3 1.0
O A:SER132 4.7 17.7 1.0
C C:SER132 4.8 17.8 1.0
C A:SER132 4.8 18.6 1.0

Sodium binding site 2 out of 5 in 3hb7

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Sodium binding site 2 out of 5 in the The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:31.3
occ:1.00
 OG B:SER132 3.2 22.8 1.0
OG1 D:THR135 3.5 18.3 1.0
OG1 B:THR135 3.6 22.9 1.0
CA B:SER132 3.7 20.3 1.0
CB D:THR135 3.8 18.7 1.0
CA D:SER132 3.8 20.0 1.0
CB B:THR135 3.9 20.6 1.0
CG2 D:THR135 3.9 18.9 1.0
CB B:SER132 4.0 20.4 1.0
CG2 B:THR135 4.0 18.6 1.0
OG D:SER132 4.1 22.0 1.0
O D:ARG131 4.2 19.4 1.0
NE D:ARG131 4.2 19.3 1.0
CG D:ARG131 4.3 18.8 1.0
N B:SER132 4.3 20.4 1.0
CG B:ARG131 4.3 23.1 1.0
N D:SER132 4.3 19.7 1.0
CB D:SER132 4.3 19.6 1.0
CD B:ARG131 4.4 25.8 1.0
C D:ARG131 4.5 19.1 1.0
O B:ARG131 4.5 20.2 1.0
NH1 B:ARG131 4.6 35.8 1.0
C B:ARG131 4.6 20.9 1.0
CZ D:ARG131 4.7 15.6 1.0
NE B:ARG131 4.7 29.8 1.0
CD D:ARG131 4.7 19.2 1.0
NH2 D:ARG131 4.8 14.3 1.0
O B:SER132 4.8 18.9 1.0
C B:SER132 4.8 19.6 1.0
O D:SER132 4.8 20.8 1.0
C D:SER132 4.8 20.1 1.0
CZ B:ARG131 4.8 30.8 1.0

Sodium binding site 3 out of 5 in 3hb7

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Sodium binding site 3 out of 5 in the The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:41.6
occ:1.00
 OG1 F:THR135 3.6 22.4 1.0
OG1 E:THR135 3.6 23.9 1.0
OG F:SER132 3.6 23.6 1.0
CA F:SER132 3.8 20.8 1.0
CB F:THR135 3.8 20.1 1.0
OG E:SER132 3.9 25.7 1.0
NE F:ARG131 3.9 24.7 1.0
CA E:SER132 4.0 24.2 1.0
CB E:THR135 4.0 22.9 1.0
CD E:ARG131 4.0 26.2 1.0
CG F:ARG131 4.2 20.8 1.0
O F:ARG131 4.2 20.6 1.0
CG2 F:THR135 4.2 20.6 1.0
CB F:SER132 4.2 21.0 1.0
CG E:ARG131 4.2 25.0 1.0
N F:SER132 4.2 20.9 1.0
CG2 E:THR135 4.3 23.1 1.0
NH1 E:ARG131 4.4 27.7 1.0
C F:ARG131 4.5 20.7 1.0
CB E:SER132 4.5 24.0 1.0
N E:SER132 4.5 23.9 1.0
O E:ARG131 4.5 25.1 1.0
CZ F:ARG131 4.5 22.3 1.0
NH2 F:ARG131 4.5 23.2 1.0
CD F:ARG131 4.6 22.3 1.0
O F:SER132 4.7 19.6 1.0
C E:ARG131 4.7 24.6 1.0
C F:SER132 4.8 20.4 1.0
O E:HOH233 4.8 19.5 1.0
NE E:ARG131 4.8 28.8 1.0
O E:SER132 4.9 23.2 1.0
C E:SER132 4.9 23.6 1.0
CZ E:ARG131 5.0 28.5 1.0

Sodium binding site 4 out of 5 in 3hb7

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Sodium binding site 4 out of 5 in the The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:29.7
occ:1.00
 O F:HOH207 2.6 24.2 1.0
OG F:SER148 3.1 16.6 1.0
N B:TRP77 3.3 23.4 1.0
O B:HOH287 3.3 34.6 1.0
CB F:SER148 3.4 16.9 1.0
CA B:THR76 3.7 23.3 1.0
CB B:THR76 3.7 23.5 1.0
C F:SER148 3.9 18.1 1.0
N F:ASP149 3.9 18.1 1.0
C B:THR76 4.0 23.3 1.0
CB F:ASP149 4.0 18.5 1.0
O B:HOH210 4.0 16.9 1.0
O F:SER148 4.0 18.7 1.0
CB B:TRP77 4.1 23.1 1.0
CG2 B:THR76 4.2 22.4 1.0
CA F:ASP149 4.3 18.6 1.0
CA B:TRP77 4.3 23.3 1.0
CA F:SER148 4.3 17.2 1.0
CG F:ASP149 4.5 19.7 1.0
CG2 F:THR174 4.6 17.4 1.0
O B:GLY75 4.8 24.8 1.0
N B:THR76 4.9 23.7 1.0
OD1 F:ASP149 4.9 22.0 1.0
OG1 B:THR76 4.9 24.4 1.0

Sodium binding site 5 out of 5 in 3hb7

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Sodium binding site 5 out of 5 in the The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:49.1
occ:1.00
 OG1 G:THR135 3.2 21.3 1.0
OG H:SER132 3.5 23.9 1.0
CB G:THR135 3.7 20.1 1.0
CA H:SER132 3.7 22.4 1.0
CG2 G:THR135 3.9 20.4 1.0
OG1 H:THR135 3.9 23.9 1.0
CA G:SER132 3.9 22.4 1.0
NE G:ARG131 3.9 27.8 1.0
CB H:THR135 4.0 23.1 1.0
NE H:ARG131 4.0 25.4 1.0
CB H:SER132 4.0 22.1 1.0
CG G:ARG131 4.1 23.3 1.0
CG2 H:THR135 4.2 23.1 1.0
OG G:SER132 4.2 24.9 1.0
CG H:ARG131 4.2 23.4 1.0
N H:SER132 4.3 21.8 1.0
CB G:SER132 4.3 22.6 1.0
CD G:ARG131 4.4 26.1 1.0
O G:ARG131 4.5 22.9 1.0
N G:SER132 4.5 22.3 1.0
O H:ARG131 4.6 21.9 1.0
O H:SER132 4.6 22.3 1.0
CD H:ARG131 4.6 25.3 1.0
C H:SER132 4.7 22.2 1.0
CZ H:ARG131 4.7 25.6 1.0
CZ G:ARG131 4.7 26.8 1.0
NH2 H:ARG131 4.7 25.5 1.0
C G:ARG131 4.7 22.8 1.0
C H:ARG131 4.7 21.8 1.0
O G:SER132 4.8 21.1 1.0
NH2 G:ARG131 4.9 25.8 1.0
C G:SER132 4.9 21.4 1.0

Reference:

A.J.Stein, X.Xu, H.Cui, J.Ng, A.Edwards, A.Savchenko, A.Joachimiak. The Crystal Structure of An Isochorismatase-Like Hydrolase From Alkaliphilus Metalliredigens to 2.3A To Be Published.
Page generated: Mon Oct 7 10:22:59 2024

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