Atomistry » Sodium » PDB 3h0n-3hwd » 3hb7
Atomistry »
  Sodium »
    PDB 3h0n-3hwd »
      3hb7 »

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

Go back to Sodium Binding Sites List in 3hb7
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

Go back to Sodium Binding Sites List in 3hb7
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

Go back to Sodium Binding Sites List in 3hb7
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

Go back to Sodium Binding Sites List in 3hb7
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

Go back to Sodium Binding Sites List in 3hb7
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: Tue Dec 15 06:13:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy