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Sodium in PDB 7rnq: Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation

Enzymatic activity of Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation

All present enzymatic activity of Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation:
4.2.1.20;

Protein crystallography data

The structure of Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation, PDB code: 7rnq was solved by P.M.Higgins, A.R.Buller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.013, 82.683, 322.558, 90, 90, 90
R / Rfree (%) 21.4 / 24.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation (pdb code 7rnq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation, PDB code: 7rnq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7rnq

Go back to Sodium Binding Sites List in 7rnq
Sodium binding site 1 out of 4 in the Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:57.6
occ:1.00
 O A:SER263 2.7 62.8 1.0
O A:TYR301 2.7 61.4 1.0
O A:GLY303 2.8 58.3 1.0
OG A:SER265 3.0 62.5 1.0
O A:HOH515 3.1 48.5 1.0
O A:GLY227 3.2 50.6 1.0
C A:TYR301 3.9 61.9 1.0
C A:SER263 3.9 63.3 1.0
CB A:SER265 3.9 62.5 1.0
C A:GLY303 3.9 59.0 1.0
CB A:SER263 4.2 64.1 1.0
C A:GLY227 4.2 48.7 1.0
N A:SER265 4.3 63.3 1.0
O A:LEU299 4.4 79.1 1.0
CB A:VAL304 4.4 56.9 1.0
CG2 A:VAL304 4.5 55.4 1.0
CA A:SER263 4.5 63.8 1.0
C A:PRO302 4.5 64.3 1.0
CB A:TYR301 4.5 58.6 1.0
N A:GLY303 4.5 62.4 1.0
OE2 A:GLU251 4.6 57.3 1.0
CA A:TYR301 4.6 60.4 1.0
N A:VAL304 4.6 57.9 1.0
O A:PRO302 4.6 65.3 1.0
CA A:VAL304 4.7 56.1 1.0
CA A:GLY227 4.7 48.5 1.0
CA A:SER265 4.7 63.3 1.0
N A:TYR301 4.8 59.6 1.0
CA A:GLY303 4.8 61.0 1.0
N A:PRO302 4.8 64.0 1.0
O A:VAL226 4.9 51.0 1.0
N A:ALA264 5.0 63.6 1.0
CA A:PRO302 5.0 65.5 1.0

Sodium binding site 2 out of 4 in 7rnq

Go back to Sodium Binding Sites List in 7rnq
Sodium binding site 2 out of 4 in the Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:22.3
occ:1.00
 O B:HOH509 2.2 43.4 1.0
O B:HOH556 2.2 30.5 1.0
O B:TYR301 2.5 33.3 0.5
O B:GLY303 2.5 30.5 1.0
O B:TYR301 2.6 33.3 0.5
O B:SER263 2.6 26.6 1.0
OG B:SER265 2.6 29.1 1.0
C B:GLY303 3.6 31.6 1.0
O B:GLY227 3.6 25.8 1.0
C B:TYR301 3.7 34.3 0.5
C B:TYR301 3.7 34.4 0.5
O B:HOH575 3.7 27.5 1.0
C B:SER263 3.8 27.2 1.0
CB B:SER265 3.8 29.3 1.0
CB B:SER263 4.0 26.9 1.0
N B:GLY303 4.0 34.0 1.0
C B:PRO302 4.1 35.1 1.0
N B:SER265 4.2 28.4 1.0
CA B:SER263 4.3 27.7 1.0
O B:PRO302 4.3 35.1 1.0
CA B:GLY303 4.4 33.4 1.0
CB B:TYR301 4.4 33.4 0.5
CB B:TYR301 4.4 33.2 0.5
C B:GLY227 4.4 25.3 1.0
CD2 B:TYR301 4.4 33.2 0.5
O B:LEU299 4.5 30.5 1.0
CA B:TYR301 4.5 34.1 0.5
CA B:TYR301 4.5 34.0 0.5
N B:VAL304 4.5 31.1 1.0
OE2 B:GLU251 4.6 27.9 1.0
N B:PRO302 4.6 35.8 1.0
CB B:VAL304 4.6 28.8 1.0
CA B:SER265 4.6 29.6 1.0
CA B:PRO302 4.7 36.2 1.0
N B:TYR301 4.7 33.2 0.5
CG B:TYR301 4.7 34.0 0.5
N B:TYR301 4.7 33.3 0.5
CA B:VAL304 4.7 29.5 1.0
N B:ALA264 4.8 27.9 1.0
CA B:GLY227 4.9 25.0 1.0

Sodium binding site 3 out of 4 in 7rnq

Go back to Sodium Binding Sites List in 7rnq
Sodium binding site 3 out of 4 in the Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:47.8
occ:1.00
 O C:HOH518 2.3 42.1 1.0
O C:GLY303 2.6 47.2 1.0
O C:TYR301 2.7 63.2 1.0
O C:SER263 2.7 58.4 1.0
OG C:SER265 2.9 56.5 1.0
O C:GLY227 3.4 41.2 1.0
C C:GLY303 3.7 47.1 1.0
CB C:SER265 3.8 56.3 1.0
C C:SER263 3.9 59.1 1.0
C C:TYR301 3.9 63.7 1.0
CB C:SER263 4.1 60.4 1.0
N C:SER265 4.2 57.8 1.0
C C:PRO302 4.2 52.8 1.0
N C:GLY303 4.3 50.7 1.0
O C:PRO302 4.3 53.5 1.0
C C:GLY227 4.3 40.1 1.0
O C:LEU299 4.4 59.1 1.0
CA C:SER263 4.4 60.1 1.0
OE2 C:GLU251 4.5 47.0 1.0
CB C:VAL304 4.6 44.2 1.0
CA C:GLY303 4.6 49.3 1.0
CA C:SER265 4.6 57.5 1.0
N C:VAL304 4.7 45.6 1.0
CA C:TYR301 4.7 63.6 1.0
CA C:GLY227 4.7 40.0 1.0
CB C:TYR301 4.7 64.7 1.0
O C:VAL226 4.7 40.6 1.0
CD2 C:TYR301 4.8 68.1 1.0
N C:TYR301 4.8 61.9 1.0
N C:PRO302 4.8 53.4 1.0
CA C:VAL304 4.8 43.8 1.0
CA C:PRO302 4.8 54.5 1.0
N C:ALA264 4.9 59.3 1.0

Sodium binding site 4 out of 4 in 7rnq

Go back to Sodium Binding Sites List in 7rnq
Sodium binding site 4 out of 4 in the Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Holo Structure of Engineered Trpb, 2B9-H275E, From Pyrococcus Furiosus in the Extended-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:52.5
occ:1.00
 O D:HOH523 2.3 44.0 1.0
O D:GLY303 2.6 53.5 1.0
O D:TYR301 2.7 66.4 1.0
O D:SER263 2.8 65.0 1.0
OG D:SER265 2.9 66.0 1.0
O D:GLY227 3.3 48.8 1.0
C D:TYR301 3.7 67.3 1.0
C D:GLY303 3.8 54.0 1.0
CB D:SER265 3.9 66.4 1.0
C D:SER263 3.9 65.8 1.0
CB D:SER263 4.2 65.6 1.0
C D:GLY227 4.2 47.4 1.0
CB D:TYR301 4.3 66.5 0.6
O D:LEU299 4.3 63.6 1.0
N D:SER265 4.3 66.6 1.0
CB D:TYR301 4.3 66.4 0.4
N D:GLY303 4.4 56.8 1.0
C D:PRO302 4.4 57.9 1.0
CA D:TYR301 4.4 67.2 0.6
CA D:TYR301 4.4 67.1 0.4
O D:PRO302 4.5 58.5 1.0
CA D:SER263 4.5 66.3 1.0
CB D:VAL304 4.6 51.5 1.0
N D:TYR301 4.6 66.6 1.0
N D:VAL304 4.6 53.2 1.0
CA D:GLY227 4.7 46.7 1.0
CA D:GLY303 4.7 55.9 1.0
CD2 D:TYR301 4.7 66.2 0.6
CA D:VAL304 4.7 51.5 1.0
CA D:SER265 4.8 67.3 1.0
N D:PRO302 4.8 57.2 1.0
OE2 D:GLU251 4.8 53.4 1.0
CG D:TYR301 4.8 67.0 0.6
O D:VAL226 4.9 47.3 1.0
CG2 D:VAL304 4.9 50.1 1.0
CA D:PRO302 4.9 58.8 1.0

Reference:

P.M.Higgins, A.R.Buller. Direct Assessment of Promiscuity During Protein Engineering By Substrate Multiplexed Screening To Be Published.
Page generated: Mon Aug 18 11:42:21 2025

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