Atomistry » Sodium » PDB 7rc3-7rsv » 7rnp
Atomistry »
  Sodium »
    PDB 7rc3-7rsv »
      7rnp »

Sodium in PDB 7rnp: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound:
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound, PDB code: 7rnp 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 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.162, 81.198, 321.014, 90, 90, 90
R / Rfree (%) 22.7 / 26.7

Other elements in 7rnp:

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound (pdb code 7rnp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound, PDB code: 7rnp:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 1 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:47.4
occ:1.00
 O A:SER263 2.6 51.8 1.0
O A:GLY303 2.6 50.2 1.0
O A:TYR301 2.7 55.6 1.0
OG A:SER265 3.0 53.4 1.0
O A:GLY227 3.2 46.5 1.0
C A:GLY303 3.7 51.1 1.0
C A:SER263 3.8 51.4 1.0
C A:TYR301 3.8 56.2 1.0
CB A:SER263 4.0 51.7 1.0
CB A:SER265 4.0 53.2 1.0
OE2 A:GLU251 4.1 62.1 1.0
C A:GLY227 4.2 46.0 1.0
N A:GLY303 4.3 53.9 1.0
N A:SER265 4.3 52.8 1.0
O A:LEU299 4.3 61.0 1.0
CA A:SER263 4.4 51.5 1.0
C A:PRO302 4.4 55.1 1.0
CB A:TYR301 4.6 55.7 1.0
CA A:GLY227 4.6 44.5 1.0
CA A:GLY303 4.6 53.2 1.0
CA A:TYR301 4.6 56.2 1.0
O A:PRO302 4.6 56.4 1.0
N A:VAL304 4.6 50.3 1.0
CB A:VAL304 4.6 49.1 1.0
N A:TYR301 4.7 55.0 1.0
O A:VAL226 4.7 47.4 1.0
CA A:VAL304 4.8 49.2 1.0
CA A:SER265 4.8 53.5 1.0
N A:PRO302 4.8 55.8 1.0
CD2 A:TYR301 4.8 57.1 1.0
N A:ALA264 4.9 51.7 1.0
CA A:PRO302 4.9 56.2 1.0
CD A:GLU251 5.0 59.0 1.0

Sodium binding site 2 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 2 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:64.1
occ:1.00
 O B:TYR301 2.5 75.4 1.0
O B:GLY303 2.6 70.5 1.0
O B:SER263 2.6 94.9 1.0
O B:GLY227 2.9 69.9 1.0
OG B:SER265 3.1 80.9 1.0
C B:TYR301 3.6 76.7 1.0
C B:GLY303 3.8 69.2 1.0
C B:SER263 3.8 93.5 1.0
OE2 B:GLU251 3.9 100.3 1.0
C B:GLY227 4.0 66.1 1.0
CB B:SER265 4.1 81.6 1.0
CB B:TYR301 4.2 73.1 1.0
CB B:SER263 4.2 93.3 1.0
N B:GLY303 4.2 73.3 1.0
CA B:TYR301 4.3 75.3 1.0
O B:LEU299 4.3 71.7 1.0
C B:PRO302 4.3 75.9 1.0
N B:SER265 4.4 83.2 1.0
CA B:GLY227 4.4 64.4 1.0
N B:TYR301 4.4 75.8 1.0
CA B:SER263 4.5 93.0 1.0
O B:PRO302 4.6 76.2 1.0
CA B:GLY303 4.6 72.1 1.0
N B:PRO302 4.6 77.3 1.0
CD2 B:TYR301 4.6 71.8 1.0
N B:VAL304 4.7 67.5 1.0
O B:VAL226 4.7 64.1 1.0
CD B:GLU251 4.8 99.0 1.0
CG B:TYR301 4.8 73.2 1.0
CA B:PRO302 4.8 78.5 1.0
CB B:VAL304 4.9 65.9 1.0
CA B:VAL304 4.9 65.7 1.0
CA B:SER265 4.9 82.9 1.0
N B:ALA264 4.9 83.0 1.0

Sodium binding site 3 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 3 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:71.2
occ:1.00
 O C:TYR301 2.6 77.0 1.0
O C:SER263 2.6 76.3 1.0
O C:GLY303 2.6 72.6 1.0
O C:GLY227 3.0 63.1 1.0
OG C:SER265 3.2 77.5 1.0
OE2 C:GLU251 3.4 74.5 1.0
C C:TYR301 3.7 79.5 1.0
C C:SER263 3.8 78.7 1.0
C C:GLY303 3.9 72.6 1.0
C C:GLY227 4.0 60.7 1.0
CB C:SER265 4.0 77.6 1.0
N C:SER265 4.2 78.2 1.0
O C:LEU299 4.2 72.7 1.0
CB C:TYR301 4.2 76.4 1.0
CB C:SER263 4.3 81.1 1.0
CD C:GLU251 4.4 73.0 1.0
CA C:TYR301 4.4 78.8 1.0
CA C:GLY227 4.4 61.2 1.0
O C:VAL226 4.6 63.1 1.0
C C:PRO302 4.6 80.6 1.0
CB C:VAL304 4.6 68.5 1.0
CA C:SER263 4.6 80.6 1.0
N C:GLY303 4.6 78.0 1.0
CD2 C:TYR301 4.6 75.5 1.0
N C:TYR301 4.6 78.1 1.0
N C:VAL304 4.7 71.1 1.0
O C:PRO302 4.7 81.1 1.0
CA C:VAL304 4.8 68.3 1.0
CA C:SER265 4.8 78.3 1.0
N C:PRO302 4.8 81.8 1.0
CG2 C:VAL304 4.8 66.5 1.0
CA C:GLY303 4.8 76.0 1.0
CG C:TYR301 4.9 77.8 1.0
CG C:GLU251 4.9 69.1 1.0
N C:ALA264 4.9 78.7 1.0

Sodium binding site 4 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 4 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:80.4
occ:1.00
 O D:SER263 2.6 86.2 1.0
O D:GLY303 2.8 79.4 1.0
O D:TYR301 2.9 85.3 1.0
O D:GLY227 3.0 70.3 1.0
OG D:SER265 3.7 89.3 1.0
C D:SER263 3.9 86.8 1.0
OE2 D:GLU251 4.0 85.7 1.0
C D:GLY303 4.0 79.4 1.0
C D:TYR301 4.0 86.2 1.0
C D:GLY227 4.1 69.3 1.0
O D:LEU299 4.1 82.7 1.0
CB D:TYR301 4.3 84.0 1.0
N D:SER265 4.3 91.1 1.0
CB D:SER265 4.3 89.6 1.0
CA D:GLY227 4.5 69.6 1.0
O D:VAL226 4.5 74.8 1.0
CA D:TYR301 4.5 85.3 1.0
CB D:SER263 4.5 87.8 1.0
N D:TYR301 4.6 85.5 1.0
CD D:GLU251 4.6 84.9 1.0
N D:GLY303 4.7 82.8 1.0
CB D:VAL304 4.7 76.1 1.0
CA D:SER263 4.7 87.8 1.0
C D:PRO302 4.8 85.7 1.0
CD2 D:TYR301 4.8 83.9 1.0
N D:ALA264 4.8 88.2 1.0
N D:VAL304 4.8 77.6 1.0
CA D:GLY303 4.9 81.7 1.0
CG D:GLU251 4.9 81.3 1.0
CA D:VAL304 4.9 74.4 1.0
O D:PRO302 4.9 87.2 1.0
CA D:ALA264 4.9 90.6 1.0
CA D:SER265 5.0 90.3 1.0
CG D:TYR301 5.0 85.0 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 11:42:11 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy