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Sodium in PDB 6qf3: X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip

Enzymatic activity of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip

All present enzymatic activity of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip:
3.4.24.27;

Protein crystallography data

The structure of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip, PDB code: 6qf3 was solved by J.Lieske, M.Cerv, S.Kreida, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.58 / 1.52
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.154, 93.154, 129.294, 90.00, 90.00, 120.00
R / Rfree (%) 12.3 / 15

Other elements in 6qf3:

The structure of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip (pdb code 6qf3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip, PDB code: 6qf3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6qf3

Go back to Sodium Binding Sites List in 6qf3
Sodium binding site 1 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:20.7
occ:1.00
 O A:HOH525 2.0 18.2 1.0
HO1 A:EDO419 2.2 45.0 1.0
O A:HOH842 2.3 32.6 1.0
O A:HOH866 2.4 30.0 1.0
O1 A:EDO419 2.5 37.5 1.0
O A:HOH541 2.5 17.3 1.0
O A:TYR211 2.5 17.2 1.0
H12 A:EDO419 2.9 41.9 1.0
HB3 A:TYR211 3.1 15.6 1.0
O A:HOH688 3.1 31.1 1.0
C1 A:EDO419 3.2 34.9 1.0
C A:TYR211 3.7 16.1 1.0
O A:HOH761 3.8 28.2 1.0
CB A:TYR211 3.9 13.0 1.0
O A:HOH543 3.9 38.6 1.0
HB2 A:TYR211 4.0 15.6 1.0
H21 A:EDO419 4.0 52.6 1.0
H11 A:EDO419 4.0 41.9 1.0
O A:HOH690 4.0 36.3 1.0
OD1 A:ASP213 4.1 13.9 1.0
C2 A:EDO419 4.2 43.8 1.0
O A:HOH858 4.3 35.2 1.0
CA A:TYR211 4.3 12.7 1.0
OD2 A:ASP213 4.4 13.4 1.0
HA3 A:GLY212 4.5 17.5 1.0
O A:LEU202 4.5 13.1 1.0
CG A:ASP213 4.5 13.2 1.0
HA A:TYR211 4.5 15.3 1.0
O A:HOH896 4.6 33.8 1.0
N A:GLY212 4.7 14.0 1.0
H22 A:EDO419 4.9 52.6 1.0
CA A:GLY212 5.0 14.6 1.0

Sodium binding site 2 out of 4 in 6qf3

Go back to Sodium Binding Sites List in 6qf3
Sodium binding site 2 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:23.0
occ:1.00
 HB2 A:ASP427 1.9 44.1 0.9
H A:TRP115 2.1 13.5 1.0
OD2 A:ASP427 2.4 41.0 0.9
CB A:ASP427 2.5 36.7 0.9
HA A:ASP427 2.5 41.1 0.9
CA A:ASP427 2.6 34.2 0.9
HB2 A:PHE114 2.8 10.9 1.0
H11 A:EDO421 2.8 43.6 1.0
CG A:ASP427 2.8 35.7 0.9
HA A:PHE114 2.8 11.4 1.0
N A:ASP427 2.9 22.6 0.9
N A:TRP115 3.0 11.3 1.0
H21 A:EDO421 3.0 36.7 1.0
H22 A:EDO421 3.0 36.7 1.0
OE1 A:GLU143 3.1 13.6 0.4
HD2 A:HIS146 3.3 11.4 1.0
C2 A:EDO421 3.3 30.6 1.0
HB3 A:TRP115 3.3 15.2 1.0
HB3 A:ASP427 3.4 44.1 0.9
CB A:PHE114 3.4 9.1 1.0
CA A:PHE114 3.4 9.5 1.0
O A:TRP115 3.5 13.8 1.0
C1 A:EDO421 3.6 36.4 1.0
HB3 A:PHE114 3.6 10.9 1.0
CD2 A:HIS146 3.6 9.5 1.0
C A:PHE114 3.7 10.2 1.0
OE1 A:GLU143 3.8 11.0 0.6
CA A:TRP115 3.9 11.0 1.0
CB A:TRP115 4.0 12.7 1.0
OD1 A:ASP427 4.1 39.4 0.9
NE2 A:HIS146 4.1 8.5 1.0
C A:ASP427 4.1 28.9 0.9
C A:TRP115 4.1 14.1 1.0
CD A:GLU143 4.2 12.9 0.4
H12 A:EDO421 4.3 43.6 1.0
CG A:HIS146 4.4 10.2 1.0
HB2 A:TRP115 4.4 15.2 1.0
O1 A:EDO421 4.5 44.0 1.0
OE2 A:GLU143 4.5 14.2 0.4
ZN A:ZN401 4.6 11.1 1.0
HB2 A:HIS146 4.7 10.7 1.0
O A:ASP427 4.7 17.1 0.9
O A:ALA113 4.7 11.1 1.0
HD2 A:PHE114 4.7 13.9 1.0
O2 A:EDO421 4.7 46.4 1.0
N A:PHE114 4.8 8.7 1.0
HA A:TRP115 4.8 13.2 1.0
HB3 A:HIS146 4.8 10.7 1.0
CG A:PHE114 4.8 9.8 1.0
HA A:GLU143 4.8 10.4 1.0
CB A:HIS146 4.9 8.9 1.0
OXT A:ASP427 4.9 30.2 0.9
CE1 A:HIS146 4.9 10.8 1.0
O A:PHE114 4.9 11.0 1.0
CD A:GLU143 4.9 10.0 0.6
HO1 A:EDO421 5.0 52.8 1.0

Sodium binding site 3 out of 4 in 6qf3

Go back to Sodium Binding Sites List in 6qf3
Sodium binding site 3 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:36.2
occ:0.79
 O A:HOH737 2.3 41.9 1.0
OG A:SER279 2.6 12.7 1.0
HA A:SER279 2.9 11.3 1.0
HB3 A:GLN283 3.0 13.7 1.0
HG A:SER279 3.1 15.2 1.0
O A:HOH755 3.1 28.6 1.0
OG1 A:THR276 3.3 17.4 1.0
CB A:SER279 3.5 10.1 1.0
OE1 A:GLN283 3.6 14.4 1.0
CA A:SER279 3.6 9.4 1.0
CD A:GLN283 3.6 17.3 1.0
H A:THR276 3.6 13.3 1.0
HB3 A:SER279 3.7 12.1 1.0
HG23 A:THR276 3.7 19.8 1.0
HG1 A:THR276 3.7 20.8 1.0
CB A:GLN283 3.8 11.4 1.0
HB2 A:GLN283 3.9 13.7 1.0
NE2 A:GLN283 4.0 25.1 1.0
N A:SER279 4.1 9.6 1.0
CG A:GLN283 4.1 15.2 1.0
HE22 A:GLN283 4.1 30.2 1.0
HA A:LEU275 4.1 10.8 1.0
H A:SER279 4.1 11.5 1.0
HG2 A:GLN283 4.2 18.2 1.0
N A:THR276 4.2 11.1 1.0
CB A:THR276 4.3 14.1 1.0
CG2 A:THR276 4.3 16.5 1.0
HG21 A:THR276 4.3 19.8 1.0
O A:HOH630 4.3 20.3 1.0
HE21 A:GLN283 4.3 30.2 1.0
HB2 A:SER279 4.4 12.1 1.0
H A:ASN280 4.6 12.5 1.0
O A:TYR274 4.6 13.5 1.0
HD23 A:LEU275 4.8 13.9 1.0
CA A:THR276 4.8 9.6 1.0
C A:THR278 4.9 12.5 1.0
C A:SER279 4.9 9.4 1.0
CA A:LEU275 5.0 9.0 1.0

Sodium binding site 4 out of 4 in 6qf3

Go back to Sodium Binding Sites List in 6qf3
Sodium binding site 4 out of 4 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:23.3
occ:0.74
 OD1 A:ASP150 2.1 15.0 0.5
HD21 A:ASN165 2.3 12.4 1.0
HD1 A:HIS146 2.8 12.8 1.0
HB3 A:HIS146 2.9 10.7 1.0
O A:HIS146 2.9 9.7 1.0
CG A:ASP150 2.9 18.1 0.5
O2 A:EDO421 3.0 46.4 1.0
HO2 A:EDO421 3.0 55.6 1.0
OD1 A:ASP150 3.0 18.9 0.5
ND2 A:ASN165 3.1 10.3 1.0
HA A:HIS146 3.1 9.9 1.0
HB A:THR149 3.2 11.4 1.0
OD2 A:ASP150 3.3 20.7 0.5
ND1 A:HIS146 3.4 10.7 1.0
OD1 A:ASN165 3.5 11.9 1.0
CB A:HIS146 3.5 8.9 1.0
CA A:HIS146 3.6 8.2 1.0
C A:HIS146 3.6 8.3 1.0
H A:ASP150 3.6 13.3 0.5
O A:HOH508 3.7 32.1 1.0
H22 A:EDO421 3.7 36.7 1.0
CG A:ASN165 3.7 10.5 1.0
HG22 A:THR149 3.7 12.7 1.0
HD22 A:ASN165 3.7 12.4 1.0
H A:ASP150 3.8 12.9 0.5
H12 A:EDO421 3.8 43.6 1.0
C2 A:EDO421 3.9 30.6 1.0
CG A:HIS146 3.9 10.2 1.0
HG21 A:THR149 3.9 12.7 1.0
O A:HOH843 3.9 25.0 1.0
CB A:THR149 4.0 9.5 1.0
CG A:ASP150 4.0 17.9 0.5
N A:ASP150 4.0 11.1 0.5
CG2 A:THR149 4.1 10.6 1.0
N A:ASP150 4.1 10.7 0.5
O A:HOH503 4.1 32.4 1.0
CB A:ASP150 4.2 15.6 0.5
HA A:ASP150 4.3 16.7 0.5
C1 A:EDO421 4.4 36.4 1.0
HB2 A:HIS146 4.4 10.7 1.0
HA A:ASP150 4.4 12.7 0.5
O A:HOH634 4.5 10.1 1.0
CA A:ASP150 4.5 10.6 0.5
HB2 A:ASP150 4.5 18.7 0.5
CA A:ASP150 4.5 13.9 0.5
CE1 A:HIS146 4.6 10.8 1.0
HD1 A:TRP115 4.6 20.1 1.0
C A:THR149 4.7 10.4 1.0
CB A:ASP150 4.7 14.9 0.5
HB2 A:ASP150 4.7 17.9 0.5
H21 A:EDO421 4.8 36.7 1.0
OD2 A:ASP150 4.8 16.9 0.5
HG1 A:THR149 4.8 12.7 1.0
N A:ALA147 4.8 9.0 1.0
CA A:THR149 4.9 8.8 1.0
O A:HOH559 4.9 29.8 1.0
HE1 A:HIS146 4.9 13.0 1.0
HD1 A:TYR157 4.9 15.6 1.0
HB3 A:ASP150 4.9 18.7 0.5
OG1 A:THR149 5.0 10.6 1.0
N A:HIS146 5.0 9.3 1.0
H A:THR149 5.0 10.4 1.0
O1 A:EDO421 5.0 44.0 1.0

Reference:

J.Lieske, M.Cerv, S.Kreida, D.Komadina, J.Fischer, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents. On-Chip Crystallization For Serial Crystallography Experiments and on-Chip Ligand-Binding Studies. Iucrj V. 6 714 2019.
ISSN: ESSN 2052-2525
PubMed: 31316815
DOI: 10.1107/S2052252519007395
Page generated: Tue Oct 8 12:53:21 2024

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