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Chlorine in PDB 4brk: Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp

Enzymatic activity of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp

All present enzymatic activity of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp, PDB code: 4brk was solved by M.Zebisch, P.Schaefer, P.Lauble, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.43 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.600, 82.967, 109.578, 90.00, 90.00, 90.00
R / Rfree (%) 12.877 / 17.791

Other elements in 4brk:

The structure of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp (pdb code 4brk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp, PDB code: 4brk:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4brk

Go back to Chlorine Binding Sites List in 4brk
Chlorine binding site 1 out of 3 in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1399

b:11.5
occ:1.00
 O A:HOH2113 3.2 27.1 1.0
N B:GLN89 3.3 12.9 1.0
N A:GLN89 3.4 12.4 1.0
NE2 B:GLN89 3.4 14.0 1.0
NE2 A:GLN89 3.4 15.2 1.0
CG A:GLN89 3.6 11.7 1.0
CG B:GLN89 3.8 13.5 1.0
CA A:ILE88 3.9 12.0 1.0
CG2 B:THR94 3.9 13.0 1.0
CA B:ILE88 3.9 12.5 1.0
CG2 A:THR94 4.0 16.8 1.0
CB A:ILE88 4.0 12.4 1.0
CB A:GLN89 4.0 11.6 1.0
CB B:GLN89 4.0 15.1 1.0
CD A:GLN89 4.0 13.3 1.0
CB B:ILE88 4.0 12.8 1.0
CD B:GLN89 4.1 14.2 1.0
C B:ILE88 4.1 13.4 1.0
C A:ILE88 4.2 12.4 1.0
CA A:GLN89 4.3 12.8 1.0
CA B:GLN89 4.3 12.5 1.0
O A:HOH2092 4.6 16.6 1.0
CG2 A:ILE88 4.6 12.0 1.0
CG2 B:ILE88 4.7 14.8 1.0
OG1 B:THR94 4.8 20.6 1.0
OG1 A:THR94 4.8 16.5 1.0
O A:HOH2091 4.8 18.1 1.0

Chlorine binding site 2 out of 3 in 4brk

Go back to Chlorine Binding Sites List in 4brk
Chlorine binding site 2 out of 3 in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1400

b:15.8
occ:0.50
 CG A:ASP253 0.6 13.3 0.5
OD2 A:ASP253 1.0 16.5 0.5
OD1 A:ASP253 1.2 16.7 0.5
CB A:ASP253 2.1 12.7 0.5
O A:HOH2278 3.0 10.7 1.0
CA A:ASP253 3.1 12.0 0.5
O A:HOH2276 3.2 34.6 1.0
CA A:ASP253 3.2 14.6 0.5
CB A:ASP253 3.3 13.3 0.5
N B:GLY156 3.3 8.1 1.0
NE B:ARG122 3.4 20.3 1.0
N A:ASP253 3.5 12.1 1.0
ND2 A:ASN240 3.6 10.6 1.0
O A:HOH2258 3.7 23.2 1.0
CD B:ARG122 3.7 19.6 1.0
CA B:GLY156 3.8 8.2 1.0
C A:PRO252 3.9 12.6 1.0
CZ B:ARG122 4.1 14.0 1.0
O A:PRO252 4.1 17.9 1.0
NH2 B:ARG122 4.3 9.9 1.0
C B:THR155 4.4 8.1 1.0
CG A:ASN240 4.5 10.3 1.0
CB A:PRO252 4.5 13.5 1.0
OD1 A:ASN240 4.5 10.8 1.0
C A:ASP253 4.6 13.8 1.0
OG B:SER225 4.6 8.6 1.0
CA B:THR155 4.6 8.2 1.0
CB B:SER225 4.7 7.5 1.0
CG A:ASP253 4.7 13.2 0.5
CB B:THR155 4.8 9.5 1.0
CA A:PRO252 4.9 12.4 1.0
CD2 B:LEU227 4.9 8.9 1.0
CB B:LEU227 4.9 8.0 1.0
C B:GLY156 4.9 6.9 1.0

Chlorine binding site 3 out of 3 in 4brk

Go back to Chlorine Binding Sites List in 4brk
Chlorine binding site 3 out of 3 in the Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Legionella Pneumophila NTPDASE1 N302Y Variant Crystal Form III (Closed) in Complex with Mg Umppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1396

b:14.1
occ:1.00
 O A:HOH2191 2.9 18.7 1.0
O A:HOH2134 3.1 10.9 1.0
O A:HOH2190 3.2 22.9 1.0
ND2 B:ASN240 3.4 13.6 1.0
CD A:ARG122 3.6 16.9 1.0
N B:ASP253 3.8 10.5 1.0
CA B:ASP253 3.8 12.8 1.0
C B:PRO252 3.9 10.5 1.0
CB B:ASP253 3.9 15.5 1.0
CB B:PRO252 4.1 11.9 1.0
O B:PRO252 4.1 12.6 1.0
CB A:LEU227 4.1 7.9 1.0
CD2 A:LEU227 4.3 7.4 1.0
CG B:ASN240 4.3 8.4 1.0
NE A:ARG122 4.3 20.2 1.0
OD1 B:ASN240 4.4 9.7 1.0
CA B:PRO252 4.6 10.0 1.0
NH1 A:ARG122 4.7 8.9 1.0
N A:GLY156 4.7 8.5 1.0
CG A:LEU227 4.7 7.1 1.0
CG B:PRO252 4.9 12.0 1.0
CA A:GLY156 4.9 9.9 1.0
CG A:ARG122 4.9 14.9 1.0
CZ A:ARG122 4.9 10.3 1.0
OG A:SER225 4.9 9.9 1.0
O A:SER225 5.0 10.8 1.0
O A:HOH2192 5.0 19.2 1.0

Reference:

M.Zebisch, M.Krauss, P.Schaefer, P.Lauble, N.Straeter. Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases Structure V. 21 1460 2013.
ISSN: ISSN 0969-2126
PubMed: 23830739
DOI: 10.1016/J.STR.2013.05.016
Page generated: Sat Dec 12 10:27:20 2020

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