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Chlorine in PDB 4brl: Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate, PDB code: 4brl 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) 19.88 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.994, 83.463, 109.289, 90.00, 90.00, 90.00
R / Rfree (%) 14.416 / 19.773

Other elements in 4brl:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Vanadium (V) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate (pdb code 4brl). 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 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate, PDB code: 4brl:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4brl

Go back to Chlorine Binding Sites List in 4brl
Chlorine binding site 1 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate


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 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1397

b:29.5
occ:1.00
NE2 B:GLN89 3.5 27.3 1.0
NE2 A:GLN89 3.5 23.7 1.0
N B:GLN89 3.5 31.9 1.0
N A:GLN89 3.5 26.1 1.0
CG B:GLN89 3.6 30.3 1.0
CG A:GLN89 3.8 27.9 1.0
CA B:ILE88 3.9 32.5 1.0
CA A:ILE88 4.0 25.6 1.0
CD B:GLN89 4.0 30.6 1.0
CB B:ILE88 4.1 28.7 1.0
CG2 A:THR94 4.1 28.2 1.0
CB A:ILE88 4.1 23.3 1.0
CD A:GLN89 4.1 24.4 1.0
CB A:GLN89 4.2 31.0 1.0
C B:ILE88 4.2 31.3 1.0
CB B:GLN89 4.2 31.4 1.0
C A:ILE88 4.3 27.1 1.0
CA A:GLN89 4.4 25.8 1.0
CA B:GLN89 4.5 25.7 1.0
O A:HOH2052 4.6 37.0 1.0
CG2 A:ILE88 4.6 23.5 1.0
CG2 B:ILE88 4.7 32.6 1.0
O A:HOH2051 4.7 29.5 1.0
O B:SER87 5.0 32.4 1.0
CG2 B:THR94 5.0 29.3 1.0

Chlorine binding site 2 out of 3 in 4brl

Go back to Chlorine Binding Sites List in 4brl
Chlorine binding site 2 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate


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 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1398

b:28.8
occ:1.00
O A:HOH2161 2.9 31.3 1.0
O B:HOH2063 3.1 17.4 1.0
ND2 A:ASN240 3.2 22.1 1.0
O B:HOH2085 3.3 25.4 0.5
CD B:ARG122 3.5 22.8 1.0
N A:ASP253 3.7 21.0 1.0
CB A:ASP253 3.8 26.7 1.0
CA A:ASP253 3.8 22.2 1.0
C A:PRO252 3.8 21.1 1.0
O A:PRO252 4.0 22.9 1.0
CB A:PRO252 4.1 24.2 1.0
CG A:ASN240 4.2 19.3 1.0
NE B:ARG122 4.3 30.8 1.0
OD1 A:ASN240 4.4 18.7 1.0
N B:GLY156 4.4 19.3 1.0
CD2 B:LEU227 4.4 18.0 1.0
CB B:LEU227 4.4 16.6 1.0
CA A:PRO252 4.6 24.2 1.0
CA B:GLY156 4.6 19.1 1.0
O B:HOH2085 4.6 22.0 0.5
CG A:PRO252 4.7 20.0 1.0
NH1 B:ARG122 4.8 18.5 1.0
CG B:ARG122 4.9 18.5 1.0
CG B:LEU227 4.9 13.8 1.0
CZ B:ARG122 4.9 22.4 1.0
OG B:SER225 4.9 17.2 1.0

Chlorine binding site 3 out of 3 in 4brl

Go back to Chlorine Binding Sites List in 4brl
Chlorine binding site 3 out of 3 in the Legionella Pneumophila NTPDASE1 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate


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 Crystal Form III (Closed) in Complex with Transition State Mimic Guanosine 5'-Phosphovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1395

b:32.3
occ:1.00
O A:HOH2075 3.1 16.6 1.0
CB B:ASP253 3.2 37.1 1.0
CA B:ASP253 3.2 26.2 1.0
N B:ASP253 3.4 19.3 1.0
ND2 B:ASN240 3.4 17.9 1.0
N A:GLY156 3.5 13.6 1.0
NE A:ARG122 3.5 26.4 1.0
CD A:ARG122 3.7 26.0 1.0
O A:HOH2134 3.7 33.4 1.0
C B:PRO252 3.8 21.3 1.0
CA A:GLY156 4.0 16.0 1.0
O B:PRO252 4.0 23.4 1.0
CB B:PRO252 4.3 20.3 1.0
CZ A:ARG122 4.3 19.4 1.0
CG B:ASN240 4.3 16.9 1.0
OD1 B:ASN240 4.4 16.8 1.0
NH2 A:ARG122 4.6 17.6 1.0
C A:THR155 4.6 14.8 1.0
C B:ASP253 4.7 19.6 1.0
CG B:ASP253 4.7 33.4 1.0
OG A:SER225 4.7 14.3 1.0
CA B:PRO252 4.7 17.4 1.0
CD2 A:LEU227 4.7 16.5 1.0
CB A:SER225 4.8 16.6 1.0
CA A:THR155 4.8 15.8 1.0
CB A:LEU227 4.9 14.5 1.0
CB A:THR155 5.0 16.5 1.0
CG A:ARG122 5.0 15.8 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: Wed Oct 28 11:36:37 2020

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