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Chlorine in PDB 5nx9: Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate

Enzymatic activity of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate

All present enzymatic activity of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate:
4.3.2.2;

Protein crystallography data

The structure of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate, PDB code: 5nx9 was solved by B.Van Laer, U.Kapp, M.Soler-Lopez, G.Leonard, C.Mueller-Dieckmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.740, 107.490, 209.660, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate (pdb code 5nx9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate, PDB code: 5nx9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5nx9

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Chlorine binding site 1 out of 6 in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:49.1
occ:1.00
 O A:HOH621 2.8 28.9 1.0
N A:THR201 3.3 33.0 1.0
OG1 A:THR201 3.3 47.3 1.0
OG A:SER207 3.4 45.2 1.0
N A:SER207 3.4 32.8 1.0
CA A:GLY200 3.6 29.5 1.0
CB A:SER207 3.7 35.4 1.0
N A:ALA206 3.8 30.9 1.0
C A:GLY200 3.9 30.1 1.0
CG B:GLN164 4.0 59.2 1.0
CB A:ALA206 4.0 30.5 1.0
CA A:SER207 4.1 33.0 1.0
CA A:ALA206 4.2 30.8 1.0
CB A:THR201 4.3 38.4 1.0
C A:ALA206 4.3 30.5 1.0
CA A:THR201 4.3 38.5 1.0
C A:GLN205 4.5 32.3 1.0
CB B:GLN164 4.6 52.5 1.0
CG2 A:THR201 4.6 41.7 1.0
NE2 B:GLN164 4.6 74.9 1.0
OG1 A:THR204 4.6 27.3 1.0
N A:THR202 4.8 35.1 1.0
N A:GLN205 4.8 28.2 1.0
CD B:GLN164 4.8 69.9 1.0
CA A:GLN205 4.9 30.4 1.0
N A:GLY200 5.0 28.9 1.0

Chlorine binding site 2 out of 6 in 5nx9

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Chlorine binding site 2 out of 6 in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:28.0
occ:1.00
 N A:GLY200 3.2 28.9 1.0
NH1 A:ARG196 3.3 29.5 1.0
N A:LYS199 3.4 32.6 1.0
N A:THR111 3.5 34.0 1.0
NH2 A:ARG196 3.6 27.6 1.0
CB A:TYR114 3.7 27.9 1.0
CG2 A:THR111 3.8 36.5 1.0
CA A:GLY200 3.8 29.5 1.0
CA A:ALA110 3.9 32.5 1.0
CZ A:ARG196 3.9 27.7 1.0
CE2 A:PHE208 4.0 36.5 1.0
CA A:VAL198 4.1 29.2 1.0
CB A:ALA110 4.1 31.5 1.0
C A:LYS199 4.1 28.4 1.0
C A:VAL198 4.2 31.3 1.0
CA A:LYS199 4.2 30.1 1.0
C A:ALA110 4.3 31.5 1.0
CZ A:PHE208 4.3 35.0 1.0
O A:THR111 4.3 30.2 1.0
CA A:TYR114 4.4 27.7 1.0
C A:GLY200 4.4 30.1 1.0
O A:GLY200 4.4 28.4 1.0
N A:TYR114 4.5 30.5 1.0
CA A:THR111 4.5 32.1 1.0
CG A:TYR114 4.5 28.7 1.0
CB A:VAL198 4.6 31.6 1.0
CB A:THR111 4.6 33.0 1.0
CD1 A:TYR114 4.6 28.7 1.0
O A:GLY197 4.7 27.0 1.0
C A:THR111 4.8 29.9 1.0
CB A:LYS199 4.9 31.8 1.0
O A:GLY109 5.0 28.7 1.0

Chlorine binding site 3 out of 6 in 5nx9

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Chlorine binding site 3 out of 6 in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:24.1
occ:1.00
 N B:GLY200 3.2 26.8 1.0
NH1 B:ARG196 3.3 26.0 1.0
N B:LYS199 3.4 26.7 1.0
N B:THR111 3.5 27.7 1.0
NH2 B:ARG196 3.7 31.1 1.0
CB B:TYR114 3.7 25.4 1.0
CA B:ALA110 3.8 29.1 1.0
CA B:GLY200 3.9 26.9 1.0
CG2 B:THR111 3.9 29.3 1.0
CE2 B:PHE208 3.9 36.2 1.0
CB B:ALA110 4.0 30.2 1.0
CZ B:ARG196 4.0 26.6 1.0
CA B:VAL198 4.0 27.5 1.0
C B:VAL198 4.2 26.6 1.0
C B:LYS199 4.2 27.3 1.0
C B:ALA110 4.2 27.9 1.0
CZ B:PHE208 4.2 37.2 1.0
CA B:LYS199 4.3 28.4 1.0
O B:THR111 4.3 27.4 1.0
CA B:TYR114 4.4 28.5 1.0
C B:GLY200 4.5 29.4 1.0
O B:GLY200 4.5 32.5 1.0
N B:TYR114 4.5 28.5 1.0
CG B:TYR114 4.5 23.0 1.0
CB B:VAL198 4.5 28.5 1.0
CA B:THR111 4.5 27.0 1.0
CD1 B:TYR114 4.6 23.1 1.0
CB B:THR111 4.6 29.4 1.0
O B:GLY197 4.7 24.8 1.0
C B:THR111 4.9 26.0 1.0
O B:GLY109 4.9 30.1 1.0
CB B:LYS199 5.0 30.5 1.0

Chlorine binding site 4 out of 6 in 5nx9

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Chlorine binding site 4 out of 6 in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:45.5
occ:1.00
 O C:HOH624 3.2 24.5 1.0
N C:SER207 3.3 29.5 1.0
OG C:SER207 3.3 37.6 1.0
N C:THR201 3.4 30.4 1.0
CB C:SER207 3.5 30.5 1.0
CA C:GLY200 3.8 27.8 1.0
N C:ALA206 3.9 27.7 1.0
CB C:ALA206 3.9 28.4 1.0
CA C:SER207 4.0 28.8 1.0
OG1 C:THR201 4.0 39.9 1.0
C C:GLY200 4.1 28.1 1.0
C C:ALA206 4.2 28.4 1.0
CA C:ALA206 4.2 28.0 1.0
CB C:THR201 4.2 34.3 1.0
CG D:GLN164 4.3 54.1 1.0
CA C:THR201 4.4 30.9 1.0
C C:GLN205 4.6 27.6 1.0
CB D:GLN164 4.8 44.8 1.0
OG1 C:THR204 4.8 25.1 1.0

Chlorine binding site 5 out of 6 in 5nx9

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Chlorine binding site 5 out of 6 in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:26.4
occ:1.00
 N C:GLY200 3.1 26.1 1.0
NH1 C:ARG196 3.2 24.4 1.0
N C:LYS199 3.3 26.0 1.0
N C:THR111 3.5 26.2 1.0
NH2 C:ARG196 3.6 24.8 1.0
CG2 C:THR111 3.7 26.5 1.0
CB C:TYR114 3.8 28.0 1.0
CA C:GLY200 3.8 27.8 1.0
CZ C:ARG196 3.9 24.9 1.0
CA C:ALA110 4.0 27.2 1.0
CE2 C:PHE208 4.0 28.1 1.0
C C:LYS199 4.1 24.0 1.0
CA C:VAL198 4.1 27.4 1.0
C C:VAL198 4.2 26.2 1.0
CA C:LYS199 4.2 25.1 1.0
CB C:ALA110 4.2 27.2 1.0
C C:ALA110 4.3 26.2 1.0
C C:GLY200 4.3 28.1 1.0
O C:GLY200 4.3 27.1 1.0
CZ C:PHE208 4.4 28.9 1.0
O C:THR111 4.4 23.6 1.0
CA C:TYR114 4.4 26.7 1.0
CA C:THR111 4.5 26.4 1.0
N C:TYR114 4.5 26.5 1.0
CB C:THR111 4.5 27.0 1.0
CG C:TYR114 4.6 26.9 1.0
CB C:VAL198 4.6 29.2 1.0
CD1 C:TYR114 4.7 26.3 1.0
O C:GLY197 4.7 31.3 1.0
CB C:LYS199 4.8 27.6 1.0
C C:THR111 4.9 25.6 1.0
O C:GLY109 5.0 30.5 1.0

Chlorine binding site 6 out of 6 in 5nx9

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Chlorine binding site 6 out of 6 in the Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Neanderthal Adenylosuccinate Lyase (Adsl) in Complex with Its Products Amp and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:35.6
occ:1.00
 N D:GLY200 3.1 31.4 1.0
NH1 D:ARG196 3.3 40.7 1.0
N D:LYS199 3.3 34.7 1.0
N D:THR111 3.6 33.5 1.0
NH2 D:ARG196 3.7 33.2 1.0
CB D:TYR114 3.7 29.4 1.0
CA D:GLY200 3.8 32.7 1.0
CA D:ALA110 3.9 38.0 1.0
CG2 D:THR111 3.9 31.0 1.0
CZ D:ARG196 3.9 34.5 1.0
CE2 D:PHE208 4.0 38.5 1.0
CA D:VAL198 4.0 39.0 1.0
CB D:ALA110 4.1 39.1 1.0
C D:LYS199 4.1 32.4 1.0
C D:VAL198 4.1 35.1 1.0
CA D:LYS199 4.2 32.9 1.0
CZ D:PHE208 4.2 39.9 1.0
C D:ALA110 4.3 35.1 1.0
CA D:TYR114 4.4 30.3 1.0
C D:GLY200 4.4 35.4 1.0
O D:THR111 4.4 31.7 1.0
CG D:TYR114 4.4 26.6 1.0
O D:GLY200 4.4 33.3 1.0
CB D:VAL198 4.5 40.0 1.0
CD1 D:TYR114 4.5 26.2 1.0
N D:TYR114 4.5 33.9 1.0
CA D:THR111 4.6 32.4 1.0
O D:GLY197 4.6 32.3 1.0
CB D:THR111 4.7 30.9 1.0
CB D:LYS199 4.9 30.2 1.0
O D:GLY109 4.9 43.8 1.0
C D:THR111 5.0 33.1 1.0

Reference:

B.Van Laer, U.Kapp, M.Soler-Lopez, K.Moczulska, S.Paabo, G.Leonard, C.Mueller-Dieckmann. Molecular Comparison of Neanderthal and Modern Human Adenylosuccinate Lyase. Sci Rep V. 8 18008 2018.
ISSN: ESSN 2045-2322
PubMed: 30573755
DOI: 10.1038/S41598-018-36195-5
Page generated: Fri Jul 26 13:56:05 2024

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