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Chlorine in PDB 2vd6: Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate.

Enzymatic activity of Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate.

All present enzymatic activity of Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate.:
4.3.2.2;

Protein crystallography data

The structure of Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate., PDB code: 2vd6 was solved by P.Stenmark, M.Moche, C.Arrowsmith, H.Berglund, R.Busam, R.Collins, L.G.Dahlgren, A.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, B.M.Hallberg, L.Holmberg-Schiavone, I.Johansson, A.Kallas, T.Karlberg, T.Kotenyova, L.Lehtio, M.Nilsson, T.Nyman, D.Ogg, C.Persson, J.Sagemark, M.Sundstrom, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, P.Nordlund, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.300, 128.100, 190.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. (pdb code 2vd6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate., PDB code: 2vd6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 2vd6

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Chlorine binding site 1 out of 7 in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and 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 Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2001

b:55.2
occ:1.00
 C8 A:AMP1000 3.5 36.5 1.0
ND2 D:ASN297 3.7 35.8 1.0
CB D:MET299 3.7 34.1 1.0
CG D:MET299 3.8 34.4 1.0
SD D:MET299 3.9 35.3 1.0
CE1 B:HIS159 4.0 31.1 1.0
CB D:ASN297 4.0 35.8 1.0
N7 A:AMP1000 4.0 37.1 1.0
O2' A:AMP1000 4.0 36.6 1.0
CG D:ASN297 4.3 35.8 1.0
NE2 B:HIS159 4.4 32.0 1.0
C2' A:AMP1000 4.5 36.0 1.0
N9 A:AMP1000 4.7 37.0 1.0
ND1 B:HIS159 4.7 30.9 1.0
CA D:MET299 4.9 34.0 1.0

Chlorine binding site 2 out of 7 in 2vd6

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Chlorine binding site 2 out of 7 in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and 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 Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2002

b:35.7
occ:1.00
 N A:GLY200 3.2 29.5 1.0
NH1 A:ARG196 3.3 32.5 1.0
N A:THR111 3.5 32.0 1.0
N A:LYS199 3.5 29.8 1.0
NH2 A:ARG196 3.5 31.4 1.0
CB A:TYR114 3.6 31.2 1.0
CA A:ALA110 3.9 31.9 1.0
CA A:GLY200 3.9 29.2 1.0
CE2 A:PHE208 3.9 27.6 1.0
CZ A:ARG196 3.9 32.4 1.0
CZ A:PHE208 4.1 27.4 1.0
CB A:ALA110 4.1 31.7 1.0
C A:ALA110 4.2 31.9 1.0
CA A:VAL198 4.2 30.7 1.0
C A:LYS199 4.2 29.6 1.0
C A:VAL198 4.3 30.4 1.0
CA A:TYR114 4.3 31.8 1.0
O A:THR111 4.3 32.1 1.0
CA A:LYS199 4.4 29.6 1.0
N A:TYR114 4.5 31.9 1.0
CG A:TYR114 4.5 31.4 1.0
CA A:THR111 4.5 32.2 1.0
C A:GLY200 4.5 29.1 1.0
O A:GLY200 4.5 29.2 1.0
CB A:THR111 4.5 32.2 1.0
CD1 A:TYR114 4.6 30.5 1.0
OG1 A:THR111 4.6 34.0 1.0
CB A:VAL198 4.7 30.8 1.0
O A:GLY197 4.7 31.1 1.0
C A:THR111 4.8 32.3 1.0
O A:GLY109 4.9 32.1 1.0

Chlorine binding site 3 out of 7 in 2vd6

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Chlorine binding site 3 out of 7 in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and 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 Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2001

b:31.4
occ:1.00
 O B:HOH2166 2.8 44.0 1.0
C8 B:2SA1002 3.5 23.5 1.0
ND2 C:ASN297 3.6 33.1 1.0
CB C:MET299 3.7 32.4 1.0
CE1 A:HIS159 3.9 33.1 1.0
CB C:ASN297 3.9 34.5 1.0
CG C:MET299 3.9 32.6 1.0
N7 B:2SA1002 4.1 23.9 1.0
SD C:MET299 4.1 34.6 1.0
O2' B:2SA1002 4.1 26.2 1.0
O C:HOH2150 4.2 32.5 1.0
CG C:ASN297 4.3 33.2 1.0
NE2 A:HIS159 4.3 33.2 1.0
C2' B:2SA1002 4.5 26.2 1.0
ND1 A:HIS159 4.7 31.1 1.0
N9 B:2SA1002 4.7 23.8 1.0
O B:HOH2165 4.7 27.5 1.0
O B:HOH2037 4.7 47.1 1.0
CA C:MET299 4.9 32.3 1.0

Chlorine binding site 4 out of 7 in 2vd6

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Chlorine binding site 4 out of 7 in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and 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 Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2002

b:25.0
occ:1.00
 N B:GLY200 3.2 30.9 1.0
NH1 B:ARG196 3.3 32.4 1.0
N B:LYS199 3.5 31.3 1.0
N B:THR111 3.6 33.6 1.0
CB B:TYR114 3.6 32.1 1.0
NH2 B:ARG196 3.6 31.0 1.0
CE2 B:PHE208 3.8 33.5 1.0
CA B:GLY200 3.8 30.6 1.0
CG2 B:THR111 3.9 33.4 1.0
CA B:ALA110 3.9 33.9 1.0
CZ B:ARG196 3.9 31.2 1.0
CZ B:PHE208 4.1 33.6 1.0
CA B:VAL198 4.1 31.8 1.0
CB B:ALA110 4.2 34.1 1.0
C B:LYS199 4.2 31.2 1.0
CA B:TYR114 4.2 32.5 1.0
C B:VAL198 4.3 31.4 1.0
C B:ALA110 4.3 33.8 1.0
CA B:LYS199 4.4 31.1 1.0
CG B:TYR114 4.4 31.8 1.0
O B:THR111 4.4 33.4 1.0
CD1 B:TYR114 4.4 31.6 1.0
N B:TYR114 4.4 32.7 1.0
C B:GLY200 4.5 30.4 1.0
CA B:THR111 4.6 33.6 1.0
O B:GLY197 4.6 32.1 1.0
O B:GLY200 4.7 29.9 1.0
CB B:THR111 4.7 33.5 1.0
CB B:VAL198 4.7 31.9 1.0
C B:THR111 4.9 33.4 1.0
O B:GLY109 4.9 33.8 1.0

Chlorine binding site 5 out of 7 in 2vd6

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Chlorine binding site 5 out of 7 in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and 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 Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2002

b:38.3
occ:1.00
 N C:GLY200 3.2 29.7 1.0
NH1 C:ARG196 3.2 33.7 1.0
N C:LYS199 3.3 30.4 1.0
NH2 C:ARG196 3.5 33.4 1.0
CB C:TYR114 3.6 29.9 1.0
N C:THR111 3.7 31.0 1.0
CZ C:ARG196 3.8 33.6 1.0
CA C:ALA110 3.9 31.5 1.0
CE2 C:PHE208 3.9 31.5 1.0
CA C:GLY200 3.9 29.5 1.0
CA C:VAL198 3.9 31.3 1.0
C C:VAL198 4.1 31.0 1.0
CB C:ALA110 4.1 31.6 1.0
CG2 C:THR111 4.1 30.0 1.0
CZ C:PHE208 4.2 30.8 1.0
C C:LYS199 4.2 29.7 1.0
CA C:LYS199 4.2 30.1 1.0
CG C:TYR114 4.3 29.7 1.0
CD1 C:TYR114 4.3 29.1 1.0
CA C:TYR114 4.3 30.6 1.0
C C:ALA110 4.3 31.3 1.0
O C:GLY197 4.4 31.6 1.0
O C:THR111 4.5 31.0 1.0
CB C:VAL198 4.5 31.4 1.0
N C:TYR114 4.6 30.4 1.0
C C:GLY200 4.6 29.5 1.0
O C:GLY200 4.6 29.7 1.0
CA C:THR111 4.8 30.8 1.0
CG1 C:VAL198 4.8 31.9 1.0
O C:GLY109 4.8 32.0 1.0
CB C:THR111 4.9 30.9 1.0
CB C:LYS199 4.9 29.8 1.0

Chlorine binding site 6 out of 7 in 2vd6

Go back to Chlorine Binding Sites List in 2vd6
Chlorine binding site 6 out of 7 in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and 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 Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2001

b:29.9
occ:1.00
 O D:HOH2026 3.0 42.6 1.0
O D:HOH2067 3.1 40.5 1.0
ND2 A:ASN297 3.5 34.3 1.0
CB A:MET299 3.6 32.2 1.0
C8 D:2SA1002 3.6 19.8 1.0
CB A:ASN297 3.8 35.3 1.0
CG A:MET299 3.9 32.6 1.0
CE1 C:HIS159 3.9 34.9 1.0
SD A:MET299 4.0 33.6 1.0
O A:HOH2146 4.1 36.2 1.0
N7 D:2SA1002 4.2 19.3 1.0
CG A:ASN297 4.2 35.9 1.0
NE2 C:HIS159 4.3 33.3 1.0
O2' D:2SA1002 4.3 19.9 1.0
O D:HOH2065 4.6 41.2 1.0
ND1 C:HIS159 4.6 33.4 1.0
C2' D:2SA1002 4.6 21.2 1.0
N9 D:2SA1002 4.8 19.7 1.0
CA A:MET299 4.8 32.1 1.0
O D:HOH2244 4.9 37.9 1.0
O A:ASN297 4.9 33.3 1.0

Chlorine binding site 7 out of 7 in 2vd6

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Chlorine binding site 7 out of 7 in the Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and 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 7 of Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2002

b:18.4
occ:1.00
 N D:GLY200 3.2 31.5 1.0
NH1 D:ARG196 3.3 30.5 1.0
N D:LYS199 3.4 31.7 1.0
NH2 D:ARG196 3.5 29.1 1.0
N D:THR111 3.6 29.6 1.0
CB D:TYR114 3.6 29.4 1.0
CE2 D:PHE208 3.9 29.7 1.0
CG2 D:THR111 3.9 27.7 1.0
CA D:GLY200 3.9 31.1 1.0
CZ D:ARG196 3.9 30.2 1.0
CA D:ALA110 3.9 29.6 1.0
CA D:VAL198 4.1 31.7 1.0
CZ D:PHE208 4.1 30.0 1.0
CB D:ALA110 4.1 29.6 1.0
C D:LYS199 4.2 31.4 1.0
C D:VAL198 4.2 31.9 1.0
CA D:TYR114 4.2 30.1 1.0
C D:ALA110 4.3 29.6 1.0
CA D:LYS199 4.3 31.2 1.0
O D:THR111 4.4 30.0 1.0
CG D:TYR114 4.4 29.6 1.0
N D:TYR114 4.4 30.1 1.0
CD1 D:TYR114 4.5 28.8 1.0
C D:GLY200 4.5 31.3 1.0
CA D:THR111 4.5 29.6 1.0
O D:GLY200 4.6 31.2 1.0
O D:GLY197 4.6 30.5 1.0
CB D:VAL198 4.6 32.2 1.0
CB D:THR111 4.7 29.3 1.0
C D:THR111 4.9 30.0 1.0
CB D:LYS199 4.9 30.9 1.0
O D:GLY109 5.0 29.6 1.0

Reference:

P.Stenmark, M.Moche, C.Arrowsmith, H.Berglund, R.Busam, R.Collins, L.G.Dahlgren, A.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, B.M.Hallberg, L.Holmberg-Schiavone, I.Johansson, A.Kallas, T.Karlberg, T.Kotenyova, L.Lehtio, M.Nilsson, T.Nyman, D.Ogg, C.Persson, J.Sagemark, M.Sundstrom, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, P.Nordlund. Human Adenylosuccinate Lyase in Complex with Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, and Its Products Amp and Fumarate. To Be Published.
Page generated: Fri Jul 11 00:45:24 2025

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