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Chlorine in PDB 3zzf: Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate

Enzymatic activity of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate

All present enzymatic activity of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate:
2.7.2.8;

Protein crystallography data

The structure of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate, PDB code: 3zzf was solved by S.De Cima, F.Gil-Ortiz, M.Crabeel, I.Fita, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.701, 99.299, 190.644, 90.00, 90.00, 90.00
R / Rfree (%) 17.87 / 21.812

Other elements in 3zzf:

The structure of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate also contains other interesting chemical elements:

Mercury (Hg) 11 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate (pdb code 3zzf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate, PDB code: 3zzf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3zzf

Go back to Chlorine Binding Sites List in 3zzf
Chlorine binding site 1 out of 7 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1361

b:31.6
occ:1.00
 HG A:HG1359 1.9 41.2 0.4
CG A:ARG143 3.4 30.2 1.0
CD A:LYS170 3.6 36.2 1.0
CG A:LYS170 3.7 31.6 1.0
CB A:LYS170 3.7 29.1 1.0
CG1 A:VAL167 3.9 19.0 1.0
CD A:ARG143 4.0 34.5 1.0
CA A:VAL167 4.0 20.5 1.0
O A:VAL167 4.0 21.0 1.0
SG A:CYS171 4.2 31.3 1.0
NE A:ARG143 4.3 38.1 1.0
CB A:VAL167 4.4 20.0 1.0
CE A:LYS170 4.4 38.4 1.0
CB A:ARG143 4.4 28.1 1.0
CG2 A:VAL167 4.5 19.9 1.0
OE2 A:GLU174 4.5 39.4 1.0
C A:VAL167 4.5 20.4 1.0
N A:CYS171 4.7 25.6 1.0
CA A:LYS170 4.9 26.4 1.0
O A:ALA166 4.9 22.8 1.0
C A:LYS170 4.9 25.5 1.0

Chlorine binding site 2 out of 7 in 3zzf

Go back to Chlorine Binding Sites List in 3zzf
Chlorine binding site 2 out of 7 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1362

b:61.5
occ:1.00
 NE2 A:GLN335 2.9 36.6 1.0
SG A:CYS119 3.1 14.3 0.5
SG A:CYS119 3.1 22.3 0.5
HG A:HG1358 3.3 33.0 0.7
O A:HOH2019 3.4 26.6 1.0
CB A:CYS119 3.4 16.2 0.5
CA A:CYS119 3.6 16.2 0.5
CA A:CYS119 3.7 17.7 0.5
CB A:GLN335 3.7 31.7 1.0
CB A:CYS119 3.8 17.8 0.5
CD A:GLN335 4.0 35.8 1.0
O A:HOH2018 4.1 22.6 1.0
CG A:GLN335 4.2 33.3 1.0
NE2 A:GLN73 4.2 36.2 1.0
CB A:PHE122 4.4 16.6 1.0
N A:CYS119 4.5 17.4 0.5
O A:CYS119 4.5 16.4 0.5
N A:CYS119 4.5 18.1 0.5
C A:CYS119 4.6 16.5 0.5
O A:CYS119 4.7 15.7 0.5
C A:CYS119 4.7 15.8 0.5
CG A:PHE122 4.7 17.0 1.0
CA A:GLN335 4.8 29.8 1.0
N A:GLN335 4.8 28.5 1.0
CD2 A:PHE122 4.9 17.9 1.0
O A:SER118 4.9 18.4 1.0
CD A:GLN73 4.9 32.5 1.0

Chlorine binding site 3 out of 7 in 3zzf

Go back to Chlorine Binding Sites List in 3zzf
Chlorine binding site 3 out of 7 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1362

b:30.1
occ:1.00
 HG B:HG1360 2.7 39.5 0.5
OE1 B:GLU174 2.9 35.2 1.0
NH2 B:ARG143 3.3 31.8 1.0
CZ B:ARG143 3.3 31.8 1.0
O B:HOH2072 3.4 23.4 1.0
CL B:CL1363 3.6 10.6 1.0
O B:LYS170 3.6 20.1 1.0
NE B:ARG143 3.6 30.2 1.0
C B:LYS170 3.6 19.8 1.0
N B:CYS171 3.7 18.4 1.0
NH1 B:ARG143 3.7 33.2 1.0
CD B:GLU174 3.8 33.6 1.0
CA B:CYS171 3.9 18.8 1.0
CB B:LYS170 3.9 20.4 1.0
SG B:CYS171 4.1 22.7 1.0
CB B:GLU174 4.1 24.1 1.0
O B:HOH2071 4.4 16.1 1.0
CA B:LYS170 4.4 20.2 1.0
CD B:ARG143 4.4 28.3 1.0
OE2 B:GLU174 4.6 38.5 1.0
O B:HOH2055 4.6 17.6 1.0
CG B:GLU174 4.6 27.3 1.0
CB B:CYS171 4.6 18.1 1.0

Chlorine binding site 4 out of 7 in 3zzf

Go back to Chlorine Binding Sites List in 3zzf
Chlorine binding site 4 out of 7 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1363

b:10.6
occ:1.00
 HG B:HG1360 2.3 39.5 0.5
CL B:CL1362 3.6 30.1 1.0
CD B:ARG143 3.7 28.3 1.0
CE B:LYS170 3.8 24.9 1.0
CG1 B:VAL167 4.0 13.2 1.0
CB B:LYS170 4.0 20.4 1.0
NH1 B:ARG143 4.0 33.2 1.0
CA B:VAL167 4.1 14.7 1.0
NE B:ARG143 4.2 30.2 1.0
O B:VAL167 4.2 14.8 1.0
CG B:ARG143 4.3 24.5 1.0
CZ B:ARG143 4.3 31.8 1.0
CB B:VAL167 4.4 14.5 1.0
CG2 B:VAL167 4.4 13.2 1.0
CD B:LYS170 4.5 25.3 1.0
SG B:CYS171 4.6 22.7 1.0
C B:VAL167 4.7 14.7 1.0
CB B:ARG143 4.7 21.6 1.0
NZ B:LYS170 4.7 26.8 1.0
CG B:LYS170 4.8 22.4 1.0
N B:CYS171 4.9 18.4 1.0

Chlorine binding site 5 out of 7 in 3zzf

Go back to Chlorine Binding Sites List in 3zzf
Chlorine binding site 5 out of 7 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1364

b:40.3
occ:1.00
 HG B:HG1359 2.2 39.5 0.3
O B:HOH2009 3.5 16.0 1.0
O B:HOH2044 3.5 13.3 1.0
CB B:SER118 3.7 16.8 1.0
CG B:GLU115 3.8 20.6 1.0
SG B:CYS119 4.2 16.2 0.5
O B:GLU115 4.3 15.6 1.0
CA B:GLU115 4.4 17.4 1.0
OG B:SER118 4.4 18.4 1.0
CB B:GLU115 4.6 18.0 1.0
OE2 B:GLU115 4.6 26.4 1.0
CD B:GLU115 4.7 24.2 1.0
N B:CYS119 4.8 15.6 0.5
N B:CYS119 4.8 16.1 0.5
C B:GLU115 4.8 16.4 1.0
C B:SER118 5.0 16.0 1.0
CA B:SER118 5.0 16.2 1.0

Chlorine binding site 6 out of 7 in 3zzf

Go back to Chlorine Binding Sites List in 3zzf
Chlorine binding site 6 out of 7 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


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 the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1359

b:70.3
occ:1.00
 O C:HOH2024 2.8 14.2 1.0
SG C:CYS171 3.2 20.0 1.0
CG C:ARG143 3.3 33.5 1.0
HG C:HG1357 3.3 52.9 0.6
O C:HOH2027 3.4 15.8 1.0
OE1 C:GLU174 3.9 37.0 1.0
NE C:ARG143 4.1 39.8 1.0
CB C:ARG143 4.3 31.0 1.0
CD C:ARG143 4.4 37.1 1.0
CB C:CYS171 4.6 20.0 1.0
O C:GLN139 4.6 26.5 1.0
CD C:GLU174 4.8 34.6 1.0

Chlorine binding site 7 out of 7 in 3zzf

Go back to Chlorine Binding Sites List in 3zzf
Chlorine binding site 7 out of 7 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1358

b:39.2
occ:1.00
 HG D:HG1355 2.2 42.5 0.4
O D:HOH2007 3.5 20.2 1.0
O D:HOH2040 3.6 10.5 1.0
CB D:SER118 3.8 16.7 1.0
CG D:GLU115 3.9 20.6 1.0
O D:GLU115 4.2 14.6 1.0
CA D:GLU115 4.3 17.5 1.0
SG D:CYS119 4.4 16.8 0.5
OG D:SER118 4.5 19.7 1.0
CB D:GLU115 4.6 18.4 1.0
N D:CYS119 4.7 14.8 0.5
N D:CYS119 4.7 14.9 0.5
C D:GLU115 4.8 16.0 1.0
OE2 D:GLU115 4.8 27.1 1.0
CD D:GLU115 4.9 24.0 1.0
C D:SER118 4.9 15.3 1.0
CA D:SER118 5.0 15.9 1.0

Reference:

S.De Cima, F.Gil-Ortiz, M.Crabeel, I.Fita, V.Rubio. Insight on An Arginine Synthesis Metabolon From the Tetrameric Structure of Yeast Acetylglutamate Kinase Plos One V. 7 34734 2012.
ISSN: ISSN 1932-6203
PubMed: 22529931
DOI: 10.1371/JOURNAL.PONE.0034734
Page generated: Sun Jul 21 08:41:05 2024

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