Chlorine in PDB 8gqz: Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae, PDB code: 8gqz was solved by K.Nishio, K.Nakatsukasa, T.Kamura, T.Mizushima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.64 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.328, 102.398, 146.87, 90, 90, 90
R / Rfree (%) 16.6 / 19.7

Other elements in 8gqz:

The structure of Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae (pdb code 8gqz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae, PDB code: 8gqz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8gqz

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Chlorine binding site 1 out of 5 in the Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae


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 Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:23.4
occ:0.69
 CL A:CL502 0.0 23.4 0.7
CL A:CL502 2.6 24.4 0.3
O A:HOH890 2.7 33.0 1.0
N B:VAL281 3.0 11.5 1.0
O A:HOH958 3.1 44.2 1.0
CA B:ASN280 3.4 10.6 1.0
ND1 B:HIS312 3.6 17.7 1.0
CB B:ASN280 3.6 13.1 1.0
C B:ASN280 3.7 11.5 1.0
CG2 B:VAL281 3.7 12.0 1.0
CD1 A:ILE457 3.8 15.4 1.0
CE1 B:HIS312 3.8 15.1 1.0
NH2 A:ARG459 3.9 31.8 1.0
CG B:HIS312 3.9 12.9 1.0
CB B:VAL281 4.0 11.3 1.0
NE A:ARG459 4.0 46.8 1.0
CA B:VAL281 4.1 12.1 1.0
NE2 B:HIS312 4.3 13.2 1.0
CD2 B:HIS312 4.3 12.9 1.0
CZ A:ARG459 4.4 50.9 1.0
CB B:HIS312 4.4 13.9 1.0
CG1 A:ILE457 4.7 14.2 1.0
N B:ASN280 4.8 12.2 1.0
O B:GLY279 4.8 14.2 1.0
O B:HOH972 4.9 32.8 1.0
CG B:ASN280 4.9 11.9 1.0
CA B:HIS312 4.9 14.5 1.0
O B:ASN280 5.0 12.2 1.0

Chlorine binding site 2 out of 5 in 8gqz

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Chlorine binding site 2 out of 5 in the Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae


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 Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:24.4
occ:0.31
 CL A:CL502 0.0 24.4 0.3
CL A:CL502 2.6 23.4 0.7
NE A:ARG459 3.0 46.8 1.0
O A:GLU458 3.0 15.7 1.0
CG A:ARG459 3.1 32.7 1.0
O B:GLY279 3.2 14.2 1.0
CB A:ARG459 3.3 19.7 1.0
CA B:ASN280 3.5 10.6 1.0
N B:VAL281 3.6 11.5 1.0
CD A:ARG459 3.6 53.3 1.0
CA A:ARG459 3.7 16.1 1.0
CG2 B:VAL281 3.7 12.0 1.0
CZ A:ARG459 3.8 50.9 1.0
C B:ASN280 3.9 11.5 1.0
C A:GLU458 3.9 14.5 1.0
O A:HOH716 3.9 14.0 1.0
NH2 A:ARG459 4.0 31.8 1.0
O A:HOH958 4.1 44.2 1.0
C B:GLY279 4.1 12.9 1.0
CD1 A:ILE457 4.1 15.4 1.0
CG1 A:ILE457 4.2 14.2 1.0
N A:ARG459 4.2 13.9 1.0
O B:HOH972 4.3 32.8 1.0
N B:ASN280 4.3 12.2 1.0
CA B:VAL281 4.4 12.1 1.0
CB B:VAL281 4.5 11.3 1.0
CB B:ASN280 4.6 13.1 1.0
O A:HOH890 4.6 33.0 1.0
CG2 A:ILE457 4.7 15.4 1.0
O B:ASN280 4.9 12.2 1.0
NH1 A:ARG459 4.9 55.9 1.0
C A:ARG459 5.0 16.0 1.0

Chlorine binding site 3 out of 5 in 8gqz

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Chlorine binding site 3 out of 5 in the Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae


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 Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:14.7
occ:0.71
 O A:HOH945 2.9 30.9 1.0
O A:HOH882 3.0 27.6 1.0
NH1 A:ARG439 3.2 14.7 1.0
O A:HOH896 3.2 29.5 1.0
NH2 A:ARG439 3.3 14.8 1.0
CE1 A:HIS312 3.7 15.2 1.0
CZ A:ARG439 3.7 16.3 1.0
CG A:ASN280 3.8 11.5 1.0
CB A:ASN280 3.9 13.8 1.0
ND2 A:ASN280 3.9 12.9 1.0
CB A:HIS276 4.0 14.7 1.0
CZ A:PHE435 4.2 15.2 1.0
OD1 A:ASN280 4.3 12.0 1.0
ND1 A:HIS312 4.4 15.9 1.0
O A:HOH854 4.5 31.1 1.0
CG A:HIS276 4.6 15.4 1.0
NE2 A:HIS312 4.7 13.6 1.0
O A:HOH989 4.8 41.3 1.0
O A:HIS276 4.9 13.3 1.0
CE2 A:PHE435 4.9 14.2 1.0

Chlorine binding site 4 out of 5 in 8gqz

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Chlorine binding site 4 out of 5 in the Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae


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 Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:22.1
occ:0.67
 O B:HOH899 2.7 28.4 1.0
O B:HOH812 2.7 30.8 1.0
N A:VAL281 3.1 10.8 1.0
O B:HOH927 3.3 40.0 1.0
CA A:ASN280 3.5 11.2 1.0
ND1 A:HIS312 3.5 15.9 1.0
CB A:ASN280 3.6 13.8 1.0
CG2 A:VAL281 3.7 13.7 1.0
NH2 B:ARG459 3.7 31.8 1.0
C A:ASN280 3.8 11.4 1.0
CE1 A:HIS312 3.8 15.2 1.0
CD1 B:ILE457 3.9 16.1 1.0
CG A:HIS312 3.9 13.0 1.0
NE B:ARG459 4.0 39.1 1.0
CB A:VAL281 4.0 12.0 1.0
CA A:VAL281 4.1 10.5 1.0
NE2 A:HIS312 4.3 13.6 1.0
CZ B:ARG459 4.3 47.2 1.0
CD2 A:HIS312 4.3 12.6 1.0
CB A:HIS312 4.4 14.4 1.0
CG1 B:ILE457 4.6 13.0 1.0
N A:ASN280 4.8 11.5 1.0
O A:GLY279 4.9 15.1 1.0
CA A:HIS312 4.9 12.3 1.0
CG A:ASN280 4.9 11.5 1.0
O A:HOH957 4.9 31.5 1.0
O A:ASN280 5.0 12.4 1.0

Chlorine binding site 5 out of 5 in 8gqz

Go back to Chlorine Binding Sites List in 8gqz
Chlorine binding site 5 out of 5 in the Crystal Structure of Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae


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 Mitochondrial Citrate Synthase (CIT1) From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:17.2
occ:0.83
 O B:HOH962 2.9 30.1 1.0
O B:HOH814 2.9 24.7 1.0
NH1 B:ARG439 3.2 14.2 1.0
O B:HOH944 3.2 28.6 1.0
NH2 B:ARG439 3.3 15.9 1.0
CE1 B:HIS312 3.7 15.1 1.0
CZ B:ARG439 3.7 14.7 1.0
CG B:ASN280 3.8 11.9 1.0
CB B:HIS276 3.8 14.7 1.0
CB B:ASN280 3.9 13.1 1.0
ND2 B:ASN280 3.9 12.2 1.0
OD1 B:ASN280 4.3 12.5 1.0
CZ B:PHE435 4.3 17.3 1.0
O A:HOH958 4.4 44.2 1.0
CG B:HIS276 4.4 15.4 1.0
ND1 B:HIS312 4.4 17.7 1.0
O B:HOH837 4.4 36.1 1.0
O B:HOH845 4.5 34.8 1.0
NE2 B:HIS312 4.7 13.2 1.0
O B:HIS276 4.8 13.0 1.0
ND1 B:HIS276 4.9 17.8 1.0
CE2 B:PHE435 4.9 14.5 1.0

Reference:

K.Nishio, T.Kawarasaki, Y.Sugiura, S.Matsumoto, A.Konoshima, Y.Takano, M.Hayashi, F.Okumura, T.Kamura, T.Mizushima, K.Nakatsukasa. Defective Import of Mitochondrial Metabolic Enzyme Elicits Ectopic Metabolic Stress. Sci Adv V. 9 F1956 2023.
ISSN: ESSN 2375-2548
PubMed: 37058555
DOI: 10.1126/SCIADV.ADF1956
Page generated: Tue Jul 30 10:07:13 2024

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