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Zinc in PDB 3git: Crystal Structure of A Truncated Acetyl-Coa Synthase

Enzymatic activity of Crystal Structure of A Truncated Acetyl-Coa Synthase

All present enzymatic activity of Crystal Structure of A Truncated Acetyl-Coa Synthase:
2.3.1.169;

Protein crystallography data

The structure of Crystal Structure of A Truncated Acetyl-Coa Synthase, PDB code: 3git was solved by A.Volbeda, C.Darnault, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 3.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.400, 166.400, 245.200, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 20.8

Other elements in 3git:

The structure of Crystal Structure of A Truncated Acetyl-Coa Synthase also contains other interesting chemical elements:

Iron (Fe) 24 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Truncated Acetyl-Coa Synthase (pdb code 3git). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Truncated Acetyl-Coa Synthase, PDB code: 3git:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3git

Go back to Zinc Binding Sites List in 3git
Zinc binding site 1 out of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn739

b:58.0
occ:0.75
SG A:CYS597 2.2 57.8 1.0
S A:H2S740 2.2 60.4 0.8
SG A:CYS509 2.3 55.6 1.0
SG A:CYS595 2.3 56.6 1.0
CB A:CYS509 3.0 55.4 1.0
CB A:CYS595 3.4 57.3 1.0
CB A:CYS597 3.5 58.0 1.0
FE4 A:SF4738 3.5 56.0 1.0
N A:CYS597 3.6 58.2 1.0
S1 A:SF4738 3.8 57.1 1.0
N A:GLY596 4.0 59.3 1.0
CA A:CYS597 4.1 58.0 1.0
NH2 A:ARG405 4.2 54.8 1.0
CA A:CYS509 4.4 55.5 1.0
C A:GLY596 4.5 58.9 1.0
CD2 A:LEU527 4.6 53.6 1.0
CA A:CYS595 4.7 58.1 1.0
CA A:GLY596 4.8 58.7 1.0
C A:CYS595 4.8 58.8 1.0
C A:CYS597 5.0 57.5 1.0

Zinc binding site 2 out of 6 in 3git

Go back to Zinc Binding Sites List in 3git
Zinc binding site 2 out of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn739

b:57.4
occ:0.75
S B:H2S740 2.2 57.7 0.8
SG B:CYS595 2.3 57.9 1.0
SG B:CYS597 2.3 58.5 1.0
SG B:CYS509 2.3 54.4 1.0
CB B:CYS509 3.1 54.9 1.0
CB B:CYS595 3.4 57.9 1.0
N B:CYS597 3.5 57.8 1.0
CB B:CYS597 3.5 58.0 1.0
FE4 B:SF4738 3.6 55.8 1.0
S1 B:SF4738 3.8 54.5 1.0
N B:GLY596 3.9 58.7 1.0
CA B:CYS597 4.0 58.0 1.0
C B:GLY596 4.4 58.2 1.0
NH2 B:ARG405 4.4 54.0 1.0
CA B:CYS509 4.5 55.0 1.0
CD2 B:LEU527 4.5 53.7 1.0
CA B:CYS595 4.6 58.3 1.0
CA B:GLY596 4.6 58.2 1.0
C B:CYS595 4.7 58.9 1.0
C B:CYS597 4.8 57.7 1.0

Zinc binding site 3 out of 6 in 3git

Go back to Zinc Binding Sites List in 3git
Zinc binding site 3 out of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn739

b:57.9
occ:0.75
SG C:CYS595 2.2 57.8 1.0
S C:H2S740 2.2 58.5 0.8
SG C:CYS509 2.3 56.2 1.0
SG C:CYS597 2.4 57.3 1.0
CB C:CYS509 3.0 55.7 1.0
CB C:CYS595 3.3 58.5 1.0
N C:CYS597 3.6 58.0 1.0
FE4 C:SF4738 3.6 55.9 1.0
CB C:CYS597 3.6 57.5 1.0
S1 C:SF4738 3.8 55.3 1.0
N C:GLY596 3.9 58.9 1.0
CA C:CYS597 4.1 57.9 1.0
CD2 C:LEU527 4.4 53.0 1.0
CA C:CYS509 4.4 55.8 1.0
C C:GLY596 4.4 58.3 1.0
NH2 C:ARG405 4.5 54.5 1.0
CA C:CYS595 4.6 58.5 1.0
CA C:GLY596 4.6 58.5 1.0
C C:CYS595 4.7 58.8 1.0
C C:CYS597 4.9 57.8 1.0
S2 C:SF4738 4.9 57.4 1.0

Zinc binding site 4 out of 6 in 3git

Go back to Zinc Binding Sites List in 3git
Zinc binding site 4 out of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn739

b:57.9
occ:0.75
S D:H2S740 2.2 58.6 0.8
SG D:CYS595 2.2 57.5 1.0
SG D:CYS597 2.3 57.8 1.0
SG D:CYS509 2.3 54.4 1.0
CB D:CYS509 3.2 55.7 1.0
CB D:CYS597 3.4 57.4 1.0
CB D:CYS595 3.4 57.8 1.0
N D:CYS597 3.5 57.8 1.0
FE4 D:SF4738 3.6 56.5 1.0
S1 D:SF4738 3.7 54.7 1.0
N D:GLY596 3.9 58.6 1.0
CA D:CYS597 4.0 57.5 1.0
NH2 D:ARG405 4.4 54.9 1.0
C D:GLY596 4.4 58.1 1.0
CA D:CYS509 4.5 55.6 1.0
CD2 D:LEU527 4.5 53.4 1.0
CA D:CYS595 4.6 57.9 1.0
CA D:GLY596 4.7 57.9 1.0
C D:CYS595 4.7 58.6 1.0
C D:CYS597 4.8 57.2 1.0

Zinc binding site 5 out of 6 in 3git

Go back to Zinc Binding Sites List in 3git
Zinc binding site 5 out of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn739

b:59.1
occ:0.75
S E:H2S740 2.2 59.8 0.8
SG E:CYS597 2.2 57.8 1.0
SG E:CYS595 2.3 57.3 1.0
SG E:CYS509 2.4 54.9 1.0
CB E:CYS509 3.1 55.0 1.0
CB E:CYS595 3.3 58.5 1.0
CB E:CYS597 3.4 57.2 1.0
N E:CYS597 3.5 57.4 1.0
FE4 E:SF4738 3.5 57.2 1.0
S1 E:SF4738 3.8 56.0 1.0
N E:GLY596 3.8 58.9 1.0
CA E:CYS597 4.0 57.3 1.0
C E:GLY596 4.4 58.0 1.0
NH2 E:ARG405 4.4 53.5 1.0
CA E:CYS509 4.4 55.2 1.0
CA E:CYS595 4.5 58.5 1.0
CD2 E:LEU527 4.5 53.7 1.0
CA E:GLY596 4.6 58.0 1.0
C E:CYS595 4.6 58.9 1.0
C E:CYS597 4.9 57.3 1.0
S2 E:SF4738 5.0 57.4 1.0

Zinc binding site 6 out of 6 in 3git

Go back to Zinc Binding Sites List in 3git
Zinc binding site 6 out of 6 in the Crystal Structure of A Truncated Acetyl-Coa Synthase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Truncated Acetyl-Coa Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn739

b:57.6
occ:0.75
SG F:CYS595 2.2 57.2 1.0
SG F:CYS597 2.2 57.3 1.0
S F:H2S740 2.3 59.1 0.8
SG F:CYS509 2.3 55.4 1.0
CB F:CYS509 3.1 55.2 1.0
CB F:CYS595 3.3 57.8 1.0
N F:CYS597 3.5 57.9 1.0
CB F:CYS597 3.5 58.0 1.0
FE4 F:SF4738 3.8 56.1 1.0
N F:GLY596 3.8 58.2 1.0
S1 F:SF4738 3.9 55.2 1.0
CA F:CYS597 4.0 57.8 1.0
C F:GLY596 4.4 58.2 1.0
NH2 F:ARG405 4.4 53.5 1.0
CA F:CYS509 4.5 55.4 1.0
CD2 F:LEU527 4.5 53.9 1.0
CA F:CYS595 4.5 58.0 1.0
CA F:GLY596 4.6 58.0 1.0
C F:CYS595 4.6 58.4 1.0
C F:CYS597 4.8 58.0 1.0

Reference:

A.Volbeda, C.Darnault, X.Tan, P.A.Lindahl, J.C.Fontecilla-Camps. Novel Domain Arrangement in the Crystal Structure of A Truncated Acetyl-Coa Synthase From Moorella Thermoacetica Biochemistry V. 48 7916 2009.
ISSN: ISSN 0006-2960
PubMed: 19650626
DOI: 10.1021/BI9003952
Page generated: Wed Dec 16 04:20:41 2020

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