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Zinc in PDB 4m6v: Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin

Enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin

All present enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin:
6.4.1.1;

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin, PDB code: 4m6v was solved by A.D.Lietzan, M.St. Maurice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.66 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.641, 157.828, 244.953, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.3

Other elements in 4m6v:

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin (pdb code 4m6v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin, PDB code: 4m6v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4m6v

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Zinc binding site 1 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:37.4
occ:1.00
 OD2 A:ASP549 2.0 35.0 1.0
OQ2 A:KCX718 2.0 39.6 1.0
O A:HOH1203 2.2 34.4 1.0
NE2 A:HIS749 2.2 30.6 1.0
OQ1 A:KCX718 2.2 34.2 1.0
NE2 A:HIS747 2.2 39.4 1.0
CX A:KCX718 2.5 38.8 1.0
CE1 A:HIS749 2.9 29.3 1.0
CG A:ASP549 3.0 34.1 1.0
CD2 A:HIS747 3.2 40.3 1.0
CE1 A:HIS747 3.2 36.7 1.0
CD2 A:HIS749 3.3 31.8 1.0
OD1 A:ASP549 3.3 36.3 1.0
O A:HOH1204 3.7 32.1 1.0
NZ A:KCX718 3.9 36.2 1.0
OE1 A:GLN783 3.9 39.2 1.0
NH1 A:ARG548 4.1 36.5 1.0
ND1 A:HIS749 4.1 32.0 1.0
ND1 A:HIS747 4.3 36.8 1.0
CG A:HIS749 4.3 30.0 1.0
CG A:HIS747 4.3 36.8 1.0
O A:HOH1271 4.4 44.8 1.0
CB A:ASP549 4.4 33.0 1.0
O3 A:PYR1104 4.4 41.9 1.0
CA A:MET720 4.9 33.2 1.0
CE A:KCX718 4.9 37.8 1.0
CD A:GLN783 5.0 34.4 1.0

Zinc binding site 2 out of 4 in 4m6v

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Zinc binding site 2 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1102

b:46.5
occ:1.00
 OD2 B:ASP549 2.0 45.2 1.0
OQ2 B:KCX718 2.1 48.5 1.0
NE2 B:HIS749 2.2 45.8 1.0
OQ1 B:KCX718 2.2 47.2 1.0
O B:HOH1205 2.2 42.0 1.0
NE2 B:HIS747 2.2 46.1 1.0
CX B:KCX718 2.5 49.8 1.0
CE1 B:HIS749 2.9 45.2 1.0
CG B:ASP549 3.0 44.2 1.0
CE1 B:HIS747 3.1 45.2 1.0
CD2 B:HIS749 3.3 46.5 1.0
CD2 B:HIS747 3.3 45.9 1.0
OD1 B:ASP549 3.4 42.6 1.0
O B:HOH1233 3.7 47.5 1.0
NZ B:KCX718 3.8 50.8 1.0
OE1 B:GLN783 3.9 41.4 1.0
NH1 B:ARG548 4.0 47.5 1.0
ND1 B:HIS749 4.1 45.0 1.0
ND1 B:HIS747 4.2 43.7 1.0
CG B:HIS749 4.3 44.2 1.0
CB B:ASP549 4.4 42.3 1.0
CG B:HIS747 4.4 43.6 1.0
O3 B:PYR1105 4.4 63.8 1.0
O B:HOH1272 4.5 53.9 1.0
CE B:KCX718 4.8 51.1 1.0
C3 B:PYR1105 4.9 66.2 1.0
CD B:GLN783 4.9 40.0 1.0
CA B:MET720 4.9 48.2 1.0

Zinc binding site 3 out of 4 in 4m6v

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Zinc binding site 3 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:49.1
occ:1.00
 OD2 C:ASP549 2.0 47.2 1.0
OQ2 C:KCX718 2.0 49.2 1.0
NE2 C:HIS749 2.1 49.6 1.0
NE2 C:HIS747 2.2 50.2 1.0
OQ1 C:KCX718 2.3 53.2 1.0
O C:HOH1203 2.3 47.7 1.0
CX C:KCX718 2.5 51.3 1.0
CE1 C:HIS749 2.7 47.7 1.0
CE1 C:HIS747 3.0 50.1 1.0
CG C:ASP549 3.0 47.1 1.0
CD2 C:HIS747 3.3 50.8 1.0
CD2 C:HIS749 3.3 51.0 1.0
OD1 C:ASP549 3.4 49.5 1.0
NZ C:KCX718 3.8 51.4 1.0
O C:HOH1250 3.8 56.2 1.0
OE1 C:GLN783 3.9 48.4 1.0
ND1 C:HIS749 3.9 48.3 1.0
NH1 C:ARG548 4.1 46.7 1.0
ND1 C:HIS747 4.2 49.3 1.0
CG C:HIS749 4.2 51.2 1.0
CG C:HIS747 4.3 50.9 1.0
CB C:ASP549 4.4 45.5 1.0
O C:HOH1236 4.4 55.5 1.0
O3 C:PYR1105 4.6 56.6 1.0
CE C:KCX718 4.9 51.6 1.0
CA C:MET720 4.9 52.3 1.0
CD C:GLN783 4.9 46.2 1.0

Zinc binding site 4 out of 4 in 4m6v

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Zinc binding site 4 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate and Biocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1101

b:57.6
occ:1.00
 OQ1 D:KCX718 2.0 58.4 1.0
OD2 D:ASP549 2.1 59.4 1.0
NE2 D:HIS749 2.1 50.1 1.0
NE2 D:HIS747 2.2 57.5 1.0
O D:HOH1202 2.3 45.6 1.0
OQ2 D:KCX718 2.4 57.0 1.0
CX D:KCX718 2.5 60.4 1.0
CE1 D:HIS747 2.7 56.0 1.0
CE1 D:HIS749 3.0 50.0 1.0
CG D:ASP549 3.1 56.5 1.0
CD2 D:HIS749 3.2 51.5 1.0
OD1 D:ASP549 3.4 53.7 1.0
CD2 D:HIS747 3.4 59.6 1.0
O D:HOH1229 3.7 56.7 1.0
NZ D:KCX718 3.8 62.8 1.0
OE1 D:GLN783 3.8 52.4 1.0
ND1 D:HIS747 3.9 56.3 1.0
ND1 D:HIS749 4.1 50.3 1.0
NH1 D:ARG548 4.1 57.8 1.0
CG D:HIS749 4.3 50.6 1.0
CG D:HIS747 4.3 57.3 1.0
O3 D:PYR1104 4.3 70.7 1.0
CB D:ASP549 4.4 57.4 1.0
O D:HOH1249 4.8 70.0 1.0
CD D:GLN783 4.8 50.8 1.0
CE D:KCX718 4.9 65.2 1.0
O D:MET720 5.0 56.4 1.0

Reference:

A.D.Lietzan, Y.Lin, M.St. Maurice. The Role of Biotin and Oxamate in the Carboxyltransferase Reaction of Pyruvate Carboxylase. Arch.Biochem.Biophys. V.562C 70 2014.
ISSN: ISSN 0003-9861
PubMed: 25157442
DOI: 10.1016/J.ABB.2014.08.008
Page generated: Sun Oct 27 02:16:27 2024

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