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Zinc in PDB 4mfe: Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate

Enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate

All present enzymatic activity of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate:
6.4.1.1;

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate, PDB code: 4mfe 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) 49.37 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.254, 157.849, 243.319, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.5

Other elements in 4mfe:

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Hydroxypyruvate (pdb code 4mfe). 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 3-Hydroxypyruvate, PDB code: 4mfe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4mfe

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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 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:44.9
occ:1.00
 OD2 A:ASP549 2.0 42.3 1.0
OQ2 A:KCX718 2.0 46.9 1.0
OQ1 A:KCX718 2.0 44.4 1.0
NE2 A:HIS747 2.1 45.5 1.0
O A:HOH1260 2.1 36.3 1.0
NE2 A:HIS749 2.1 42.3 1.0
CX A:KCX718 2.3 42.2 1.0
CE1 A:HIS747 3.0 45.6 1.0
CE1 A:HIS749 3.0 42.0 1.0
CG A:ASP549 3.1 38.4 1.0
CD2 A:HIS747 3.2 43.0 1.0
CD2 A:HIS749 3.2 43.1 1.0
OD1 A:ASP549 3.6 38.0 1.0
NZ A:KCX718 3.6 41.5 1.0
O A:HOH1233 3.9 42.5 1.0
OE1 A:GLN783 3.9 49.5 1.0
NH1 A:ARG548 4.1 42.4 1.0
ND1 A:HIS747 4.1 44.6 1.0
ND1 A:HIS749 4.2 39.5 1.0
O A:HOH1241 4.2 42.5 1.0
O3 A:3PY1102 4.2 44.2 1.0
CG A:HIS747 4.3 44.9 1.0
CG A:HIS749 4.3 38.1 1.0
CB A:ASP549 4.3 38.4 1.0
O4 A:3PY1102 4.8 62.7 1.0
CE A:KCX718 4.8 41.5 1.0
CA A:MET720 4.9 39.0 1.0
CD A:GLN783 4.9 39.8 1.0

Zinc binding site 2 out of 4 in 4mfe

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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 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1101

b:61.1
occ:1.00
 OD2 B:ASP549 1.7 66.7 1.0
OQ1 B:KCX718 2.0 64.0 1.0
NE2 B:HIS749 2.0 66.7 1.0
OQ2 B:KCX718 2.1 68.5 1.0
NE2 B:HIS747 2.1 64.4 1.0
CE1 B:HIS749 2.2 62.5 1.0
CE1 B:HIS747 2.3 59.9 1.0
CX B:KCX718 2.4 65.8 1.0
O B:HOH1234 2.4 51.6 1.0
CG B:ASP549 2.7 60.0 1.0
OD1 B:ASP549 3.2 53.9 1.0
CD2 B:HIS749 3.3 62.6 1.0
CD2 B:HIS747 3.4 63.3 1.0
ND1 B:HIS749 3.5 52.8 1.0
ND1 B:HIS747 3.6 53.8 1.0
O B:HOH1235 3.6 58.8 1.0
OE1 B:GLN783 3.7 51.5 1.0
NZ B:KCX718 3.8 60.4 1.0
NH1 B:ARG548 3.9 62.9 1.0
CB B:ASP549 4.0 56.0 1.0
CG B:HIS749 4.1 54.9 1.0
CG B:HIS747 4.1 53.9 1.0
O B:HOH1224 4.3 59.9 1.0
O3 B:3PY1102 4.4 72.2 1.0
O4 B:3PY1102 4.5 64.2 1.0
CD B:GLN783 4.7 50.7 1.0
CE B:KCX718 4.8 60.8 1.0
CA B:MET720 4.9 61.6 1.0
CZ B:ARG548 4.9 61.2 1.0
O B:MET720 5.0 56.6 1.0

Zinc binding site 3 out of 4 in 4mfe

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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 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:54.7
occ:1.00
 OQ1 C:KCX718 1.6 62.2 1.0
OD2 C:ASP549 2.0 56.9 1.0
NE2 C:HIS749 2.0 55.8 1.0
NE2 C:HIS747 2.1 56.8 1.0
CE1 C:HIS749 2.2 56.9 1.0
CX C:KCX718 2.3 54.1 1.0
O C:HOH1236 2.3 44.0 1.0
OQ2 C:KCX718 2.4 51.7 1.0
CE1 C:HIS747 2.9 52.1 1.0
CG C:ASP549 3.0 50.2 1.0
CD2 C:HIS747 3.3 48.2 1.0
CD2 C:HIS749 3.3 57.1 1.0
OD1 C:ASP549 3.4 49.2 1.0
ND1 C:HIS749 3.6 49.4 1.0
NZ C:KCX718 3.6 52.1 1.0
OE1 C:GLN783 4.0 58.8 1.0
NH1 C:ARG548 4.1 53.3 1.0
ND1 C:HIS747 4.1 48.3 1.0
CG C:HIS749 4.1 53.9 1.0
CB C:ASP549 4.3 49.9 1.0
CG C:HIS747 4.3 48.4 1.0
O3 C:3PY1102 4.4 53.8 1.0
O C:HOH1203 4.5 51.5 1.0
CE C:KCX718 4.6 50.6 1.0
O4 C:3PY1102 4.9 68.5 1.0
CA C:MET720 4.9 50.5 1.0
CD C:GLN783 4.9 50.8 1.0

Zinc binding site 4 out of 4 in 4mfe

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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 3-Hydroxypyruvate


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 3-Hydroxypyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1102

b:69.3
occ:1.00
 OD2 D:ASP549 1.7 87.4 1.0
OQ2 D:KCX718 2.0 87.2 1.0
OQ1 D:KCX718 2.0 90.3 1.0
NE2 D:HIS749 2.0 76.6 1.0
NE2 D:HIS747 2.1 75.3 1.0
CX D:KCX718 2.2 83.6 1.0
CE1 D:HIS747 2.2 69.6 1.0
CE1 D:HIS749 2.2 68.8 1.0
CG D:ASP549 2.7 78.1 1.0
OD1 D:ASP549 3.0 75.0 1.0
CD2 D:HIS749 3.4 71.7 1.0
CD2 D:HIS747 3.4 71.3 1.0
NZ D:KCX718 3.5 79.1 1.0
ND1 D:HIS749 3.5 59.7 1.0
ND1 D:HIS747 3.5 65.9 1.0
O D:HOH1232 3.8 63.0 1.0
CB D:ASP549 4.0 66.8 1.0
NH1 D:ARG548 4.1 59.4 1.0
CG D:HIS749 4.1 64.0 1.0
CG D:HIS747 4.2 65.8 1.0
O3 D:3PY1103 4.2 74.5 1.0
OE1 D:GLN783 4.3 58.0 1.0
O D:HOH1207 4.5 72.4 1.0
CE D:KCX718 4.6 80.2 1.0
O4 D:3PY1103 4.7 88.9 1.0
CA D:MET720 4.9 69.3 1.0
O D:MET720 4.9 65.4 1.0
CZ D:ARG548 5.0 59.1 1.0

Reference:

A.D.Lietzan, M.St. Maurice. Insights Into the Carboxyltransferase Reaction of Pyruvate Carboxylase From the Structures of Bound Product and Intermediate Analogs. Biochem.Biophys.Res.Commun. V. 441 377 2013.
ISSN: ISSN 0006-291X
PubMed: 24157795
DOI: 10.1016/J.BBRC.2013.10.066
Page generated: Sun Oct 27 02:26:10 2024

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