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Zinc in PDB 4jx5: Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate

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

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

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate, PDB code: 4jx5 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) 46.88 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.130, 157.253, 245.320, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.2

Other elements in 4jx5:

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Pyruvate 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 (pdb code 4jx5). 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, PDB code: 4jx5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4jx5

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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


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

b:43.4
occ:1.00
 OD2 A:ASP549 2.0 42.6 1.0
NE2 A:HIS747 2.1 42.7 1.0
NE2 A:HIS749 2.1 39.0 1.0
OQ1 A:KCX718 2.2 46.8 1.0
OQ2 A:KCX718 2.2 46.7 1.0
O A:HOH1284 2.2 41.7 1.0
CX A:KCX718 2.7 47.7 1.0
CE1 A:HIS749 3.0 36.3 1.0
CE1 A:HIS747 3.0 37.9 1.0
CD2 A:HIS747 3.0 37.8 1.0
CG A:ASP549 3.1 39.6 1.0
CD2 A:HIS749 3.1 35.9 1.0
OD1 A:ASP549 3.5 39.9 1.0
O A:HOH1256 3.7 39.0 1.0
NZ A:KCX718 4.0 41.8 1.0
OE1 A:GLN783 4.1 37.1 1.0
ND1 A:HIS747 4.1 37.0 1.0
ND1 A:HIS749 4.1 36.6 1.0
CG A:HIS747 4.2 37.2 1.0
NH1 A:ARG548 4.2 34.4 1.0
CG A:HIS749 4.2 35.8 1.0
O A:HOH1283 4.4 48.1 1.0
CB A:ASP549 4.4 37.1 1.0
O3 A:PYR1104 4.4 44.6 1.0
CA A:MET720 4.8 30.2 1.0
O A:MET720 4.9 30.4 1.0

Zinc binding site 2 out of 4 in 4jx5

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1104

b:51.7
occ:1.00
 NE2 B:HIS749 2.0 52.0 1.0
OD2 B:ASP549 2.0 58.6 1.0
NE2 B:HIS747 2.0 59.9 1.0
OQ1 B:KCX718 2.1 61.8 1.0
OQ2 B:KCX718 2.2 55.4 1.0
O B:HOH1246 2.3 46.8 1.0
CX B:KCX718 2.5 57.1 1.0
CE1 B:HIS747 2.8 56.8 1.0
CE1 B:HIS749 2.9 49.8 1.0
CD2 B:HIS749 3.0 49.6 1.0
CG B:ASP549 3.0 54.5 1.0
CD2 B:HIS747 3.2 57.1 1.0
OD1 B:ASP549 3.4 58.1 1.0
NZ B:KCX718 3.9 60.9 1.0
O B:HOH1239 3.9 53.5 1.0
OE1 B:GLN783 3.9 47.8 1.0
ND1 B:HIS747 4.0 55.5 1.0
ND1 B:HIS749 4.1 48.6 1.0
NH1 B:ARG548 4.1 45.1 1.0
CG B:HIS749 4.1 51.2 1.0
CG B:HIS747 4.2 57.7 1.0
CB B:ASP549 4.3 52.2 1.0
O B:HOH1245 4.5 63.5 1.0
O3 B:PYR1105 4.6 48.4 1.0
CD B:GLN783 4.9 45.7 1.0
CA B:MET720 4.9 53.7 1.0

Zinc binding site 3 out of 4 in 4jx5

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1104

b:54.9
occ:1.00
 OD2 C:ASP549 2.0 54.9 1.0
NE2 C:HIS749 2.0 63.6 1.0
NE2 C:HIS747 2.1 60.9 1.0
OQ1 C:KCX718 2.1 66.1 1.0
OQ2 C:KCX718 2.2 70.1 1.0
O C:HOH1242 2.2 46.4 1.0
CX C:KCX718 2.6 64.6 1.0
CE1 C:HIS749 2.9 57.7 1.0
CE1 C:HIS747 3.0 52.3 1.0
CG C:ASP549 3.1 54.1 1.0
CD2 C:HIS747 3.1 56.8 1.0
CD2 C:HIS749 3.2 58.2 1.0
OD1 C:ASP549 3.5 54.6 1.0
NZ C:KCX718 3.9 66.7 1.0
OE1 C:GLN783 4.0 49.5 1.0
NH1 C:ARG548 4.1 56.2 1.0
ND1 C:HIS749 4.1 54.6 1.0
ND1 C:HIS747 4.1 49.9 1.0
CG C:HIS749 4.2 54.6 1.0
CG C:HIS747 4.2 54.5 1.0
CB C:ASP549 4.4 52.2 1.0
O C:HOH1241 4.4 49.9 1.0
C3 C:PYR1105 4.5 30.9 0.5
O3 C:PYR1105 4.6 32.8 0.5
CA C:MET720 4.7 57.8 1.0
O C:MET720 4.8 61.3 1.0
CE C:KCX718 4.9 65.3 1.0
C2 C:PYR1105 5.0 32.6 0.5

Zinc binding site 4 out of 4 in 4jx5

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1103

b:60.2
occ:1.00
 OD2 D:ASP549 2.0 72.5 1.0
NE2 D:HIS749 2.0 64.6 1.0
NE2 D:HIS747 2.0 70.2 1.0
OQ1 D:KCX718 2.1 75.0 1.0
OQ2 D:KCX718 2.2 73.7 1.0
CX D:KCX718 2.5 70.3 1.0
CE1 D:HIS749 2.9 59.0 1.0
CE1 D:HIS747 2.9 64.6 1.0
CG D:ASP549 3.0 67.5 1.0
CD2 D:HIS749 3.1 60.2 1.0
CD2 D:HIS747 3.1 65.3 1.0
OD1 D:ASP549 3.4 66.0 1.0
NZ D:KCX718 3.9 71.2 1.0
NH1 D:ARG548 4.0 57.3 1.0
ND1 D:HIS749 4.1 56.6 1.0
ND1 D:HIS747 4.1 63.0 1.0
OE1 D:GLN783 4.2 55.7 1.0
CG D:HIS749 4.2 57.3 1.0
CG D:HIS747 4.2 62.7 1.0
O3 D:PYR1104 4.3 60.4 1.0
CB D:ASP549 4.3 63.8 1.0
O D:HOH1233 4.6 60.8 1.0
CA D:MET720 4.8 60.2 1.0
O D:MET720 4.9 57.2 1.0
CZ D:ARG548 5.0 58.2 1.0
CE D:KCX718 5.0 70.4 1.0

Reference:

A.D.Lietzan, M.St Maurice. A Substrate-Induced Biotin Binding Pocket in the Carboxyltransferase Domain of Pyruvate Carboxylase. J.Biol.Chem. V. 288 19915 2013.
ISSN: ISSN 0021-9258
PubMed: 23698000
DOI: 10.1074/JBC.M113.477828
Page generated: Sun Oct 27 01:30:43 2024

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