Atomistry » Zinc » PDB 4m2w-4mhq » 4m6v
Atomistry »
  Zinc »
    PDB 4m2w-4mhq »
      4m6v »

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

Go back to Zinc Binding Sites List in 4m6v
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

Go back to Zinc Binding Sites List in 4m6v
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

Go back to Zinc Binding Sites List in 4m6v
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

Go back to Zinc Binding Sites List in 4m6v
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy