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

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

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

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxalate, PDB code: 4mfd 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) 48.26 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.657, 157.368, 244.827, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24

Other elements in 4mfd:

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

Zinc binding site 1 out of 4 in 4mfd

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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 Oxalate


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

b:37.5
occ:0.75
 OQ1 A:KCX718 2.0 39.0 1.0
OD2 A:ASP549 2.1 37.1 1.0
OQ2 A:KCX718 2.1 44.9 1.0
NE2 A:HIS749 2.1 40.7 1.0
NE2 A:HIS747 2.1 38.5 1.0
CX A:KCX718 2.2 42.6 1.0
O A:HOH1286 2.3 43.7 1.0
CE1 A:HIS749 2.3 37.6 1.0
CE1 A:HIS747 3.0 37.3 1.0
CG A:ASP549 3.1 35.5 1.0
CD2 A:HIS747 3.2 38.1 1.0
OD1 A:ASP549 3.4 39.2 1.0
CD2 A:HIS749 3.4 40.1 1.0
O A:HOH1230 3.6 32.1 1.0
NZ A:KCX718 3.6 39.5 1.0
ND1 A:HIS749 3.6 35.0 1.0
OE1 A:GLN783 3.8 39.5 1.0
ND1 A:HIS747 4.2 39.5 1.0
CG A:HIS749 4.2 38.0 1.0
CG A:HIS747 4.3 37.2 1.0
NH1 A:ARG548 4.3 41.3 1.0
CB A:ASP549 4.4 35.5 1.0
O A:HOH1216 4.5 41.9 1.0
O1 A:OXL1102 4.5 44.5 1.0
CE A:KCX718 4.8 37.0 1.0
CD A:GLN783 4.9 37.3 1.0
CA A:MET720 4.9 29.6 1.0
O A:MET720 5.0 31.1 1.0

Zinc binding site 2 out of 4 in 4mfd

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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 Oxalate


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

b:43.0
occ:0.75
 OQ1 B:KCX718 2.0 59.9 1.0
OD2 B:ASP549 2.1 68.6 1.0
NE2 B:HIS749 2.1 64.0 1.0
NE2 B:HIS747 2.2 51.5 1.0
OQ2 B:KCX718 2.2 49.6 1.0
O B:HOH1246 2.5 38.8 1.0
CX B:KCX718 2.6 55.1 1.0
CG B:ASP549 2.7 56.5 1.0
OD1 B:ASP549 2.7 54.2 1.0
CE1 B:HIS747 2.8 49.0 1.0
CE1 B:HIS749 3.0 61.7 1.0
CD2 B:HIS749 3.1 58.2 1.0
CD2 B:HIS747 3.4 51.1 1.0
OE1 B:GLN783 3.6 51.0 1.0
NZ B:KCX718 3.9 55.1 1.0
ND1 B:HIS747 4.0 49.9 1.0
CB B:ASP549 4.1 54.5 1.0
ND1 B:HIS749 4.1 57.7 1.0
CG B:HIS749 4.2 55.4 1.0
NH1 B:ARG548 4.3 49.2 1.0
CG B:HIS747 4.4 50.0 1.0
O B:HOH1236 4.6 66.4 1.0
O2 B:OXL1102 4.6 47.9 1.0
CD B:GLN783 4.7 50.5 1.0

Zinc binding site 3 out of 4 in 4mfd

Go back to Zinc Binding Sites List in 4mfd
Zinc binding site 3 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxalate


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

b:58.5
occ:0.75
 OD2 C:ASP549 2.0 74.8 1.0
OQ1 C:KCX718 2.0 79.7 1.0
OQ2 C:KCX718 2.1 90.5 1.0
NE2 C:HIS749 2.1 75.0 1.0
NE2 C:HIS747 2.2 73.6 1.0
CX C:KCX718 2.2 85.9 1.0
CE1 C:HIS749 2.3 75.7 1.0
CG C:ASP549 2.7 70.0 1.0
OD1 C:ASP549 2.9 64.8 1.0
CE1 C:HIS747 3.0 65.9 1.0
CD2 C:HIS747 3.3 68.4 1.0
CD2 C:HIS749 3.5 70.4 1.0
ND1 C:HIS749 3.5 68.9 1.0
NZ C:KCX718 3.6 81.0 1.0
OE1 C:GLN783 3.9 53.3 1.0
NH1 C:ARG548 4.0 64.8 1.0
CB C:ASP549 4.0 66.0 1.0
CG C:HIS749 4.1 67.1 1.0
ND1 C:HIS747 4.2 63.5 1.0
CG C:HIS747 4.3 64.0 1.0
O C:HOH1205 4.5 48.5 1.0
O4 C:OXL1102 4.6 74.8 1.0
CE C:KCX718 4.6 81.3 1.0
O C:MET720 4.8 70.5 1.0
CD C:GLN783 4.9 51.7 1.0
CZ C:ARG548 4.9 67.5 1.0
CA C:MET720 4.9 70.9 1.0

Zinc binding site 4 out of 4 in 4mfd

Go back to Zinc Binding Sites List in 4mfd
Zinc binding site 4 out of 4 in the Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with Oxalate


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

b:56.8
occ:0.75
 NE2 D:HIS749 1.8 84.8 1.0
OQ1 D:KCX718 2.0 79.7 1.0
OD2 D:ASP549 2.1 82.9 1.0
OQ2 D:KCX718 2.1 80.9 1.0
NE2 D:HIS747 2.2 72.2 1.0
CX D:KCX718 2.2 79.4 1.0
O D:HOH1223 2.5 47.1 1.0
CD2 D:HIS749 2.7 79.0 1.0
CG D:ASP549 2.7 75.1 1.0
CE1 D:HIS749 2.7 79.7 1.0
OD1 D:ASP549 2.9 69.7 1.0
CE1 D:HIS747 3.0 67.6 1.0
CD2 D:HIS747 3.3 69.8 1.0
NZ D:KCX718 3.6 78.0 1.0
OE1 D:GLN783 3.6 59.9 1.0
ND1 D:HIS749 3.8 71.9 1.0
CG D:HIS749 3.8 71.7 1.0
CB D:ASP549 4.0 70.2 1.0
ND1 D:HIS747 4.2 67.4 1.0
CG D:HIS747 4.3 67.7 1.0
NH1 D:ARG548 4.4 67.0 1.0
O2 D:OXL1102 4.6 68.1 1.0
CD D:GLN783 4.6 60.2 1.0
CE D:KCX718 4.7 79.2 1.0
O D:HOH1216 4.7 59.5 1.0
CA D:MET720 5.0 69.1 1.0
O D:MET720 5.0 67.0 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: Wed Aug 20 20:22:34 2025

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