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

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

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

Protein crystallography data

The structure of Structure of the Carboxyl Transferase Domain From Rhizobium Etli Pyruvate Carboxylase with 3-Bromopyruvate, PDB code: 4mim 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) 48.13 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.592, 157.060, 243.098, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.5

Other elements in 4mim:

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

Bromine (Br) 2 atoms
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 3-Bromopyruvate (pdb code 4mim). 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-Bromopyruvate, PDB code: 4mim:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4mim

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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-Bromopyruvate


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

b:47.1
occ:1.00
OQ2 A:KCX718 2.0 47.2 1.0
BR A:BPV1102 2.1 38.3 0.2
OD2 A:ASP549 2.2 46.8 1.0
NE2 A:HIS747 2.2 43.4 1.0
OQ1 A:KCX718 2.3 42.9 1.0
NE2 A:HIS749 2.4 39.3 1.0
CX A:KCX718 2.6 45.0 1.0
CE1 A:HIS747 3.1 43.0 1.0
CG A:ASP549 3.1 44.4 1.0
CD2 A:HIS747 3.2 44.1 1.0
CD2 A:HIS749 3.3 40.9 1.0
CE1 A:HIS749 3.3 39.8 1.0
OD1 A:ASP549 3.4 40.0 1.0
C3 A:BPV1102 3.7 35.4 0.2
O A:HOH1237 3.8 42.5 1.0
OE1 A:GLN783 3.8 45.7 1.0
NZ A:KCX718 3.9 42.4 1.0
NH1 A:ARG548 4.1 48.6 1.0
ND1 A:HIS747 4.2 41.7 1.0
O3 A:BPV1102 4.2 53.7 0.8
CG A:HIS747 4.3 41.6 1.0
CB A:ASP549 4.4 43.8 1.0
O A:HOH1216 4.4 47.4 1.0
ND1 A:HIS749 4.4 39.2 1.0
CG A:HIS749 4.5 38.7 1.0
CA A:MET720 4.8 39.7 1.0
C2 A:BPV1102 4.8 35.4 0.2
O A:MET720 4.9 46.8 1.0
O3 A:BPV1102 4.9 33.4 0.2
CD A:GLN783 4.9 43.0 1.0
CE A:KCX718 5.0 40.4 1.0

Zinc binding site 2 out of 4 in 4mim

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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-Bromopyruvate


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-Bromopyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1102

b:64.2
occ:1.00
OD2 B:ASP549 1.8 58.8 1.0
OQ1 B:KCX718 2.0 57.7 1.0
NE2 B:HIS749 2.2 58.3 1.0
NE2 B:HIS747 2.3 61.4 1.0
OQ2 B:KCX718 2.4 68.2 1.0
CX B:KCX718 2.6 64.3 1.0
CG B:ASP549 2.8 58.3 1.0
CE1 B:HIS749 2.9 56.0 1.0
CE1 B:HIS747 3.1 53.8 1.0
OD1 B:ASP549 3.1 59.3 1.0
CD2 B:HIS749 3.4 55.6 1.0
CD2 B:HIS747 3.5 60.4 1.0
OE1 B:GLN783 3.6 54.5 1.0
NZ B:KCX718 3.9 61.2 1.0
NH1 B:ARG548 4.0 57.2 1.0
O3 B:BPV1103 4.0 75.6 1.0
ND1 B:HIS749 4.1 56.3 1.0
CB B:ASP549 4.2 55.9 1.0
ND1 B:HIS747 4.3 54.2 1.0
CG B:HIS749 4.4 56.1 1.0
O B:HOH1223 4.5 59.9 1.0
CG B:HIS747 4.5 55.5 1.0
C3 B:BPV1103 4.6 52.6 1.0
C2 B:BPV1103 4.7 67.7 1.0
CD B:GLN783 4.8 54.2 1.0
CA B:MET720 4.9 65.2 1.0
O B:MET720 4.9 71.3 1.0
CE B:KCX718 4.9 62.1 1.0
CZ B:ARG548 5.0 58.2 1.0

Zinc binding site 3 out of 4 in 4mim

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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-Bromopyruvate


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

b:61.3
occ:1.00
OD2 C:ASP549 2.0 70.0 1.0
OQ2 C:KCX718 2.0 50.4 1.0
NE2 C:HIS749 2.1 48.5 1.0
NE2 C:HIS747 2.3 56.0 1.0
OQ1 C:KCX718 2.4 53.5 1.0
CX C:KCX718 2.6 54.9 1.0
CE1 C:HIS749 2.8 51.8 1.0
CE1 C:HIS747 3.0 53.5 1.0
CG C:ASP549 3.1 58.5 1.0
CD2 C:HIS749 3.2 49.5 1.0
CD2 C:HIS747 3.4 56.2 1.0
OD1 C:ASP549 3.5 58.9 1.0
OE1 C:GLN783 3.8 57.9 1.0
NZ C:KCX718 3.9 54.9 1.0
ND1 C:HIS749 4.0 50.4 1.0
NH1 C:ARG548 4.1 55.9 1.0
O3 C:BPV1102 4.2 65.4 1.0
ND1 C:HIS747 4.2 51.7 1.0
CG C:HIS749 4.2 52.2 1.0
CB C:ASP549 4.3 59.1 1.0
CG C:HIS747 4.4 55.1 1.0
O C:HOH1206 4.5 65.0 1.0
CA C:MET720 4.8 54.3 1.0
CD C:GLN783 4.8 52.4 1.0
O C:MET720 5.0 54.8 1.0
CE C:KCX718 5.0 55.6 1.0

Zinc binding site 4 out of 4 in 4mim

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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-Bromopyruvate


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

b:68.2
occ:1.00
OQ2 D:KCX718 1.9 66.8 1.0
NE2 D:HIS749 2.2 64.2 1.0
OD2 D:ASP549 2.2 72.5 1.0
NE2 D:HIS747 2.2 70.5 1.0
OQ1 D:KCX718 2.3 71.1 1.0
CX D:KCX718 2.5 67.0 1.0
CG D:ASP549 3.0 71.5 1.0
CE1 D:HIS747 3.1 67.5 1.0
CE1 D:HIS749 3.1 63.2 1.0
OD1 D:ASP549 3.1 68.6 1.0
CD2 D:HIS749 3.2 64.6 1.0
CD2 D:HIS747 3.3 70.3 1.0
NZ D:KCX718 3.8 68.9 1.0
O3 D:BPV1102 3.8 74.3 1.0
NH1 D:ARG548 4.1 60.6 1.0
OE1 D:GLN783 4.2 67.4 1.0
ND1 D:HIS747 4.2 65.7 1.0
ND1 D:HIS749 4.2 61.1 1.0
CB D:ASP549 4.3 67.6 1.0
CG D:HIS749 4.3 63.9 1.0
CG D:HIS747 4.4 66.5 1.0
O D:HOH1212 4.6 80.0 1.0
CA D:MET720 4.7 66.8 1.0
C2 D:BPV1102 4.8 72.8 1.0
C3 D:BPV1102 4.9 72.5 1.0
O D:MET720 4.9 66.7 1.0
CE D:KCX718 4.9 71.2 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 Dec 16 05:35:29 2020

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