Zinc in PDB 6siz: Paak Family Amp-Ligase with Anp and Substrate

Protein crystallography data

The structure of Paak Family Amp-Ligase with Anp and Substrate, PDB code: 6siz was solved by J.H.Naismith, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.80 / 1.77
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.450, 138.810, 130.700, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.8

Other elements in 6siz:

The structure of Paak Family Amp-Ligase with Anp and Substrate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Paak Family Amp-Ligase with Anp and Substrate (pdb code 6siz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Paak Family Amp-Ligase with Anp and Substrate, PDB code: 6siz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6siz

Go back to Zinc Binding Sites List in 6siz
Zinc binding site 1 out of 2 in the Paak Family Amp-Ligase with Anp and Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Paak Family Amp-Ligase with Anp and Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:59.5
occ:1.00
NE2 A:HIS254 2.1 49.6 1.0
SG A:CYS248 2.2 53.5 1.0
SG A:CYS310 2.4 66.3 1.0
SG A:CYS308 2.5 68.0 1.0
CB A:CYS248 3.0 49.3 1.0
CD2 A:HIS254 3.0 49.5 1.0
CB A:CYS310 3.1 65.2 1.0
CE1 A:HIS254 3.1 53.2 1.0
CB A:CYS308 3.2 72.0 1.0
CG A:HIS254 4.1 50.4 1.0
ND1 A:HIS254 4.2 51.8 1.0
N A:CYS310 4.2 71.8 1.0
CA A:CYS310 4.3 69.6 1.0
CB A:GLU250 4.4 67.7 1.0
CA A:CYS248 4.4 48.4 1.0
CB A:ARG252 4.5 61.1 1.0
O A:ARG252 4.6 49.1 1.0
CA A:CYS308 4.6 72.6 1.0
CG A:GLU250 4.6 73.1 1.0
C A:CYS308 4.9 71.8 1.0
N A:CYS248 4.9 45.5 1.0
CG2 A:THR316 5.0 58.9 1.0

Zinc binding site 2 out of 2 in 6siz

Go back to Zinc Binding Sites List in 6siz
Zinc binding site 2 out of 2 in the Paak Family Amp-Ligase with Anp and Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Paak Family Amp-Ligase with Anp and Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:49.2
occ:1.00
NE2 B:HIS254 2.0 44.1 1.0
SG B:CYS248 2.3 48.8 1.0
SG B:CYS310 2.4 51.5 1.0
SG B:CYS308 2.5 54.2 1.0
CD2 B:HIS254 3.0 43.0 1.0
CE1 B:HIS254 3.1 47.1 1.0
CB B:CYS248 3.1 45.6 1.0
CB B:CYS308 3.2 54.6 1.0
CB B:CYS310 3.2 52.3 1.0
CG B:HIS254 4.1 42.4 1.0
ND1 B:HIS254 4.1 43.7 1.0
N B:CYS310 4.3 54.9 1.0
CA B:CYS310 4.3 54.5 1.0
CB B:ARG252 4.4 50.0 1.0
CB B:GLU250 4.5 57.8 1.0
O B:ARG252 4.5 41.4 1.0
CA B:CYS248 4.5 43.0 1.0
CA B:CYS308 4.6 55.1 1.0
CG B:GLU250 4.8 62.4 1.0
CG2 B:THR316 4.8 50.4 1.0
C B:CYS308 4.9 55.3 1.0
N B:CYS248 4.9 41.2 1.0

Reference:

H.Song, C.Rao, Z.Deng, Y.Yi, J.H.Naismith. The Biosynthetic Pathway of the Benzoxazole in Nataxazole Proceeds Via An Unstable Ester and Has Synthetic Utility. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 31903677
DOI: 10.1002/ANIE.201915685
Page generated: Wed Dec 16 12:48:36 2020

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