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Zinc in PDB 6six: Paak Family Amp-Ligase with Anp

Protein crystallography data

The structure of Paak Family Amp-Ligase with Anp, PDB code: 6six 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) 84.92 / 1.88
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.380, 138.139, 130.524, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.1

Other elements in 6six:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Paak Family Amp-Ligase with Anp (pdb code 6six). 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, PDB code: 6six:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6six

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:42.8
occ:0.80
NE2 A:HIS254 2.0 42.6 1.0
SG A:CYS310 2.3 55.3 1.0
SG A:CYS248 2.3 43.7 1.0
SG A:CYS308 2.4 60.4 1.0
CD2 A:HIS254 3.0 41.7 1.0
CE1 A:HIS254 3.0 44.5 1.0
CB A:CYS248 3.0 41.9 1.0
CB A:CYS308 3.0 61.4 1.0
CB A:CYS310 3.2 58.7 1.0
ND1 A:HIS254 4.1 44.6 1.0
CG A:HIS254 4.1 42.2 1.0
N A:CYS310 4.2 61.8 1.0
CA A:CYS310 4.3 60.4 1.0
CA A:CYS308 4.4 60.8 1.0
CB A:ARG252 4.5 54.6 1.0
CA A:CYS248 4.5 38.6 1.0
CB A:GLU250 4.5 58.9 1.0
O A:ARG252 4.6 40.6 1.0
CG A:GLU250 4.7 62.6 1.0
C A:CYS308 4.8 60.0 1.0
NH1 A:ARG252 4.8 82.2 1.0
CG2 A:THR316 4.9 47.5 1.0
N A:CYS248 5.0 35.9 1.0

Zinc binding site 2 out of 2 in 6six

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:42.1
occ:1.00
NE2 B:HIS254 2.1 41.1 1.0
SG B:CYS248 2.2 41.4 1.0
SG B:CYS310 2.3 43.0 1.0
SG B:CYS308 2.4 45.2 1.0
CB B:CYS248 3.0 40.1 1.0
CD2 B:HIS254 3.0 39.8 1.0
CE1 B:HIS254 3.1 42.7 1.0
CB B:CYS308 3.1 45.2 1.0
CB B:CYS310 3.2 45.7 1.0
CG B:HIS254 4.1 38.1 1.0
ND1 B:HIS254 4.1 40.6 1.0
N B:CYS310 4.2 47.5 1.0
CA B:CYS310 4.3 47.1 1.0
CB B:ARG252 4.4 42.6 1.0
CB B:GLU250 4.4 52.6 1.0
CA B:CYS248 4.4 38.0 1.0
O B:ARG252 4.5 38.9 1.0
CA B:CYS308 4.5 45.4 1.0
CG B:GLU250 4.6 56.4 1.0
C B:CYS308 4.8 46.5 1.0
N B:CYS248 4.9 34.8 1.0
CG2 B:THR316 4.9 43.0 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: Tue Oct 29 07:24:45 2024

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