Zinc in PDB 7e44: Crystal Structure of Nudc Complexed with Dpcoa

All present enzymatic activity of Crystal Structure of Nudc Complexed with Dpcoa:
3.6.1.22;

The structure of Crystal Structure of Nudc Complexed with Dpcoa, PDB code: 7e44 was solved by W.Zhou, Z.Y.Guan, P.Yin, D.L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.33 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.837, 61.651, 93.893, 97.24, 100.39, 111.14
R / Rfree (%)	23.4 / 24.8

The binding sites of Zinc atom in the Crystal Structure of Nudc Complexed with Dpcoa (pdb code 7e44). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Nudc Complexed with Dpcoa, PDB code: 7e44:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Nudc Complexed with Dpcoa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Nudc Complexed with Dpcoa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:37.3 occ:1.00 SG A:CYS119 2.2 38.5 1.0 SG A:CYS116 2.3 37.0 1.0 SG A:CYS101 2.3 38.8 1.0 SG A:CYS98 2.4 33.4 1.0 CB A:CYS119 2.8 66.0 1.0 CB A:CYS98 3.2 37.9 1.0 CB A:CYS116 3.3 37.2 1.0 CB A:CYS101 3.4 40.7 1.0 N A:CYS119 3.6 44.3 1.0 CA A:CYS119 3.7 48.4 1.0 N A:CYS101 3.8 40.4 1.0 CA A:CYS101 4.1 38.1 1.0 CB A:TYR100 4.6 45.5 1.0 CA A:CYS98 4.6 37.3 1.0 CA A:CYS116 4.7 37.1 1.0 C A:HIS118 4.7 45.8 1.0 C A:CYS119 4.8 44.2 1.0 C A:TYR100 4.8 39.0 1.0 C A:CYS101 4.8 39.6 1.0 CB A:HIS118 4.8 42.9 1.0 CB A:HIS103 4.8 41.5 1.0 N A:GLY102 4.9 39.1 1.0 N A:HIS103 4.9 38.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Nudc Complexed with Dpcoa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Nudc Complexed with Dpcoa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:42.0 occ:1.00 SG B:CYS101 2.3 44.1 1.0 SG B:CYS116 2.3 45.6 1.0 SG B:CYS98 2.3 36.9 1.0 SG B:CYS119 2.4 45.5 1.0 CB B:CYS98 3.2 37.6 1.0 CB B:CYS116 3.3 43.6 1.0 CB B:CYS101 3.4 42.6 1.0 CB B:CYS119 3.4 49.9 1.0 N B:CYS119 3.8 50.1 1.0 N B:CYS101 3.8 36.4 1.0 CA B:CYS119 4.1 55.0 1.0 CA B:CYS101 4.2 42.4 1.0 CB B:TYR100 4.5 38.4 1.0 C B:CYS119 4.6 50.6 1.0 O B:CYS119 4.6 53.3 1.0 CA B:CYS98 4.7 38.9 1.0 CA B:CYS116 4.7 44.3 1.0 C B:TYR100 4.8 41.8 1.0 C B:HIS118 4.9 54.4 1.0 CB B:HIS118 5.0 57.8 1.0 N B:GLY102 5.0 42.5 1.0 C B:CYS101 5.0 40.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Nudc Complexed with Dpcoa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Nudc Complexed with Dpcoa within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn302 b:30.3 occ:1.00 SG E:CYS101 2.3 28.2 1.0 SG E:CYS98 2.3 25.1 1.0 SG E:CYS116 2.4 29.6 1.0 SG E:CYS119 2.4 31.8 1.0 CB E:CYS98 3.1 25.1 1.0 CB E:CYS116 3.3 26.9 1.0 CB E:CYS101 3.4 29.0 1.0 CB E:CYS119 3.4 31.3 1.0 N E:CYS119 3.7 33.5 1.0 N E:CYS101 3.8 26.3 1.0 CA E:CYS119 4.0 31.5 1.0 CA E:CYS101 4.1 29.0 1.0 CB E:TYR100 4.3 25.6 1.0 CA E:CYS98 4.6 29.1 1.0 O F:HOH522 4.6 42.0 1.0 C E:CYS119 4.7 33.4 1.0 C E:TYR100 4.7 29.3 1.0 CA E:CYS116 4.7 27.6 1.0 O E:CYS119 4.8 37.7 1.0 C E:HIS118 4.8 40.0 1.0 CB E:HIS118 4.8 35.4 1.0 C E:CYS101 4.9 27.9 1.0 CA E:TYR100 4.9 27.7 1.0 N E:GLY102 5.0 29.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Nudc Complexed with Dpcoa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Nudc Complexed with Dpcoa within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn302 b:25.1 occ:1.00 SG F:CYS101 2.3 27.0 1.0 SG F:CYS116 2.3 25.1 1.0 SG F:CYS119 2.3 23.1 1.0 SG F:CYS98 2.4 23.1 1.0 CB F:CYS98 3.1 23.8 1.0 CB F:CYS116 3.3 23.8 1.0 CB F:CYS119 3.4 29.1 1.0 CB F:CYS101 3.5 30.7 1.0 N F:CYS119 3.7 34.1 1.0 N F:CYS101 4.0 27.2 1.0 CA F:CYS119 4.0 26.4 1.0 CA F:CYS101 4.3 29.4 1.0 CA F:CYS98 4.6 23.7 1.0 O F:HOH537 4.6 32.4 1.0 CB F:TYR100 4.6 24.7 1.0 C F:CYS119 4.6 24.7 1.0 CA F:CYS116 4.7 24.0 1.0 O F:CYS119 4.7 25.2 1.0 C F:HIS118 4.9 35.2 1.0 C F:CYS101 4.9 30.9 1.0 C F:TYR100 4.9 29.4 1.0 CB F:HIS118 4.9 34.1 1.0

W.Zhou, Z.Guan, F.Zhao, Y.Ye, F.Yang, P.Yin, D.Zhang. Structural Insights Into Dpcoa-Rna Decapping By Nudc. Rna Biol. 1 2021.
ISSN: ESSN 1555-8584
PubMed: 34074215
DOI: 10.1080/15476286.2021.1936837