Zinc in PDB 5vjj: Crystal Structure of the Flax-Rust Effector Avrp

The structure of Crystal Structure of the Flax-Rust Effector Avrp, PDB code: 5vjj was solved by X.Zhang, D.J.Ericsson, S.J.Williams, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.01 / 2.52
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.937, 88.937, 45.782, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26.4

The binding sites of Zinc atom in the Crystal Structure of the Flax-Rust Effector Avrp (pdb code 5vjj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Flax-Rust Effector Avrp, PDB code: 5vjj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Flax-Rust Effector Avrp


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 the Flax-Rust Effector Avrp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:30.0 occ:1.00 SG A:CYS81 2.3 34.8 1.0 SG A:CYS38 2.3 46.3 1.0 SG A:CYS78 2.3 35.2 1.0 SG A:CYS36 2.4 34.5 1.0 HB3 A:CYS36 2.9 39.4 1.0 HB3 A:CYS38 3.1 35.5 1.0 CB A:CYS36 3.2 32.8 1.0 HB2 A:CYS78 3.2 41.5 1.0 CB A:CYS78 3.2 34.6 1.0 HB2 A:CYS81 3.2 36.3 1.0 H A:CYS81 3.2 64.0 1.0 HB3 A:CYS78 3.3 41.5 1.0 CB A:CYS38 3.4 29.6 1.0 CB A:CYS81 3.4 30.2 1.0 H A:CYS38 3.4 36.3 1.0 HB2 A:CYS36 3.4 39.4 1.0 HB3 A:ASN80 3.5 36.7 1.0 HD22 A:ASN80 3.7 35.2 1.0 HH11 A:ARG84 3.7 46.3 1.0 HB2 A:ARG40 3.8 46.1 1.0 N A:CYS81 3.9 53.3 1.0 HB2 A:CYS38 4.1 35.5 1.0 HD2 A:ARG40 4.1 60.3 1.0 HB3 A:CYS81 4.1 36.3 1.0 N A:CYS38 4.1 30.2 1.0 CA A:CYS81 4.3 43.7 1.0 CA A:CYS38 4.3 33.4 1.0 HD3 A:ARG84 4.4 40.5 1.0 H A:ARG40 4.4 39.7 1.0 H A:ASN80 4.4 29.4 1.0 HH11 A:ARG40 4.4 52.0 1.0 CB A:ASN80 4.5 30.6 1.0 NH1 A:ARG84 4.5 38.6 1.0 ND2 A:ASN80 4.6 29.3 1.0 HE2 A:TYR76 4.6 41.4 1.0 CA A:CYS36 4.6 34.2 1.0 HH12 A:ARG84 4.6 46.3 1.0 CA A:CYS78 4.7 25.1 1.0 HD2 A:ARG84 4.7 40.5 1.0 CB A:ARG40 4.7 38.4 1.0 H A:LEU37 4.8 37.6 1.0 C A:CYS36 4.9 39.4 1.0 HA A:CYS81 4.9 52.4 1.0 HA A:CYS78 4.9 30.2 1.0 N A:LEU37 4.9 31.3 1.0 C A:ASN80 4.9 35.0 1.0 C A:CYS38 5.0 42.7 1.0 CD A:ARG40 5.0 50.2 1.0 HB2 A:ASN80 5.0 36.7 1.0 H A:ARG39 5.0 43.6 1.0 CD A:ARG84 5.0 33.7 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Flax-Rust Effector Avrp


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 the Flax-Rust Effector Avrp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:36.3 occ:1.00 NE2 A:HIS93 2.0 33.7 1.0 SG A:CYS89 2.2 37.5 1.0 SG A:CYS53 2.3 29.4 1.0 SG A:CYS67 2.3 37.0 1.0 CE1 A:HIS93 3.0 40.2 1.0 HB3 A:CYS67 3.0 34.4 1.0 CD2 A:HIS93 3.0 57.9 1.0 HB3 A:CYS89 3.1 31.8 1.0 CB A:CYS53 3.2 19.9 1.0 HE1 A:HIS93 3.2 48.3 1.0 CB A:CYS67 3.2 28.7 1.0 HB2 A:CYS53 3.2 23.9 1.0 HB3 A:CYS53 3.2 23.9 1.0 CB A:CYS89 3.2 26.4 1.0 HD2 A:HIS93 3.2 69.5 1.0 HB2 A:CYS67 3.3 34.4 1.0 HB2 A:CYS89 3.4 31.8 1.0 HA3 A:GLY91 3.7 51.9 1.0 H A:GLY91 3.8 62.7 1.0 HA2 A:GLY69 3.9 42.8 1.0 HB3 A:ALA55 3.9 28.1 1.0 H A:GLY69 4.0 41.9 1.0 ND1 A:HIS93 4.1 56.2 1.0 CG A:HIS93 4.2 59.7 1.0 HB2 A:ALA71 4.2 37.0 1.0 CA A:GLY91 4.4 43.2 1.0 N A:GLY91 4.4 52.2 1.0 CA A:CYS67 4.6 39.1 1.0 CA A:CYS53 4.6 27.2 1.0 CA A:CYS89 4.6 27.5 1.0 HB2 A:ALA55 4.6 28.1 1.0 CA A:GLY69 4.7 35.6 1.0 H A:ALA55 4.7 33.2 1.0 N A:GLY69 4.7 34.9 1.0 CB A:ALA55 4.7 23.4 1.0 C A:GLY91 4.8 41.2 1.0 O A:GLY91 4.8 54.4 1.0 HA A:CYS53 4.9 32.7 1.0 HD1 A:HIS93 4.9 67.4 1.0 HA A:CYS89 4.9 33.0 1.0 C A:CYS89 5.0 41.6 1.0 C A:CYS67 5.0 31.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Flax-Rust Effector Avrp


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 the Flax-Rust Effector Avrp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:47.5 occ:1.00 HE1 A:HIS101 1.8 49.9 1.0 NE2 A:HIS101 1.9 79.2 1.0 CE1 A:HIS101 2.1 41.6 1.0 SG A:CYS97 2.3 51.9 1.0 SG A:CYS59 2.4 60.6 1.0 SG A:CYS61 2.4 36.4 1.0 HB2 A:CYS59 2.9 39.3 1.0 HB3 A:CYS97 3.0 58.2 1.0 HA A:CYS97 3.0 72.6 1.0 CB A:CYS97 3.1 48.5 1.0 CB A:CYS59 3.2 32.8 1.0 CD2 A:HIS101 3.3 61.5 1.0 H A:CYS61 3.3 60.2 1.0 ND1 A:HIS101 3.4 41.0 1.0 HB3 A:TYR63 3.4 40.2 1.0 HB3 A:CYS61 3.5 40.9 1.0 CA A:CYS97 3.5 60.5 1.0 CB A:CYS61 3.6 34.1 1.0 HB2 A:TYR63 3.6 40.2 1.0 HB3 A:CYS59 3.7 39.3 1.0 HD2 A:PRO60 3.8 75.7 1.0 HD2 A:HIS101 3.9 73.8 1.0 HB2 A:CYS97 3.9 58.2 1.0 CG A:HIS101 4.0 40.3 1.0 CB A:TYR63 4.0 33.5 1.0 HD1 A:HIS101 4.0 49.2 1.0 N A:CYS61 4.1 50.1 1.0 H A:TYR63 4.1 65.0 1.0 CA A:CYS61 4.3 47.6 1.0 HB2 A:CYS61 4.4 40.9 1.0 N A:CYS97 4.5 63.9 1.0 HG2 A:PRO60 4.5 78.5 1.0 CA A:CYS59 4.5 33.6 1.0 C A:CYS97 4.6 51.7 1.0 CD A:PRO60 4.6 63.1 1.0 H A:CYS97 4.6 76.7 1.0 C A:CYS59 4.6 50.7 1.0 O A:CYS97 4.7 60.5 1.0 N A:PRO60 4.7 67.3 1.0 C A:CYS61 4.7 48.5 1.0 N A:TYR63 4.8 54.2 1.0 CG A:TYR63 4.9 30.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Flax-Rust Effector Avrp


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 the Flax-Rust Effector Avrp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:30.7 occ:1.00 SG B:CYS38 2.3 29.1 1.0 SG B:CYS81 2.3 24.3 1.0 SG B:CYS78 2.3 27.1 1.0 SG B:CYS36 2.3 30.1 1.0 HB3 B:CYS38 2.9 22.3 1.0 HB2 B:CYS81 3.1 26.3 1.0 HB3 B:CYS36 3.1 25.6 1.0 H B:CYS81 3.2 38.1 1.0 HB2 B:CYS78 3.2 26.4 1.0 CB B:CYS78 3.2 22.0 1.0 CB B:CYS38 3.2 18.6 1.0 HB3 B:CYS78 3.2 26.4 1.0 CB B:CYS36 3.3 21.4 1.0 CB B:CYS81 3.3 21.9 1.0 HB3 B:ASN80 3.3 57.7 1.0 HD22 B:ASN80 3.3 71.8 1.0 H B:CYS38 3.4 28.2 1.0 HB2 B:ARG40 3.5 28.4 1.0 HB2 B:CYS36 3.5 25.6 1.0 N B:CYS81 3.7 31.8 1.0 HH11 B:ARG84 3.9 28.6 1.0 HB2 B:CYS38 3.9 22.3 1.0 HB3 B:CYS81 4.1 26.3 1.0 N B:CYS38 4.1 23.5 1.0 CA B:CYS81 4.2 37.5 1.0 ND2 B:ASN80 4.2 59.9 1.0 H B:ASN80 4.2 37.9 1.0 CA B:CYS38 4.2 32.6 1.0 CB B:ASN80 4.3 48.1 1.0 H B:ARG40 4.4 43.4 1.0 CB B:ARG40 4.4 23.6 1.0 HD3 B:ARG84 4.5 38.3 1.0 HG3 B:ARG40 4.5 38.1 1.0 HE2 B:TYR76 4.6 27.4 1.0 NH1 B:ARG84 4.6 23.8 1.0 CA B:CYS78 4.6 26.1 1.0 C B:ASN80 4.7 45.4 1.0 CA B:CYS36 4.7 21.6 1.0 HA B:CYS81 4.7 45.0 1.0 HH12 B:ARG84 4.7 28.6 1.0 HD21 B:ASN80 4.8 71.8 1.0 CG B:ASN80 4.8 61.3 1.0 HB3 B:ARG40 4.8 28.4 1.0 CA B:ASN80 4.8 38.1 1.0 HB2 B:ASN80 4.9 57.7 1.0 N B:ASN80 4.9 31.6 1.0 C B:CYS38 4.9 33.3 1.0 HD2 B:ARG84 4.9 38.3 1.0 HA B:CYS78 4.9 31.4 1.0 H B:ARG39 4.9 29.3 1.0 H B:LEU37 4.9 47.2 1.0 CG B:ARG40 5.0 31.8 1.0 C B:CYS36 5.0 32.0 1.0 HA B:CYS38 5.0 39.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Flax-Rust Effector Avrp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Flax-Rust Effector Avrp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:27.7 occ:1.00 NE2 B:HIS93 2.0 35.0 1.0 SG B:CYS53 2.3 26.1 1.0 SG B:CYS67 2.3 38.5 1.0 SG B:CYS89 2.3 30.1 1.0 CD2 B:HIS93 2.8 28.0 1.0 HD2 B:HIS93 2.9 33.6 1.0 HB3 B:CYS67 3.0 38.0 1.0 CE1 B:HIS93 3.1 42.1 1.0 CB B:CYS67 3.1 31.6 1.0 HB3 B:CYS89 3.1 35.9 1.0 CB B:CYS53 3.2 23.2 1.0 HB3 B:CYS53 3.2 27.9 1.0 CB B:CYS89 3.2 29.9 1.0 HB2 B:CYS53 3.2 27.9 1.0 HB2 B:CYS67 3.3 38.0 1.0 HB3 B:ALA55 3.3 35.6 1.0 HB2 B:CYS89 3.4 35.9 1.0 HE1 B:HIS93 3.4 50.5 1.0 HA3 B:GLY91 4.0 44.7 1.0 H B:GLY91 4.0 53.3 1.0 CG B:HIS93 4.0 40.2 1.0 HA2 B:GLY69 4.1 40.6 1.0 ND1 B:HIS93 4.1 45.5 1.0 H B:GLY69 4.2 34.4 1.0 CB B:ALA55 4.2 29.7 1.0 HB2 B:ALA55 4.3 35.6 1.0 H B:ALA55 4.5 40.6 1.0 HB2 B:ALA71 4.5 31.6 1.0 CA B:CYS67 4.6 39.4 1.0 CA B:GLY91 4.6 37.3 1.0 CA B:CYS53 4.6 25.5 1.0 N B:GLY91 4.6 44.4 1.0 CA B:CYS89 4.7 23.4 1.0 HB1 B:ALA55 4.7 35.6 1.0 N B:GLY69 4.8 28.7 1.0 CA B:GLY69 4.8 33.8 1.0 C B:GLY91 4.9 31.4 1.0 O B:GLY91 4.9 43.0 1.0 HA B:CYS53 4.9 30.6 1.0 HA B:CYS67 4.9 47.3 1.0 HD1 B:HIS93 5.0 54.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Flax-Rust Effector Avrp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Flax-Rust Effector Avrp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:38.1 occ:1.00 NE2 B:HIS101 2.0 50.9 1.0 SG B:CYS61 2.2 41.6 1.0 SG B:CYS59 2.3 34.3 1.0 SG B:CYS97 2.3 29.6 1.0 H B:CYS61 2.9 35.7 1.0 CE1 B:HIS101 3.0 34.7 1.0 HA B:CYS97 3.0 48.5 1.0 HB2 B:CYS59 3.0 29.3 1.0 HB3 B:CYS61 3.1 32.2 1.0 CD2 B:HIS101 3.1 42.5 1.0 HE1 B:HIS101 3.1 41.6 1.0 HB3 B:CYS97 3.2 37.1 1.0 CB B:CYS61 3.2 26.9 1.0 CB B:CYS97 3.2 30.9 1.0 CB B:CYS59 3.3 24.4 1.0 HD2 B:HIS101 3.3 51.0 1.0 HB3 B:TYR63 3.5 50.4 1.0 CA B:CYS97 3.6 40.4 1.0 HD2 B:PRO60 3.6 44.4 1.0 HB2 B:TYR63 3.6 50.4 1.0 N B:CYS61 3.6 29.8 1.0 HB3 B:CYS59 3.8 29.3 1.0 CA B:CYS61 4.0 25.9 1.0 HB2 B:CYS61 4.0 32.2 1.0 H B:TYR63 4.0 57.6 1.0 CB B:TYR63 4.1 42.0 1.0 HB2 B:CYS97 4.1 37.1 1.0 ND1 B:HIS101 4.1 40.4 1.0 CG B:HIS101 4.2 48.2 1.0 CD B:PRO60 4.4 37.0 1.0 HG2 B:PRO60 4.4 56.0 1.0 N B:PRO60 4.4 31.1 1.0 N B:CYS97 4.4 30.0 1.0 CA B:CYS59 4.5 23.6 1.0 C B:CYS59 4.5 24.4 1.0 C B:CYS61 4.6 26.6 1.0 H B:CYS97 4.6 36.0 1.0 C B:CYS97 4.7 41.1 1.0 C B:PRO60 4.8 29.3 1.0 HA B:CYS61 4.8 31.1 1.0 N B:TYR63 4.8 48.0 1.0 O B:CYS97 4.9 67.3 1.0 HD1 B:HIS101 4.9 48.5 1.0 CG B:PRO60 4.9 46.7 1.0 HB B:VAL100 4.9 35.4 1.0 CG B:TYR63 5.0 38.2 1.0

X.Zhang, N.Farah, L.Rolston, D.J.Ericsson, A.M.Catanzariti, M.Bernoux, T.Ve, K.Bendak, C.Chen, J.P.Mackay, G.J.Lawrence, A.Hardham, J.G.Ellis, S.J.Williams, P.N.Dodds, D.A.Jones, B.Kobe. Crystal Structure of the Melampsora Lini Effector Avrp Reveals Insights Into A Possible Nuclear Function and Recognition By the Flax Disease Resistance Protein P. Mol. Plant Pathol. V. 19 1196 2018.
ISSN: ISSN 1364-3703
PubMed: 28817232
DOI: 10.1111/MPP.12597