Zinc in PDB 8pfc: Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana

The structure of Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana, PDB code: 8pfc was solved by W.Huang, Q.Liu, A.Maqbool, C.E.M.Stevenson, D.M.Lawson, S.Kamoun, S.A.Hogenhout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.21 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.686, 165.019, 80.862, 90, 109.65, 90
R / Rfree (%)	22.3 / 25.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana (pdb code 8pfc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana, PDB code: 8pfc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


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 Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:66.5 occ:1.00 OE1 A:GLU80 2.1 59.5 1.0 OE2 D:GLU118 2.1 71.4 1.0 NE2 B:HIS82 2.1 59.8 1.0 O D:HOH317 2.3 36.1 1.0 CD D:GLU118 2.8 68.0 1.0 OE1 D:GLU118 2.9 65.3 1.0 CD2 B:HIS82 2.9 50.3 1.0 CD A:GLU80 3.0 66.7 1.0 CE1 B:HIS82 3.2 52.0 1.0 OE2 A:GLU80 3.2 70.8 1.0 NH1 B:ARG109 3.9 58.4 1.0 CG B:HIS82 4.1 46.1 1.0 ND1 B:HIS82 4.2 51.9 1.0 CG D:GLU118 4.3 68.7 1.0 NH2 B:ARG109 4.3 63.2 1.0 CG B:ARG81 4.4 59.6 1.0 CG A:GLU80 4.4 55.8 1.0 N A:GLU80 4.4 44.7 1.0 CB A:ALA79 4.5 56.1 1.0 CZ B:ARG109 4.5 57.7 1.0 CB A:GLU80 4.8 52.6 1.0 CA A:ALA79 4.9 49.7 1.0 CD B:ARG81 5.0 68.5 1.0

Zinc binding site 2 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


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 Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:47.6 occ:1.00 ND1 B:HIS88 1.9 51.5 1.0 SG B:CYS68 2.3 44.6 1.0 SG B:CYS63 2.4 45.9 1.0 SG B:CYS85 2.4 52.8 1.0 CE1 B:HIS88 2.8 50.5 1.0 CG B:HIS88 3.0 43.3 1.0 CB B:CYS68 3.2 43.3 1.0 CB B:CYS63 3.2 38.6 1.0 CB B:CYS85 3.3 47.1 1.0 CB B:HIS88 3.5 48.4 1.0 NE2 B:HIS88 4.0 51.4 1.0 N B:CYS85 4.0 40.6 1.0 CD2 B:HIS88 4.1 46.3 1.0 CA B:CYS85 4.2 44.2 1.0 CB B:VAL65 4.3 38.7 1.0 CG2 B:VAL65 4.4 36.0 1.0 CG2 B:VAL70 4.6 44.4 1.0 CA B:CYS68 4.6 43.5 1.0 CA B:CYS63 4.7 42.0 1.0 CA B:HIS88 4.7 42.6 1.0 N B:HIS88 4.8 46.9 1.0 CB B:VAL70 4.8 48.1 1.0 C B:CYS85 5.0 42.6 1.0

Zinc binding site 3 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


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 Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:63.8 occ:1.00 NE2 B:HIS111 2.2 62.5 1.0 SG B:CYS104 2.2 61.1 1.0 SG B:CYS123 2.3 70.5 1.0 SG B:CYS107 2.4 66.0 1.0 CD2 B:HIS111 2.8 61.1 1.0 CB B:CYS104 3.0 58.4 1.0 CB B:CYS107 3.2 67.0 1.0 CB B:CYS123 3.3 67.9 1.0 CE1 B:HIS111 3.4 68.0 1.0 N B:CYS123 4.0 62.0 1.0 CG B:HIS111 4.1 63.8 1.0 N B:CYS107 4.2 58.0 1.0 CG B:GLN106 4.2 70.2 1.0 CA B:CYS123 4.2 69.7 1.0 CA B:CYS107 4.3 61.6 1.0 ND1 B:HIS111 4.4 67.5 1.0 NE2 B:GLN106 4.4 73.9 1.0 CA B:CYS104 4.5 54.7 1.0 NZ D:LYS120 4.7 117.2 1.0 CD B:GLN106 4.9 79.3 1.0

Zinc binding site 4 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


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 Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:57.0 occ:1.00 ND1 D:HIS88 1.9 56.4 1.0 SG D:CYS68 2.3 68.1 1.0 SG D:CYS63 2.4 58.2 1.0 SG D:CYS85 2.4 45.0 1.0 CE1 D:HIS88 2.8 58.4 1.0 CG D:HIS88 3.0 64.1 1.0 CB D:CYS68 3.2 63.5 1.0 CB D:CYS63 3.3 59.9 1.0 CB D:CYS85 3.3 48.8 1.0 CB D:HIS88 3.4 57.8 1.0 N D:CYS85 3.9 51.4 1.0 NE2 D:HIS88 4.0 57.9 1.0 CD2 D:HIS88 4.1 64.5 1.0 CA D:CYS85 4.2 49.1 1.0 CB D:VAL65 4.4 69.9 1.0 CG2 D:VAL65 4.4 63.2 1.0 CG2 D:VAL70 4.6 60.5 1.0 CA D:CYS68 4.7 73.2 1.0 CA D:HIS88 4.7 54.0 1.0 CA D:CYS63 4.7 63.1 1.0 N D:HIS88 4.7 53.4 1.0 CB D:VAL70 4.8 63.9 1.0 C D:CYS85 4.9 47.5 1.0

Zinc binding site 5 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


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 Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:60.2 occ:1.00 NE2 D:HIS111 2.1 56.9 1.0 SG D:CYS107 2.3 74.6 1.0 SG D:CYS104 2.4 61.5 1.0 SG D:CYS123 2.4 68.4 1.0 CD2 D:HIS111 2.8 59.0 1.0 CB D:CYS104 3.1 51.7 1.0 CB D:CYS107 3.1 66.1 1.0 CE1 D:HIS111 3.3 63.5 1.0 CB D:CYS123 3.4 65.7 1.0 CG D:HIS111 4.0 62.5 1.0 NH2 D:ARG125 4.0 103.4 1.0 N D:CYS123 4.1 64.7 1.0 N D:CYS107 4.2 57.8 1.0 ND1 D:HIS111 4.2 61.6 1.0 CA D:CYS107 4.3 62.6 1.0 CG D:GLN106 4.3 74.3 1.0 CA D:CYS123 4.4 68.4 1.0 NE2 D:GLN106 4.5 82.7 1.0 CA D:CYS104 4.6 54.9 1.0 CZ D:ARG125 4.7 117.5 1.0 CD D:ARG125 4.7 109.9 1.0 CD D:GLN106 4.9 77.6 1.0 NE D:ARG125 5.0 117.9 1.0

Zinc binding site 6 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


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 Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:83.1 occ:1.00 OE1 E:GLU80 2.2 83.1 1.0 NE2 F:HIS82 2.2 60.8 1.0 O F:HOH327 2.3 42.1 1.0 OE1 N:GLU118 2.3 94.3 1.0 OE2 N:GLU118 2.8 92.6 1.0 CD N:GLU118 2.8 93.6 1.0 CD2 F:HIS82 3.0 45.9 1.0 CD E:GLU80 3.1 79.0 1.0 CE1 F:HIS82 3.1 53.1 1.0 OE2 E:GLU80 3.4 82.6 1.0 NH1 F:ARG109 4.0 69.8 1.0 CG F:HIS82 4.1 48.8 1.0 ND1 F:HIS82 4.1 53.9 1.0 CG F:ARG81 4.2 64.6 1.0 CG N:GLU118 4.3 90.6 1.0 NH2 F:ARG109 4.4 78.0 1.0 N E:GLU80 4.5 55.8 1.0 CG E:GLU80 4.5 67.0 1.0 CB E:ALA79 4.5 57.1 1.0 CZ F:ARG109 4.7 74.7 1.0 CD F:ARG81 4.7 64.0 1.0 CB E:GLU80 4.8 62.1 1.0

Zinc binding site 7 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:48.4 occ:1.00 ND1 F:HIS88 2.0 50.1 1.0 SG F:CYS68 2.3 45.6 1.0 SG F:CYS63 2.4 42.7 1.0 SG F:CYS85 2.4 50.6 1.0 CE1 F:HIS88 2.8 49.9 1.0 CG F:HIS88 3.1 46.8 1.0 CB F:CYS68 3.2 48.8 1.0 CB F:CYS63 3.2 40.5 1.0 CB F:CYS85 3.3 42.4 1.0 CB F:HIS88 3.5 46.9 1.0 N F:CYS85 4.0 44.0 1.0 NE2 F:HIS88 4.0 45.1 1.0 CD2 F:HIS88 4.1 42.6 1.0 CA F:CYS85 4.2 41.1 1.0 CB F:VAL65 4.4 38.0 1.0 CG2 F:VAL65 4.5 37.8 1.0 CG2 J:VAL87 4.5 41.3 1.0 CG2 F:VAL70 4.6 50.7 1.0 CA F:CYS68 4.6 50.1 1.0 CA F:CYS63 4.6 41.0 1.0 CB F:VAL70 4.8 49.5 1.0 CA F:HIS88 4.8 45.1 1.0 N F:HIS88 4.8 40.6 1.0 C F:CYS85 5.0 42.8 1.0

Zinc binding site 8 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn202 b:54.5 occ:1.00 NE2 F:HIS111 2.2 56.0 1.0 SG F:CYS123 2.3 55.6 1.0 SG F:CYS104 2.3 59.2 1.0 SG F:CYS107 2.4 64.5 1.0 CD2 F:HIS111 2.8 49.6 1.0 CB F:CYS104 3.1 56.7 1.0 CB F:CYS107 3.2 57.1 1.0 CB F:CYS123 3.3 58.6 1.0 CE1 F:HIS111 3.4 55.1 1.0 NH1 F:ARG125 3.6 74.6 1.0 N F:CYS123 4.0 50.5 1.0 CG F:HIS111 4.1 56.7 1.0 CG F:GLN106 4.2 59.7 1.0 N F:CYS107 4.2 55.5 1.0 CA F:CYS123 4.3 57.4 1.0 CA F:CYS107 4.3 54.6 1.0 ND1 F:HIS111 4.3 58.5 1.0 NE2 F:GLN106 4.4 64.9 1.0 CA F:CYS104 4.5 53.4 1.0 CZ F:ARG125 4.6 85.3 1.0 CD F:GLN106 4.9 63.1 1.0 CD F:ARG125 4.9 88.9 1.0

Zinc binding site 9 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:121.6 occ:1.00 OE1 G:GLU80 2.1 117.9 1.0 NE2 H:HIS82 2.4 58.3 1.0 OE1 J:GLU118 2.8 117.7 1.0 CD G:GLU80 3.2 88.9 1.0 CD2 H:HIS82 3.3 53.8 1.0 CE1 H:HIS82 3.3 48.4 1.0 CD J:GLU118 3.6 126.5 1.0 NH1 H:ARG81 3.7 84.7 1.0 OE2 G:GLU80 3.8 100.1 1.0 N G:GLU80 3.9 46.0 1.0 CB G:ALA79 4.0 50.7 1.0 CB J:GLU118 4.0 117.9 1.0 CZ H:ARG81 4.0 86.7 1.0 NH2 H:ARG81 4.2 87.2 1.0 OE2 J:GLU118 4.2 132.8 1.0 CG J:GLU118 4.3 119.7 1.0 NH1 H:ARG109 4.3 82.6 1.0 CA G:ALA79 4.3 45.4 1.0 ND1 H:HIS82 4.4 50.9 1.0 CG H:HIS82 4.4 50.3 1.0 CG G:GLU80 4.4 69.5 1.0 CB G:GLU80 4.5 59.1 1.0 CG H:ARG81 4.6 59.2 1.0 C G:ALA79 4.6 43.3 1.0 NE H:ARG81 4.7 76.3 1.0 NH2 H:ARG109 4.7 90.8 1.0 CA G:GLU80 4.8 48.5 1.0 CZ H:ARG109 5.0 88.6 1.0

Zinc binding site 10 out of 20 in the Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Binary Complex Between Aster Yellows Witches'- Broom Phytoplasma Effector SAP05 and the Zinc Finger Domain of SPL5 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn202 b:48.8 occ:1.00 ND1 H:HIS88 2.0 53.3 1.0 SG H:CYS68 2.3 54.7 1.0 SG H:CYS63 2.4 52.4 1.0 SG H:CYS85 2.4 50.2 1.0 CE1 H:HIS88 2.9 52.5 1.0 CG H:HIS88 3.1 48.3 1.0 CB H:CYS63 3.2 49.1 1.0 CB H:CYS68 3.2 51.8 1.0 CB H:CYS85 3.3 46.6 1.0 CB H:HIS88 3.5 45.5 1.0 N H:CYS85 3.9 43.8 1.0 NE2 H:HIS88 4.1 49.6 1.0 CD2 H:HIS88 4.1 45.6 1.0 CA H:CYS85 4.2 45.5 1.0 CB H:VAL65 4.4 49.8 1.0 CG2 H:VAL65 4.5 47.4 1.0 CG2 H:VAL70 4.6 53.6 1.0 CA H:CYS68 4.6 51.8 1.0 CA H:CYS63 4.6 45.8 1.0 CA H:HIS88 4.7 49.3 1.0 N H:HIS88 4.8 45.1 1.0 CB H:VAL70 4.8 53.3 1.0 O H:HOH334 4.8 51.5 1.0 C H:CYS85 4.9 48.1 1.0

Q.Liu, A.Maqbool, F.G.Mirkin, Y.Singh, C.E.M.Stevenson, D.M.Lawson, S.Kamoun, W.Huang, S.A.Hogenhout. Bimodular Architecture of Bacterial Effector SAP05 Drives Ubiquitin-Independent Targeted Protein Degradation Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.06.19.545293