Zinc in PDB 8xku: Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State

All present enzymatic activity of Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State:
1.1.1.37;

The structure of Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State (pdb code 8xku). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State, PDB code: 8xku:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:173.2 occ:1.00 CE1 B:HIS773 1.3 141.9 1.0 NE2 B:HIS769 2.3 135.8 1.0 NE2 B:HIS773 2.3 143.5 1.0 ND1 B:HIS773 2.3 140.2 1.0 CD2 B:HIS769 2.8 136.3 1.0 OD1 B:ASP849 2.9 160.3 1.0 OD2 B:ASP849 3.4 162.6 1.0 CD2 B:HIS773 3.4 139.5 1.0 CG B:ASP849 3.4 159.5 1.0 CG B:HIS773 3.4 138.3 1.0 CE1 B:HIS769 3.5 136.2 1.0 CG B:HIS769 4.1 138.3 1.0 CA B:GLY830 4.2 139.8 1.0 OE2 B:GLU770 4.3 137.8 1.0 ND1 B:HIS769 4.4 137.4 1.0 N B:GLY830 4.6 140.2 1.0 CB B:ASP849 4.7 155.9 1.0 CB B:HIS773 4.8 135.1 1.0 O B:ALA827 4.8 141.6 1.0 C B:GLY830 4.9 140.3 1.0 O B:HIS769 4.9 133.8 1.0 N B:ARG831 5.0 136.3 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn400 b:110.9 occ:1.00 SG R:CYS102 2.3 117.0 1.0 SG R:CYS182 2.3 90.2 1.0 SG R:CYS179 2.3 87.2 1.0 CB R:CYS179 2.7 89.5 1.0 CB R:CYS182 2.7 90.5 1.0 N R:CYS182 2.9 86.8 1.0 CA R:CYS182 3.3 89.5 1.0 CB R:CYS102 3.4 114.2 1.0 O R:CYS179 3.7 89.2 1.0 CA R:CYS179 3.9 89.8 1.0 CB R:CYS99 3.9 100.8 1.0 C R:CYS179 4.0 89.6 1.0 C R:GLU181 4.0 84.0 1.0 CB R:GLU181 4.3 82.1 1.0 N R:CYS102 4.3 114.2 1.0 N R:GLU181 4.4 83.4 1.0 CA R:GLU181 4.5 84.3 1.0 SG R:CYS99 4.5 98.7 1.0 CA R:CYS102 4.5 114.3 1.0 CG R:GLN106 4.6 102.7 1.0 N R:CYS179 4.6 90.6 1.0 C R:CYS182 4.6 86.5 1.0 O R:CYS182 4.9 84.5 1.0 CB R:THR101 4.9 117.9 1.0 O R:GLU181 4.9 85.2 1.0 N R:THR180 4.9 84.4 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the YCF2-Ftshi Motor Complex From Arabidopsis in Atp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn401 b:80.7 occ:1.00 SG R:CYS168 2.3 73.0 1.0 SG R:CYS113 2.3 113.4 1.0 SG R:CYS110 2.3 85.4 1.0 SG R:CYS171 2.3 72.7 1.0 CB R:CYS171 2.5 75.3 1.0 CB R:CYS168 2.8 75.2 1.0 CB R:CYS110 3.3 92.7 1.0 N R:CYS171 3.4 74.9 1.0 CA R:CYS171 3.5 80.7 1.0 CB R:CYS113 3.7 118.5 1.0 CA R:CYS168 4.3 81.6 1.0 CA R:GLY117 4.4 99.2 1.0 N R:CYS113 4.5 125.0 1.0 C R:THR170 4.5 78.1 1.0 C R:CYS171 4.6 80.7 1.0 CA R:CYS110 4.6 95.6 1.0 O R:CYS110 4.6 102.3 1.0 CB R:THR170 4.7 78.5 1.0 O R:CYS168 4.7 73.2 1.0 C R:CYS168 4.7 82.4 1.0 CA R:CYS113 4.7 122.8 1.0 N R:GLY117 4.7 98.7 1.0 CA R:GLY175 4.8 80.2 1.0 CG R:MET112 4.9 141.1 1.0 SD R:MET112 4.9 150.8 1.0 C R:CYS110 4.9 100.3 1.0 N R:GLY175 4.9 78.4 1.0 CA R:THR170 5.0 79.6 1.0 N R:THR170 5.0 83.6 1.0

K.Liang, Z.Jin, X.Zhan, Y.Li, Q.Xu, Y.Xie, Y.Yang, S.Wang, J.Wu, Z.Yan. Structural Insights Into the Chloroplast Protein Import in Land Plants. Cell 2024.
ISSN: ISSN 1097-4172
PubMed: 39197452
DOI: 10.1016/J.CELL.2024.08.003