Zinc in PDB 7ye2: The Cryo-Em Structure of C. Crescentus Gcra-Tacdown

All present enzymatic activity of The Cryo-Em Structure of C. Crescentus Gcra-Tacdown:
2.7.7.6;

The structure of The Cryo-Em Structure of C. Crescentus Gcra-Tacdown also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the The Cryo-Em Structure of C. Crescentus Gcra-Tacdown (pdb code 7ye2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Cryo-Em Structure of C. Crescentus Gcra-Tacdown, PDB code: 7ye2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the The Cryo-Em Structure of C. Crescentus Gcra-Tacdown


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Cryo-Em Structure of C. Crescentus Gcra-Tacdown within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:68.4 occ:1.00 SG D:CYS894 2.5 29.1 1.0 SG D:CYS884 2.5 36.9 1.0 SG D:CYS810 2.7 49.9 1.0 CA D:CYS884 2.8 36.9 1.0 CB D:CYS884 2.9 36.9 1.0 CB D:CYS891 3.0 32.5 1.0 CB D:CYS894 3.4 29.1 1.0 N D:GLU885 3.8 44.5 1.0 CB D:CYS810 3.8 49.9 1.0 N D:CYS884 3.8 36.9 1.0 C D:CYS884 3.8 36.9 1.0 SG D:CYS891 4.0 32.5 1.0 CA D:CYS891 4.2 32.5 1.0 N D:CYS891 4.3 32.5 1.0 CG2 D:THR812 4.4 42.2 1.0 O D:THR883 4.4 32.9 1.0 C D:THR883 4.5 32.9 1.0 O D:SER880 4.7 26.3 1.0 N D:ALA886 4.7 38.0 1.0 CA D:CYS894 4.8 29.1 1.0 N D:CYS894 4.9 29.1 1.0 O D:CYS884 4.9 36.9 1.0

Zinc binding site 2 out of 3 in the The Cryo-Em Structure of C. Crescentus Gcra-Tacdown


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Cryo-Em Structure of C. Crescentus Gcra-Tacdown within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:72.3 occ:1.00 O D:LEU72 2.2 45.2 1.0 SG D:CYS86 2.5 45.0 1.0 SG D:CYS73 2.8 52.3 1.0 C D:LEU72 2.8 45.2 1.0 SG D:CYS71 2.8 42.9 1.0 CB D:CYS86 3.1 45.0 1.0 N D:LEU72 3.3 45.2 1.0 CA D:LEU72 3.4 45.2 1.0 SG D:CYS89 3.6 49.7 1.0 CB D:LEU72 3.6 45.2 1.0 N D:CYS73 3.8 52.3 1.0 CB D:CYS89 4.0 49.7 1.0 CB D:CYS73 4.0 52.3 1.0 CB D:LYS75 4.1 46.4 1.0 CB D:CYS71 4.1 42.9 1.0 C D:CYS71 4.1 42.9 1.0 CG1 D:VAL91 4.3 35.3 1.0 CA D:CYS73 4.3 52.3 1.0 CA D:CYS86 4.4 45.0 1.0 C D:CYS73 4.7 52.3 1.0 N D:LYS75 4.7 46.4 1.0 CA D:CYS71 4.8 42.9 1.0 O D:CYS71 4.8 42.9 1.0 N D:CYS89 4.8 49.7 1.0 CG D:LYS88 4.9 54.4 1.0 CD D:LYS75 4.9 46.4 1.0 N D:GLY74 5.0 47.7 1.0 CD2 D:TYR76 5.0 46.6 1.0 CA D:CYS89 5.0 49.7 1.0

Zinc binding site 3 out of 3 in the The Cryo-Em Structure of C. Crescentus Gcra-Tacdown


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Cryo-Em Structure of C. Crescentus Gcra-Tacdown within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:117.1 occ:1.00 ND1 G:HIS146 2.2 82.3 1.0 SG G:CYS118 2.4 85.7 1.0 SG G:CYS133 2.5 93.2 1.0 SG G:CYS143 2.8 82.0 1.0 CB G:TRP120 2.9 83.4 1.0 CE1 G:HIS146 2.9 82.3 1.0 CG G:HIS146 3.3 82.3 1.0 CB G:CYS133 3.6 93.2 1.0 CB G:HIS146 3.8 82.3 1.0 CG G:TRP120 3.8 83.4 1.0 CB G:CYS143 4.0 82.0 1.0 CA G:TRP120 4.1 83.4 1.0 N G:CYS143 4.1 82.0 1.0 N G:TRP120 4.1 83.4 1.0 CB G:CYS118 4.1 85.7 1.0 NE2 G:HIS146 4.1 82.3 1.0 CD2 G:HIS146 4.3 82.3 1.0 CD2 G:TRP120 4.4 83.4 1.0 CE3 G:TRP120 4.4 83.4 1.0 O G:TRP120 4.5 83.4 1.0 CA G:CYS143 4.7 82.0 1.0 C G:TRP120 4.8 83.4 1.0 CZ G:ARG135 4.8 87.3 1.0 CD1 G:TRP120 4.9 83.4 1.0 CA G:CYS133 4.9 93.2 1.0 CB G:TYR142 4.9 80.1 1.0 N G:CYS133 5.0 93.2 1.0

X.X.Wu, Y.Zhang. Cryo-Em Structures of Caulobacter Crescentus Transcription Activation Complex with An Essential Cell Cycle Regulator Gcra Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962