Zinc in PDB 9ekm: Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated)

The structure of Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated), PDB code: 9ekm was solved by N.Tran, A.Frenette, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.30 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.74, 91.551, 86.848, 90, 90.96, 90
R / Rfree (%)	13.9 / 18.1

The structure of Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated) also contains other interesting chemical elements:

Praseodymium

(Pr)

4 atoms

The binding sites of Zinc atom in the Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated) (pdb code 9ekm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated), PDB code: 9ekm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:13.9 occ:0.22 SG A:CYS619 2.2 15.7 1.0 SG A:CYS606 2.2 15.8 1.0 OE2 A:GLU551 2.3 20.2 1.0 SG A:CYS616 2.4 16.5 1.0 CB A:CYS606 3.2 15.6 1.0 O A:HOH1222 3.2 26.9 1.0 CD A:GLU551 3.3 22.1 1.0 CB A:CYS619 3.3 11.1 1.0 OE1 A:GLU551 3.6 24.5 1.0 CB A:CYS616 3.7 14.8 1.0 O A:HOH1238 3.9 17.2 1.0 N A:CYS616 4.0 12.8 1.0 N A:CYS619 4.3 13.4 1.0 ND2 A:ASN567 4.3 15.3 1.0 CA A:CYS619 4.4 11.5 1.0 CA A:CYS616 4.4 11.8 1.0 CG A:MET608 4.4 16.0 1.0 CB A:MET608 4.5 15.3 1.0 CG A:GLU551 4.5 20.6 1.0 CA A:CYS606 4.6 12.9 1.0 CB A:ASN567 4.8 14.0 1.0 OG A:SER602 4.9 14.1 1.0 C A:CYS616 5.0 12.2 1.0 O A:CYS616 5.0 12.1 1.0

Zinc binding site 2 out of 2 in the Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thomasclavelia Ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-Terminal Domain #1 (Metal Chelated) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:15.6 occ:0.22 OE2 B:GLU551 2.2 21.6 1.0 SG B:CYS619 2.2 17.8 1.0 SG B:CYS606 2.3 17.7 1.0 SG B:CYS616 2.3 18.6 1.0 CD B:GLU551 3.2 24.8 1.0 O B:HOH1291 3.2 31.4 1.0 CB B:CYS606 3.2 17.1 1.0 CB B:CYS619 3.3 16.5 1.0 OE1 B:GLU551 3.6 27.0 1.0 CB B:CYS616 3.7 16.6 1.0 O B:HOH1164 3.9 20.1 1.0 N B:CYS616 4.0 15.3 1.0 N B:CYS619 4.2 12.7 1.0 CA B:CYS619 4.3 12.8 1.0 ND2 B:ASN567 4.3 18.1 1.0 CA B:CYS616 4.4 15.1 1.0 CG B:GLU551 4.4 24.6 1.0 CG B:MET608 4.5 16.8 1.0 CB B:MET608 4.5 16.9 1.0 CA B:CYS606 4.7 15.5 1.0 CB B:ASN567 4.8 16.2 1.0 OG B:SER602 4.8 17.6 1.0 C B:CYS616 5.0 14.9 1.0

N.Tran, A.Frenette, T.Holyoak. Structure of the Thomasclavelia Ramosa Immunoglobulin A Protease Reveals A Modular and Minimizable Architecture Distinct From Other Immunoglobulin A Proteases Proc.Natl.Acad.Sci.Usa 2025.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2503549122