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Zinc in PDB 5hfs: Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System

Enzymatic activity of Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System

All present enzymatic activity of Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System:
3.4.22.37;

Protein crystallography data

The structure of Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System, PDB code: 5hfs was solved by P.Golik, B.Szmigielski, M.Ksiazek, Z.Nowakowska, D.Mizgalska, M.Nowak, G.Dubin, J.Potempa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.64 / 1.97
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 37.690, 37.690, 184.150, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 24.7

Other elements in 5hfs:

The structure of Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System (pdb code 5hfs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System, PDB code: 5hfs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5hfs

Go back to Zinc Binding Sites List in 5hfs
Zinc binding site 1 out of 5 in the Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System


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 C-Terminal Domain of Cargo Proteins of Type IX Secretion System within 5.0Å range:

Zinc binding site 2 out of 5 in 5hfs

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Zinc binding site 2 out of 5 in the Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System


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 C-Terminal Domain of Cargo Proteins of Type IX Secretion System within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:98.7
occ:1.00
 NH2 B:ARG721 3.6 58.3 1.0
CD B:ARG701 4.0 48.3 1.0
NH1 B:ARG721 4.0 53.0 1.0
CZ B:ARG721 4.3 57.2 1.0
NE B:ARG701 4.4 53.4 1.0
CZ B:PHE695 4.8 30.3 1.0
CG B:ARG701 4.8 51.8 1.0

Zinc binding site 3 out of 5 in 5hfs

Go back to Zinc Binding Sites List in 5hfs
Zinc binding site 3 out of 5 in the Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System


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 C-Terminal Domain of Cargo Proteins of Type IX Secretion System within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn803

b:0.2
occ:1.00
 NH1 B:ARG700 3.6 50.9 1.0
NH2 B:ARG700 4.0 61.2 1.0
CZ B:ARG700 4.3 61.6 1.0

Zinc binding site 4 out of 5 in 5hfs

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Zinc binding site 4 out of 5 in the Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System


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 C-Terminal Domain of Cargo Proteins of Type IX Secretion System within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn804

b:82.4
occ:1.00
 N B:ARG701 3.7 39.2 1.0
NE B:ARG700 3.9 58.8 1.0
NH2 B:ARG700 4.0 61.2 1.0
CB B:ARG701 4.1 47.6 1.0
NE B:ARG701 4.1 53.4 1.0
CG B:ARG701 4.4 51.8 1.0
CA B:ARG700 4.5 37.2 1.0
CZ B:ARG700 4.5 61.6 1.0
CA B:ARG701 4.5 38.9 1.0
C B:ARG700 4.6 35.6 1.0
O B:ARG701 4.7 43.7 1.0
CD B:ARG701 4.9 48.3 1.0
CB B:ARG700 4.9 35.8 1.0

Zinc binding site 5 out of 5 in 5hfs

Go back to Zinc Binding Sites List in 5hfs
Zinc binding site 5 out of 5 in the Crystal Structure of C-Terminal Domain of Cargo Proteins of Type IX Secretion System


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 C-Terminal Domain of Cargo Proteins of Type IX Secretion System within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn805

b:0.0
occ:1.00
 NZ B:LYS727 3.5 63.6 1.0
CE B:LYS727 4.2 56.5 1.0

Reference:

I.De Diego, M.Ksiazek, D.Mizgalska, L.Koneru, P.Golik, B.Szmigielski, M.Nowak, Z.Nowakowska, B.Potempa, J.A.Houston, J.J.Enghild, I.B.Thgersen, J.Gao, A.H.Kwan, J.Trewhella, G.Dubin, F.X.Gomis-Ruth, K.A.Nguyen, J.Potempa. The Outer-Membrane Export Signal of Porphyromonas Gingivalis Type IX Secretion System (T9SS) Is A Conserved C-Terminal Beta-Sandwich Domain. Sci Rep V. 6 23123 2016.
ISSN: ESSN 2045-2322
PubMed: 27005013
DOI: 10.1038/SREP23123
Page generated: Sun Oct 27 17:27:20 2024

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