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Zinc in PDB 7cje: Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase

Protein crystallography data

The structure of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase, PDB code: 7cje was solved by D.Ruiz-Carrillo, S.Lamers, Q.Feng, S.Yu, B.Sun, J.Jiang, M.Lukman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.8, 90.8, 164.5, 90, 90, 120
R / Rfree (%) 18.3 / 20.9

Other elements in 7cje:

The structure of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase (pdb code 7cje). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase, PDB code: 7cje:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7cje

Go back to Zinc Binding Sites List in 7cje
Zinc binding site 1 out of 2 in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:37.0
occ:1.00
OD2 A:ASP149 1.8 40.0 1.0
O A:HOH580 1.9 38.9 1.0
OD1 A:ASP183 2.1 36.7 1.0
NE2 A:HIS299 2.2 40.7 1.0
OD2 A:ASP183 2.6 41.3 1.0
CG A:ASP183 2.6 38.8 1.0
CG A:ASP149 2.8 38.4 1.0
CD2 A:HIS299 3.1 42.5 1.0
OD1 A:ASP149 3.1 35.9 1.0
CE1 A:HIS299 3.2 39.2 1.0
O A:HOH573 3.5 43.4 1.0
NE1 A:TRP298 3.7 40.6 1.0
O A:HOH563 3.9 38.7 1.0
O A:HOH612 4.1 50.9 1.0
CB A:ASP183 4.1 38.9 1.0
CB A:ASP149 4.1 38.4 1.0
CD1 A:TRP298 4.2 43.4 1.0
CG A:HIS299 4.2 42.4 1.0
ND1 A:HIS299 4.3 40.2 1.0
OE1 A:GLU182 4.6 37.4 1.0
O A:HOH518 4.7 40.3 1.0
CB A:ARG128 4.7 41.5 1.0
CE2 A:TRP298 4.7 40.5 1.0
CD A:ARG128 4.9 41.5 1.0
NE2 A:HIS124 5.0 37.9 1.0

Zinc binding site 2 out of 2 in 7cje

Go back to Zinc Binding Sites List in 7cje
Zinc binding site 2 out of 2 in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:48.9
occ:1.00
OD2 C:ASP183 1.9 55.0 1.0
OD2 C:ASP149 2.1 47.2 1.0
NE2 C:HIS299 2.1 51.2 1.0
O C:HOH614 2.3 51.2 1.0
CG C:ASP183 2.7 54.2 1.0
OD1 C:ASP183 2.7 56.4 1.0
CG C:ASP149 2.8 43.3 1.0
OD1 C:ASP149 3.0 40.2 1.0
CE1 C:HIS299 3.1 55.0 1.0
CD2 C:HIS299 3.1 51.2 1.0
NE1 C:TRP298 3.7 49.3 1.0
O C:HOH591 3.9 47.0 1.0
CD1 C:TRP298 4.1 49.3 1.0
CB C:ASP183 4.2 51.8 1.0
ND1 C:HIS299 4.2 57.7 1.0
CB C:ASP149 4.2 44.4 1.0
CG C:HIS299 4.2 55.2 1.0
OE1 C:GLU182 4.6 53.8 1.0
O C:HOH536 4.7 47.2 1.0
CE2 C:TRP298 4.8 51.6 1.0
O C:HOH618 4.8 58.2 1.0
CB C:ARG128 4.8 55.7 1.0
CD C:ARG128 4.9 59.1 1.0

Reference:

S.Lamers, Q.Feng, Y.Cheng, S.Yu, B.Sun, M.Lukman, J.Jiang, D.Ruiz-Carrillo. Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase. Biol.Chem. 2021.
ISSN: ISSN 1431-6730
PubMed: 33823093
DOI: 10.1515/HSZ-2020-0298
Page generated: Tue Oct 29 18:16:21 2024

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