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

The structure of Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase, PDB code: 7cjg 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)	32.06 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.117, 91.117, 165.063, 90, 90, 120
R / Rfree (%)	17.9 / 21.5

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase (pdb code 7cjg). 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: 7cjg:
Jump to Zinc binding site number: 1; 2;

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:Zn406 b:66.8 occ:1.00 OD1 A:ASP149 1.9 38.7 1.0 N1 A:DMD401 2.0 60.7 0.9 NE2 A:HIS299 2.1 34.7 1.0 OD1 A:ASP183 2.4 43.8 1.0 OD2 A:ASP183 2.5 37.0 1.0 HE1 A:TRP298 2.6 39.2 1.0 CG A:ASP183 2.7 37.0 1.0 C2 A:DMD401 2.8 49.7 0.9 CG A:ASP149 2.9 28.7 1.0 H21 A:DMD401 2.9 59.7 0.9 CE1 A:HIS299 3.0 27.7 1.0 CD2 A:HIS299 3.1 35.1 1.0 HE1 A:HIS299 3.1 33.2 1.0 C7A A:DMD401 3.1 62.5 0.9 OD2 A:ASP149 3.3 27.4 1.0 NE1 A:TRP298 3.3 32.7 1.0 HD2 A:HIS299 3.3 42.2 1.0 H71 A:DMD401 3.6 85.0 0.9 C7 A:DMD401 3.8 70.8 0.9 HD1 A:TRP298 3.8 37.4 1.0 CD1 A:TRP298 3.9 31.1 1.0 N3 A:DMD401 4.1 62.3 0.9 HB2 A:ARG128 4.1 44.2 1.0 ND1 A:HIS299 4.1 30.6 1.0 CG A:HIS299 4.1 39.4 1.0 C3A A:DMD401 4.2 60.9 0.9 CB A:ASP183 4.2 36.6 1.0 CB A:ASP149 4.3 31.4 1.0 HD2 A:ARG128 4.3 61.6 1.0 HZ3 A:TRP193 4.3 51.9 1.0 CE2 A:TRP298 4.3 30.1 1.0 O A:HOH577 4.4 40.5 1.0 OE1 A:GLU182 4.4 28.0 1.0 HB2 A:ASP149 4.5 37.7 1.0 HB3 A:ASP149 4.5 37.7 1.0 HZ2 A:TRP298 4.5 41.1 1.0 HA A:ASP183 4.6 44.9 1.0 HD3 A:ARG128 4.6 61.6 1.0 HB2 A:ASP183 4.6 43.9 1.0 HE2 A:HIS124 4.6 31.7 1.0 HB3 A:ASP183 4.7 43.9 1.0 HE2 A:MET219 4.8 42.2 1.0 HN31 A:DMD401 4.8 74.7 0.9 HD1 A:HIS299 4.8 36.8 1.0 HZ A:PHE144 4.8 95.1 1.0 CZ2 A:TRP298 4.8 34.2 1.0 O A:HOH514 4.9 38.7 1.0 CD A:ARG128 4.9 51.4 1.0 CB A:ARG128 4.9 36.8 1.0 HB3 A:ARG128 5.0 44.2 1.0

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 B:Zn705 b:184.3 occ:1.00 HE2 B:HIS299 1.8 81.7 1.0 OD2 B:ASP149 2.2 58.8 1.0 N1 B:DMD701 2.2 118.8 1.0 OD1 B:ASP183 2.4 79.4 1.0 NE2 B:HIS299 2.4 68.1 1.0 OD2 B:ASP183 2.4 69.2 1.0 HE1 B:TRP298 2.5 59.4 1.0 CG B:ASP183 2.8 71.8 1.0 H21 B:DMD701 2.8 132.2 1.0 C2 B:DMD701 2.8 110.1 1.0 CE1 B:HIS299 3.1 62.8 1.0 CG B:ASP149 3.2 42.2 1.0 HE1 B:HIS299 3.2 75.4 1.0 NE1 B:TRP298 3.3 49.5 1.0 C7A B:DMD701 3.4 113.0 1.0 CD2 B:HIS299 3.4 62.6 1.0 OD1 B:ASP149 3.4 35.2 1.0 HD2 B:HIS299 3.7 75.2 1.0 HD1 B:TRP298 3.9 62.3 1.0 H71 B:DMD701 3.9 131.8 1.0 HZ3 B:TRP193 4.0 80.0 1.0 CD1 B:TRP298 4.0 51.9 1.0 N3 B:DMD701 4.1 112.5 1.0 C7 B:DMD701 4.1 109.9 1.0 ND1 B:HIS299 4.2 65.3 1.0 CB B:ASP183 4.3 73.6 1.0 C3A B:DMD701 4.3 106.4 1.0 CE2 B:TRP298 4.3 48.8 1.0 CG B:HIS299 4.4 63.7 1.0 HB2 B:ARG128 4.4 74.2 1.0 HZ2 B:TRP298 4.4 74.2 1.0 HD2 B:ARG128 4.4 103.7 1.0 OE1 B:GLU182 4.5 41.8 1.0 CB B:ASP149 4.5 32.4 1.0 HB2 B:ASP183 4.6 88.3 1.0 HA B:ASP183 4.6 75.7 1.0 HE2 B:MET219 4.6 65.4 1.0 HE2 B:HIS124 4.6 43.3 1.0 HD3 B:ARG128 4.7 103.7 1.0 CZ3 B:TRP193 4.7 66.7 1.0 HB2 B:ASP149 4.7 38.8 1.0 HB3 B:ASP183 4.7 88.3 1.0 HN31 B:DMD701 4.8 134.9 1.0 HB3 B:ASP149 4.8 38.8 1.0 CZ2 B:TRP298 4.8 61.9 1.0 OE2 B:GLU182 4.8 64.2 1.0

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