Magnesium in PDB 7cjg: 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: 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

Other elements in 7cjg:

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

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural and Kinetic Characterization of Porphyromonas Gingivalis Glutaminyl Cyclase, PDB code: 7cjg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7cjg

Go back to Magnesium Binding Sites List in 7cjg
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg405

b:32.0
occ:1.00
O A:PHE44 2.0 37.0 1.0
O A:HOH513 2.0 35.9 1.0
OE2 A:GLU318 2.1 27.2 1.0
OD1 A:ASP314 2.2 38.8 1.0
O A:HOH558 2.2 27.6 1.0
OD1 A:ASP42 2.4 45.9 1.0
HA A:ASP42 2.8 108.5 1.0
CG A:ASP314 3.1 38.4 1.0
H A:PHE44 3.2 43.5 1.0
C A:PHE44 3.2 37.4 1.0
CD A:GLU318 3.2 39.0 1.0
OD2 A:ASP314 3.3 42.6 1.0
CG A:ASP42 3.4 69.9 1.0
HB3 A:PHE44 3.4 37.8 1.0
HG2 A:GLU318 3.5 45.4 1.0
HG3 A:GLU318 3.7 45.4 1.0
HD1 A:PHE44 3.7 38.8 1.0
CG A:GLU318 3.7 37.9 1.0
H A:ALA46 3.7 42.4 1.0
CA A:ASP42 3.7 90.4 1.0
N A:PHE44 3.8 36.2 1.0
CA A:PHE44 3.9 41.6 1.0
HA A:SER45 3.9 44.2 1.0
CB A:ASP42 4.1 77.0 1.0
CB A:PHE44 4.1 31.5 1.0
O A:HOH652 4.2 40.8 1.0
O A:ALA41 4.2 73.2 1.0
N A:SER45 4.2 29.2 1.0
C A:ASP42 4.2 61.1 1.0
OE1 A:GLU318 4.3 35.5 1.0
N A:ALA46 4.3 35.3 1.0
OD2 A:ASP42 4.3 67.8 1.0
HB2 A:ALA46 4.3 45.2 1.0
HB2 A:ASP42 4.4 92.4 1.0
CB A:ASP314 4.4 30.8 1.0
CA A:SER45 4.5 36.9 1.0
CD1 A:PHE44 4.5 32.4 1.0
HA A:ASP314 4.6 34.0 1.0
HB2 A:ASP314 4.6 37.0 1.0
N A:LEU43 4.7 51.5 1.0
O A:ASP42 4.7 55.2 1.0
O A:HOH586 4.8 45.5 1.0
C A:SER45 4.8 36.3 1.0
N A:ASP42 4.8 98.6 1.0
H A:LEU43 4.8 61.8 1.0
HA A:PHE44 4.8 49.9 1.0
CG A:PHE44 4.8 27.0 1.0
HB2 A:PHE44 4.9 37.8 1.0
C A:ALA41 4.9 94.2 1.0
HB3 A:ASP42 5.0 92.4 1.0

Magnesium binding site 2 out of 2 in 7cjg

Go back to Magnesium Binding Sites List in 7cjg
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg704

b:28.6
occ:1.00
O B:HOH835 2.0 25.9 1.0
O B:PHE44 2.0 36.5 1.0
O B:HOH815 2.1 33.0 1.0
OE2 B:GLU318 2.1 27.8 1.0
OD1 B:ASP314 2.2 32.4 1.0
OD1 B:ASP42 2.4 38.7 1.0
HA B:ASP42 2.9 88.2 1.0
CG B:ASP314 3.0 31.5 1.0
OD2 B:ASP314 3.2 33.2 1.0
C B:PHE44 3.2 27.3 1.0
H B:PHE44 3.2 40.3 1.0
CD B:GLU318 3.2 32.4 1.0
CG B:ASP42 3.5 64.6 1.0
HB3 B:PHE44 3.5 26.9 1.0
HG2 B:GLU318 3.5 36.0 1.0
HD1 B:PHE44 3.7 36.1 1.0
H B:ALA46 3.7 33.9 1.0
HG3 B:GLU318 3.7 36.0 1.0
CG B:GLU318 3.7 30.0 1.0
CA B:ASP42 3.8 73.5 1.0
N B:PHE44 3.9 33.6 1.0
HA B:SER45 3.9 36.9 1.0
CA B:PHE44 4.0 29.0 1.0
CB B:ASP42 4.1 74.1 1.0
O B:ALA41 4.2 49.2 1.0
CB B:PHE44 4.2 22.4 1.0
O B:HOH937 4.3 39.8 1.0
N B:SER45 4.3 27.7 1.0
C B:ASP42 4.3 57.5 1.0
HB2 B:ALA46 4.3 41.9 1.0
N B:ALA46 4.3 28.2 1.0
OE1 B:GLU318 4.3 30.2 1.0
OD2 B:ASP42 4.3 65.5 1.0
HB2 B:ASP42 4.4 88.9 1.0
CB B:ASP314 4.4 39.2 1.0
CD1 B:PHE44 4.5 30.1 1.0
CA B:SER45 4.5 30.8 1.0
HA B:ASP314 4.6 43.1 1.0
HB2 B:ASP314 4.6 47.0 1.0
N B:LEU43 4.8 43.8 1.0
O B:ASP42 4.8 41.4 1.0
C B:SER45 4.8 26.9 1.0
N B:ASP42 4.8 61.0 1.0
CG B:PHE44 4.9 27.8 1.0
HA B:PHE44 4.9 34.8 1.0
H B:LEU43 4.9 52.5 1.0
C B:ALA41 4.9 66.0 1.0
HB2 B:PHE44 5.0 26.9 1.0
HB3 B:ASP42 5.0 88.9 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: Sun Jul 11 16:16:21 2021

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