Zinc in PDB 5zxl: Structure of Glda From E.Coli

Enzymatic activity of Structure of Glda From E.Coli

All present enzymatic activity of Structure of Glda From E.Coli:
1.1.1.6;

Protein crystallography data

The structure of Structure of Glda From E.Coli, PDB code: 5zxl was solved by J.Zhang, L.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.61 / 2.79
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 162.446, 162.446, 293.127, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.4

Other elements in 5zxl:

The structure of Structure of Glda From E.Coli also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Glda From E.Coli (pdb code 5zxl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of Glda From E.Coli, PDB code: 5zxl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5zxl

Go back to Zinc Binding Sites List in 5zxl
Zinc binding site 1 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Glda From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:93.5
occ:1.00
H2 A:GOL402 2.1 0.1 1.0
NE2 A:HIS271 2.3 69.3 1.0
NE2 A:HIS254 2.4 86.6 1.0
OD1 A:ASP171 2.4 75.5 1.0
O3 A:GOL402 2.6 84.9 1.0
HO2 A:GOL402 2.6 0.1 1.0
C2 A:GOL402 2.8 95.9 1.0
OD2 A:ASP171 3.0 75.5 1.0
CG A:ASP171 3.0 69.2 1.0
O2 A:GOL402 3.1 0.1 1.0
CD2 A:HIS271 3.1 63.2 1.0
C3 A:GOL402 3.2 83.9 1.0
HO3 A:GOL402 3.2 0.9 1.0
CD2 A:HIS254 3.3 73.3 1.0
CE1 A:HIS254 3.3 71.2 1.0
CE1 A:HIS271 3.4 58.6 1.0
OD1 A:ASP121 3.4 69.5 1.0
H32 A:GOL402 3.6 0.6 1.0
H31 A:GOL402 4.1 0.6 1.0
C1 A:GOL402 4.2 87.9 1.0
O1 A:GOL402 4.3 0.6 1.0
CG A:ASP121 4.3 72.4 1.0
CG A:HIS271 4.3 49.9 1.0
OD2 A:ASP121 4.4 74.3 1.0
CG2 A:VAL275 4.4 49.2 1.0
ND1 A:HIS271 4.4 55.4 1.0
ND1 A:HIS254 4.5 73.6 1.0
CG A:HIS254 4.5 80.1 1.0
CB A:ASP171 4.5 56.9 1.0
O A:HOH504 4.6 66.5 1.0
H11 A:GOL402 4.7 0.4 1.0
H12 A:GOL402 4.9 0.4 1.0

Zinc binding site 2 out of 5 in 5zxl

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Zinc binding site 2 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Glda From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:0.7
occ:1.00
O3 B:GOL402 2.0 0.7 1.0
NE2 B:HIS254 2.3 86.5 1.0
HO3 B:GOL402 2.6 0.2 1.0
OD1 B:ASP171 2.6 85.0 1.0
NE2 B:HIS271 2.7 80.5 1.0
C3 B:GOL402 3.0 92.2 1.0
CE1 B:HIS254 3.0 81.7 1.0
H32 B:GOL402 3.1 0.6 1.0
OD2 B:ASP171 3.2 70.9 1.0
OD1 B:ASP121 3.2 82.4 1.0
CG B:ASP171 3.2 73.4 1.0
CD2 B:HIS271 3.4 73.0 1.0
CD2 B:HIS254 3.5 81.6 1.0
H2 B:GOL402 3.6 0.2 1.0
H12 B:GOL402 3.6 0.5 1.0
C2 B:GOL402 3.8 96.9 1.0
CE1 B:HIS271 3.8 71.2 1.0
OD2 B:ASP121 3.8 87.7 1.0
H31 B:GOL402 3.9 0.6 1.0
CG B:ASP121 3.9 82.6 1.0
C1 B:GOL402 4.2 0.1 1.0
ND1 B:HIS254 4.3 78.8 1.0
H11 B:GOL402 4.5 0.5 1.0
CG B:HIS254 4.5 81.9 1.0
CG2 B:VAL275 4.6 59.5 1.0
CB B:ASP171 4.6 69.0 1.0
CG B:HIS271 4.7 74.8 1.0
ND1 B:HIS271 4.8 63.0 1.0
O B:ASP171 5.0 60.8 1.0

Zinc binding site 3 out of 5 in 5zxl

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Zinc binding site 3 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Glda From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:93.5
occ:1.00
NE2 C:HIS254 2.3 97.3 1.0
HO3 C:GOL402 2.4 0.3 1.0
H11 C:GOL402 2.4 0.5 1.0
OD1 C:ASP171 2.4 87.5 1.0
NE2 C:HIS271 2.5 77.8 1.0
O1 C:GOL402 2.6 82.8 1.0
HO1 C:GOL402 2.6 99.3 1.0
OD2 C:ASP171 2.9 73.1 1.0
C1 C:GOL402 2.9 93.8 1.0
CG C:ASP171 3.0 76.8 1.0
HO2 C:GOL402 3.1 0.8 1.0
CE1 C:HIS254 3.2 79.2 1.0
CD2 C:HIS271 3.3 71.5 1.0
O3 C:GOL402 3.4 0.3 1.0
CD2 C:HIS254 3.4 79.0 1.0
OD1 C:ASP121 3.4 85.8 1.0
CE1 C:HIS271 3.5 64.4 1.0
C2 C:GOL402 3.8 89.9 1.0
O2 C:GOL402 3.8 88.2 1.0
H12 C:GOL402 3.8 0.5 1.0
C3 C:GOL402 4.1 0.1 1.0
CG C:ASP121 4.2 88.2 1.0
OD2 C:ASP121 4.2 85.0 1.0
ND1 C:HIS254 4.4 82.7 1.0
H31 C:GOL402 4.4 0.7 1.0
CG C:HIS254 4.5 70.6 1.0
CB C:ASP171 4.5 62.7 1.0
CG2 C:VAL275 4.5 55.9 1.0
CG C:HIS271 4.5 60.7 1.0
ND1 C:HIS271 4.6 78.7 1.0
H2 C:GOL402 4.8 0.9 1.0
O C:ASP171 4.9 59.4 1.0

Zinc binding site 4 out of 5 in 5zxl

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Zinc binding site 4 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Glda From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:0.3
occ:1.00
O2 D:GOL405 1.9 0.1 1.0
NE2 D:HIS254 2.0 68.8 1.0
O3 D:GOL405 2.2 87.9 1.0
OD1 D:ASP171 2.3 80.3 1.0
NE2 D:HIS271 2.4 67.5 1.0
H2 D:GOL405 2.4 0.4 1.0
C2 D:GOL405 2.5 94.6 1.0
HO2 D:GOL405 2.6 0.2 1.0
CE1 D:HIS254 2.7 72.6 1.0
C3 D:GOL405 2.9 82.7 1.0
HO3 D:GOL405 2.9 0.4 1.0
CG D:ASP171 3.0 66.7 1.0
CD2 D:HIS271 3.1 69.0 1.0
CD2 D:HIS254 3.1 0.7 1.0
OD2 D:ASP171 3.2 68.8 1.0
H31 D:GOL405 3.4 99.1 1.0
CE1 D:HIS271 3.5 59.4 1.0
H32 D:GOL405 3.8 99.1 1.0
OD1 D:ASP121 3.8 70.9 1.0
ND1 D:HIS254 3.9 82.8 1.0
C1 D:GOL405 3.9 75.1 1.0
CG2 D:VAL275 4.1 46.9 1.0
CG D:HIS254 4.1 0.5 1.0
CG D:HIS271 4.4 48.0 1.0
H11 D:GOL405 4.4 90.1 1.0
CB D:ASP171 4.4 60.4 1.0
O1 D:GOL405 4.4 88.6 1.0
O D:HOH510 4.5 53.0 1.0
ND1 D:HIS271 4.5 65.0 1.0
CG D:ASP121 4.6 72.8 1.0
H12 D:GOL405 4.6 90.1 1.0
OD2 D:ASP121 4.6 75.0 1.0
O D:ASP171 4.8 53.4 1.0
CA D:ASP171 4.8 54.1 1.0

Zinc binding site 5 out of 5 in 5zxl

Go back to Zinc Binding Sites List in 5zxl
Zinc binding site 5 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Glda From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:0.2
occ:1.00
NZ D:LYS274 2.9 53.7 1.0
NE2 D:HIS257 3.5 57.5 1.0
O D:HOH529 3.8 52.7 1.0
CA D:HIS271 4.0 48.2 1.0
CB D:HIS271 4.1 47.7 1.0
CE1 D:HIS257 4.1 45.5 1.0
N D:HIS271 4.1 54.6 1.0
CE D:LYS274 4.2 55.7 1.0
ND1 D:HIS271 4.2 65.0 1.0
CG2 D:THR261 4.5 43.7 1.0
CG D:HIS271 4.6 48.0 1.0
CD2 D:HIS257 4.7 57.9 1.0
O D:TYR269 4.8 52.0 1.0
C D:TYR270 4.9 51.1 1.0
CD D:LYS274 5.0 68.0 1.0

Reference:

J.Zhang, A.N.Nanjaraj Urs, L.Lin, Y.Zhou, Y.Hu, G.Hua, Q.Gao, Z.Yuchi, Y.Zhang. Structure of Glycerol Dehydrogenase (Glda) From Escherichia Coli. Acta Crystallogr F Struct V. 75 176 2019BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30839292
DOI: 10.1107/S2053230X19000037
Page generated: Wed Dec 16 11:28:14 2020

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