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Zinc in PDB 6t5l: Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation

Protein crystallography data

The structure of Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation, PDB code: 6t5l was solved by C.Frohlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.53 / 2.17
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 144.684, 144.684, 53.306, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.3

Other elements in 6t5l:

The structure of Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation (pdb code 6t5l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation, PDB code: 6t5l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6t5l

Go back to Zinc Binding Sites List in 6t5l
Zinc binding site 1 out of 4 in the Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:49.8
occ:1.00
O A:HOH416 1.3 35.4 1.0
NE2 A:HIS196 1.9 55.1 1.0
ND1 A:HIS118 2.0 53.6 1.0
NE2 A:HIS116 2.0 52.9 1.0
CD2 A:HIS196 2.8 43.5 1.0
HD2 A:HIS196 2.9 52.2 1.0
CD2 A:HIS116 2.9 44.0 1.0
HB2 A:HIS118 2.9 55.5 1.0
CE1 A:HIS118 2.9 51.7 1.0
HD2 A:HIS116 3.0 52.8 1.0
CE1 A:HIS196 3.0 49.2 1.0
CG A:HIS118 3.0 48.9 1.0
HE1 A:HIS118 3.1 62.1 1.0
CE1 A:HIS116 3.1 44.2 1.0
HE1 A:HIS196 3.3 59.0 1.0
HE1 A:HIS116 3.4 53.0 1.0
CB A:HIS118 3.4 46.2 1.0
HB3 A:HIS118 3.7 55.5 1.0
ZN A:ZN302 3.7 49.8 0.7
HG23 A:THR197 3.8 53.5 1.0
HB2 A:CYS221 3.9 61.6 1.0
OD1 A:ASP120 4.0 54.0 1.0
CG A:HIS196 4.0 46.9 1.0
ND1 A:HIS196 4.0 47.5 1.0
NE2 A:HIS118 4.1 51.5 1.0
CG A:HIS116 4.1 45.3 1.0
CD2 A:HIS118 4.1 50.0 1.0
HG21 A:THR197 4.2 53.5 1.0
ND1 A:HIS116 4.2 41.9 1.0
SG A:CYS221 4.2 65.0 1.0
HB3 A:CYS221 4.2 61.6 1.0
CB A:CYS221 4.3 51.3 1.0
CG2 A:THR197 4.4 44.6 1.0
O A:HOH445 4.4 62.9 1.0
H A:HIS118 4.5 55.8 1.0
OD2 A:ASP120 4.5 56.9 1.0
HG22 A:THR197 4.6 53.5 1.0
CG A:ASP120 4.7 54.6 1.0
HD2 A:TYR233 4.8 64.3 1.0
CA A:HIS118 4.8 49.0 1.0
HE2 A:HIS118 4.8 61.8 1.0
HD1 A:HIS196 4.9 57.0 1.0
HD1 A:HIS116 5.0 50.3 1.0
HD2 A:HIS118 5.0 60.0 1.0

Zinc binding site 2 out of 4 in 6t5l

Go back to Zinc Binding Sites List in 6t5l
Zinc binding site 2 out of 4 in the Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:49.8
occ:0.65
NE2 A:HIS263 2.1 70.0 1.0
SG A:CYS221 2.1 65.0 1.0
OD2 A:ASP120 2.3 56.9 1.0
O A:HOH445 2.3 62.9 1.0
O A:HOH416 2.7 35.4 1.0
CE1 A:HIS263 3.0 66.4 1.0
HE1 A:HIS263 3.1 79.7 1.0
CD2 A:HIS263 3.1 63.3 1.0
HB3 A:CYS221 3.2 61.6 1.0
CB A:CYS221 3.3 51.3 1.0
CG A:ASP120 3.3 54.6 1.0
HD2 A:HIS263 3.4 76.0 1.0
OD1 A:ASP120 3.6 54.0 1.0
ZN A:ZN301 3.7 49.8 1.0
HB2 A:CYS221 3.8 61.6 1.0
HE1 A:HIS116 3.8 53.0 1.0
O A:HOH446 3.9 42.5 1.0
NE2 A:HIS196 4.1 55.1 1.0
ND1 A:HIS263 4.1 67.1 1.0
HE1 A:HIS196 4.1 59.0 1.0
CE1 A:HIS196 4.2 49.2 1.0
CG A:HIS263 4.2 64.7 1.0
HA3 A:GLY262 4.4 41.9 1.0
CE1 A:HIS116 4.4 44.2 1.0
HA A:CYS221 4.5 52.1 1.0
NE2 A:HIS116 4.5 52.9 1.0
CA A:CYS221 4.5 43.4 1.0
CB A:ASP120 4.6 52.8 1.0
HB2 A:ASP120 4.7 63.4 1.0
O A:HOH419 4.8 49.1 1.0
O A:HOH506 4.8 45.1 1.0
CD2 A:HIS196 4.9 43.5 1.0
HD1 A:HIS263 4.9 80.5 1.0
H A:CYS221 5.0 46.3 1.0
HB3 A:ASP120 5.0 63.4 1.0

Zinc binding site 3 out of 4 in 6t5l

Go back to Zinc Binding Sites List in 6t5l
Zinc binding site 3 out of 4 in the Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:70.6
occ:1.00
ND1 B:HIS118 1.9 85.8 1.0
NE2 B:HIS196 2.1 68.5 1.0
NE2 B:HIS116 2.1 88.3 1.0
HB2 B:HIS118 2.7 93.2 1.0
CG B:HIS118 2.9 77.5 1.0
CE1 B:HIS118 2.9 75.8 1.0
CD2 B:HIS196 2.9 58.6 1.0
O B:HOH423 2.9 59.5 1.0
HD2 B:HIS196 3.0 70.3 1.0
CD2 B:HIS116 3.0 75.6 1.0
CE1 B:HIS116 3.1 77.7 1.0
HE1 B:HIS118 3.1 91.0 1.0
HD2 B:HIS116 3.1 90.7 1.0
CE1 B:HIS196 3.2 60.5 1.0
CB B:HIS118 3.2 77.6 1.0
HE1 B:HIS116 3.3 93.3 1.0
HE1 B:HIS196 3.5 72.6 1.0
ZN B:ZN302 3.5 79.8 0.8
HB3 B:HIS118 3.5 93.2 1.0
OD1 B:ASP120 3.7 98.6 1.0
HB2 B:CYS221 3.9 72.8 1.0
NE2 B:HIS118 4.0 76.0 1.0
CD2 B:HIS118 4.0 77.4 1.0
SG B:CYS221 4.0 71.2 1.0
CG B:HIS196 4.1 56.6 1.0
HB3 B:CYS221 4.1 72.8 1.0
ND1 B:HIS116 4.1 74.2 1.0
CG B:HIS116 4.1 73.2 1.0
HG23 B:THR197 4.2 68.7 1.0
ND1 B:HIS196 4.2 58.3 1.0
CB B:CYS221 4.3 60.6 1.0
H B:HIS118 4.3 89.2 1.0
O B:HOH428 4.3 77.6 1.0
HG21 B:THR197 4.4 68.7 1.0
CA B:HIS118 4.6 78.2 1.0
CG B:ASP120 4.7 0.0 1.0
CG2 B:THR197 4.7 57.2 1.0
HE2 B:HIS118 4.7 91.2 1.0
HD2 B:HIS118 4.8 92.9 1.0
N B:HIS118 4.9 74.3 1.0
HD1 B:HIS116 4.9 89.1 1.0
OD2 B:ASP120 5.0 0.3 1.0

Zinc binding site 4 out of 4 in 6t5l

Go back to Zinc Binding Sites List in 6t5l
Zinc binding site 4 out of 4 in the Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Myo-1 From Myroides Odoratimimus. Environmental Metallo-Beta- Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:79.8
occ:0.75
O B:HOH428 2.0 77.6 1.0
HE1 B:HIS263 2.0 0.1 1.0
SG B:CYS221 2.3 71.2 1.0
CE1 B:HIS263 2.6 0.4 1.0
HD1 B:HIS263 2.9 0.6 1.0
ND1 B:HIS263 3.0 0.3 1.0
HB3 B:CYS221 3.1 72.8 1.0
CB B:CYS221 3.3 60.6 1.0
OD2 B:ASP120 3.4 0.3 1.0
ZN B:ZN301 3.5 70.6 1.0
OD1 B:ASP120 3.6 98.6 1.0
NE2 B:HIS263 3.6 0.5 1.0
O B:HOH423 3.7 59.5 1.0
HE1 B:HIS116 3.7 93.3 1.0
CG B:ASP120 3.8 0.0 1.0
HB2 B:CYS221 3.8 72.8 1.0
NE2 B:HIS196 3.8 68.5 1.0
CG B:HIS263 4.2 0.5 1.0
CE1 B:HIS196 4.3 60.5 1.0
CE1 B:HIS116 4.4 77.7 1.0
HE1 B:HIS196 4.4 72.6 1.0
HA B:CYS221 4.4 70.2 1.0
NE2 B:HIS116 4.4 88.3 1.0
CA B:CYS221 4.5 58.5 1.0
HA3 B:GLY262 4.5 80.8 1.0
CD2 B:HIS196 4.5 58.6 1.0
CD2 B:HIS263 4.5 0.9 1.0
HD2 B:HIS196 4.7 70.3 1.0
O B:HOH425 4.9 54.0 1.0

Reference:

C.Frohlich, V.Sorum, S.Huber, O.Samuelsen, F.Berglund, E.Kristiansson, S.Kotsakis, M.P.Nachiket, J.D.G.Larsson, H.K.S.Leiros. Environmental Metallo-Beta-Lactamases Exhibit High Enzymatic Activity Under Zinc Deprivation To Be Published.
Page generated: Wed Dec 16 12:51:26 2020

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