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Zinc in PDB 6ov8: 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655

Enzymatic activity of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655

All present enzymatic activity of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655:
3.4.11.23;

Protein crystallography data

The structure of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655, PDB code: 6ov8 was solved by G.Minasov, L.Shuvalova, Z.Wawrzak, O.Kiryukhina, S.Grimshaw, K.Kwon, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.857, 148.190, 165.010, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.8

Other elements in 6ov8:

The structure of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 also contains other interesting chemical elements:

Manganese (Mn) 6 atoms
Chlorine (Cl) 21 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 (pdb code 6ov8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655, PDB code: 6ov8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6ov8

Go back to Zinc Binding Sites List in 6ov8
Zinc binding site 1 out of 6 in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:36.5
occ:1.00
 OD2 A:ASP218 2.0 34.0 1.0
OE1 A:GLU279 2.0 33.7 1.0
NZ A:LYS195 2.1 33.8 1.0
O A:HOH662 2.6 26.7 1.0
CG A:ASP218 2.8 32.5 1.0
OD2 A:ASP200 2.8 35.5 1.0
CD A:GLU279 2.9 32.5 1.0
CE A:LYS195 3.0 30.8 1.0
OD1 A:ASP218 3.0 31.8 1.0
MN A:MN502 3.0 30.3 1.0
OE2 A:GLU279 3.2 33.2 1.0
CG A:ASP200 3.5 34.1 1.0
CB A:ASP200 4.1 33.9 1.0
O A:THR304 4.2 35.9 1.0
CB A:ASP218 4.3 32.9 1.0
CG A:GLU279 4.3 32.6 1.0
OD1 A:ASP200 4.3 34.1 1.0
CD A:LYS195 4.4 30.7 1.0
N A:GLY280 4.4 30.2 1.0
O A:ASP277 4.5 33.9 1.0
CA A:GLY280 4.6 31.1 1.0
CG1 A:ILE197 4.7 30.5 1.0
CB A:ILE197 4.9 30.1 1.0
CG2 A:ILE197 5.0 30.0 1.0
O A:LEU305 5.0 41.0 1.0

Zinc binding site 2 out of 6 in 6ov8

Go back to Zinc Binding Sites List in 6ov8
Zinc binding site 2 out of 6 in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:38.3
occ:1.00
 OD2 B:ASP218 2.0 33.1 1.0
OE1 B:GLU279 2.0 36.8 1.0
NZ B:LYS195 2.2 35.8 1.0
CG B:ASP218 2.8 31.1 1.0
O B:HOH693 2.8 18.1 1.0
OD2 B:ASP200 2.9 35.4 1.0
CE B:LYS195 2.9 32.9 1.0
OD1 B:ASP218 3.0 30.4 1.0
CD B:GLU279 3.0 35.6 1.0
O B:HOH686 3.1 39.7 1.0
MN B:MN502 3.1 33.8 1.0
OE2 B:GLU279 3.4 35.5 1.0
CG B:ASP200 3.7 33.2 1.0
O B:THR304 4.2 44.5 1.0
CB B:ASP200 4.2 32.3 1.0
CB B:ASP218 4.2 31.8 1.0
CD B:LYS195 4.3 32.1 1.0
CG B:GLU279 4.3 35.3 1.0
N B:GLY280 4.4 32.1 1.0
OD1 B:ASP200 4.6 33.8 1.0
CA B:GLY280 4.6 31.2 1.0
O B:ASP277 4.7 35.8 1.0
O B:LEU305 4.7 44.0 1.0
CG1 B:ILE197 4.8 27.4 1.0
CB B:ILE197 4.8 27.8 1.0
CG2 B:ILE197 4.9 28.5 1.0

Zinc binding site 3 out of 6 in 6ov8

Go back to Zinc Binding Sites List in 6ov8
Zinc binding site 3 out of 6 in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:36.0
occ:1.00
 OD2 C:ASP218 2.0 37.2 1.0
OE1 C:GLU279 2.0 39.1 1.0
NZ C:LYS195 2.2 37.9 1.0
OD2 C:ASP200 2.7 34.9 1.0
O C:HOH688 2.7 24.8 1.0
CG C:ASP218 2.8 35.5 1.0
OD1 C:ASP218 3.0 36.1 1.0
CE C:LYS195 3.0 35.5 1.0
CD C:GLU279 3.0 37.4 1.0
MN C:MN502 3.0 31.1 1.0
O C:HOH681 3.1 26.9 1.0
OE2 C:GLU279 3.4 37.3 1.0
CG C:ASP200 3.5 32.9 1.0
CB C:ASP200 4.0 32.0 1.0
O C:THR304 4.2 40.7 1.0
CB C:ASP218 4.3 35.4 1.0
CG C:GLU279 4.4 36.4 1.0
CD C:LYS195 4.4 35.1 1.0
OD1 C:ASP200 4.5 33.6 1.0
N C:GLY280 4.6 33.5 1.0
CG1 C:ILE197 4.7 30.0 1.0
O C:ASP277 4.7 38.1 1.0
CB C:ILE197 4.8 30.0 1.0
CA C:GLY280 4.8 33.0 1.0
CG2 C:ILE197 4.8 29.9 1.0
O C:LEU305 4.9 45.0 1.0

Zinc binding site 4 out of 6 in 6ov8

Go back to Zinc Binding Sites List in 6ov8
Zinc binding site 4 out of 6 in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:38.9
occ:1.00
 OD2 D:ASP218 2.0 38.7 1.0
OE1 D:GLU279 2.0 39.3 1.0
NZ D:LYS195 2.2 38.8 1.0
OD2 D:ASP200 2.8 35.3 1.0
CG D:ASP218 2.8 38.5 1.0
O D:HOH700 2.8 29.5 1.0
MN D:MN502 3.0 34.8 1.0
CE D:LYS195 3.0 37.0 1.0
OD1 D:ASP218 3.0 39.6 1.0
CD D:GLU279 3.0 37.2 1.0
OE2 D:GLU279 3.4 37.5 1.0
CG D:ASP200 3.6 33.0 1.0
CB D:ASP200 4.1 33.4 1.0
O D:THR304 4.2 38.3 1.0
CB D:ASP218 4.3 36.9 1.0
CG D:GLU279 4.4 38.1 1.0
OD1 D:ASP200 4.4 33.0 1.0
CD D:LYS195 4.4 37.1 1.0
N D:GLY280 4.5 37.1 1.0
O D:ASP277 4.6 38.6 1.0
CA D:GLY280 4.6 36.3 1.0
CG1 D:ILE197 4.6 31.4 1.0
CB D:ILE197 4.8 31.3 1.0
CG2 D:ILE197 4.9 30.4 1.0
O D:LEU305 5.0 40.4 1.0

Zinc binding site 5 out of 6 in 6ov8

Go back to Zinc Binding Sites List in 6ov8
Zinc binding site 5 out of 6 in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:40.0
occ:1.00
 OE1 E:GLU279 2.0 37.5 1.0
OD2 E:ASP218 2.0 39.9 1.0
NZ E:LYS195 2.2 40.5 1.0
OD2 E:ASP200 2.7 35.4 1.0
O E:HOH693 2.7 20.2 1.0
CG E:ASP218 2.9 38.0 1.0
O E:HOH643 2.9 27.6 1.0
CE E:LYS195 2.9 38.5 1.0
OD1 E:ASP218 3.1 38.9 1.0
CD E:GLU279 3.1 34.9 1.0
MN E:MN502 3.1 33.6 1.0
OE2 E:GLU279 3.5 35.5 1.0
CG E:ASP200 3.7 33.2 1.0
O E:THR304 4.2 44.1 1.0
CB E:ASP200 4.2 32.8 1.0
CB E:ASP218 4.3 37.7 1.0
CD E:LYS195 4.3 36.9 1.0
CG E:GLU279 4.4 34.3 1.0
N E:GLY280 4.5 33.0 1.0
O E:ASP277 4.6 37.3 1.0
OD1 E:ASP200 4.6 32.6 1.0
CG1 E:ILE197 4.6 34.9 1.0
CA E:GLY280 4.6 33.6 1.0
CB E:ILE197 4.8 35.1 1.0
O E:LEU305 4.9 49.1 1.0
CG2 E:ILE197 4.9 35.0 1.0

Zinc binding site 6 out of 6 in 6ov8

Go back to Zinc Binding Sites List in 6ov8
Zinc binding site 6 out of 6 in the 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:37.3
occ:1.00
 OD2 F:ASP218 2.0 36.1 1.0
OE1 F:GLU279 2.0 38.3 1.0
NZ F:LYS195 2.2 36.8 1.0
OD2 F:ASP200 2.7 34.2 1.0
CG F:ASP218 2.8 34.1 1.0
CE F:LYS195 2.8 34.3 1.0
O F:HOH641 2.9 26.0 1.0
CD F:GLU279 2.9 37.3 1.0
OD1 F:ASP218 3.0 34.8 1.0
O F:HOH679 3.0 22.9 1.0
MN F:MN502 3.0 33.5 1.0
OE2 F:GLU279 3.2 39.2 1.0
CG F:ASP200 3.5 32.8 1.0
CB F:ASP200 4.1 33.0 1.0
CB F:ASP218 4.3 34.9 1.0
CD F:LYS195 4.3 34.2 1.0
O F:THR304 4.3 40.8 1.0
O F:HOH611 4.3 33.6 1.0
CG F:GLU279 4.3 35.8 1.0
N F:GLY280 4.4 33.5 1.0
OD1 F:ASP200 4.4 33.3 1.0
CA F:GLY280 4.6 33.8 1.0
CG1 F:ILE197 4.6 30.9 1.0
O F:ASP277 4.6 37.5 1.0
CG2 F:ILE197 4.7 32.0 1.0
CB F:ILE197 4.7 31.7 1.0
O F:LEU305 4.9 37.9 1.0

Reference:

G.Minasov, L.Shuvalova, Z.Wawrzak, O.Kiryukhina, S.Grimshaw, K.Kwon, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. To Be Published.
Page generated: Tue Oct 29 04:35:33 2024

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