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: Wed Dec 16 12:27:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy