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Manganese 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:

Zinc (Zn) 6 atoms
Chlorine (Cl) 21 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 6 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6ov8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:30.3
occ:1.00
 OD1 A:ASP277 2.1 34.0 1.0
O A:ASP277 2.1 33.9 1.0
OE2 A:GLU279 2.2 33.2 1.0
OD2 A:ASP200 2.2 35.5 1.0
O A:HOH662 2.2 26.7 1.0
CG A:ASP200 3.0 34.1 1.0
ZN A:ZN501 3.0 36.5 1.0
CD A:GLU279 3.0 32.5 1.0
OD1 A:ASP200 3.2 34.1 1.0
C A:ASP277 3.2 32.2 1.0
OE1 A:GLU279 3.2 33.7 1.0
CG A:ASP277 3.2 33.9 1.0
NZ A:LYS207 3.5 34.0 1.0
CA A:ASP277 3.6 33.1 1.0
CB A:ASP277 4.0 34.0 1.0
CE A:LYS207 4.1 33.7 1.0
OD2 A:ASP277 4.2 34.2 1.0
N A:ALA278 4.4 31.8 1.0
CB A:ASP200 4.4 33.9 1.0
CG A:GLU279 4.4 32.6 1.0
OD2 A:ASP218 4.4 34.0 1.0
N A:GLU279 4.5 31.7 1.0
ND2 A:ASN250 4.7 29.4 1.0
CA A:ALA278 4.8 31.1 1.0
CA A:GLY202 4.9 31.4 1.0
NZ A:LYS195 5.0 33.8 1.0
CB A:GLU279 5.0 32.0 1.0

Manganese binding site 2 out of 6 in 6ov8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:33.8
occ:1.00
 OD2 B:ASP200 2.1 35.4 1.0
OD1 B:ASP277 2.1 34.7 1.0
O B:ASP277 2.1 35.8 1.0
OE2 B:GLU279 2.1 35.5 1.0
O B:HOH693 2.6 18.1 1.0
CD B:GLU279 3.0 35.6 1.0
CG B:ASP200 3.1 33.2 1.0
ZN B:ZN501 3.1 38.3 1.0
C B:ASP277 3.2 34.3 1.0
CG B:ASP277 3.2 35.4 1.0
OE1 B:GLU279 3.2 36.8 1.0
OD1 B:ASP200 3.5 33.8 1.0
CA B:ASP277 3.6 34.5 1.0
O B:HOH686 3.7 39.7 1.0
NZ B:LYS207 3.8 33.9 1.0
CB B:ASP277 3.9 35.1 1.0
OD2 B:ASP277 4.1 36.9 1.0
CE B:LYS207 4.2 33.7 1.0
N B:ALA278 4.4 35.1 1.0
CG B:GLU279 4.4 35.3 1.0
N B:GLU279 4.4 34.4 1.0
OD2 B:ASP218 4.5 33.1 1.0
CB B:ASP200 4.5 32.3 1.0
ND2 B:ASN250 4.8 28.0 1.0
CA B:ALA278 4.8 35.1 1.0
CA B:GLY202 4.9 32.7 1.0
N B:ASP277 5.0 33.5 1.0

Manganese binding site 3 out of 6 in 6ov8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:31.1
occ:1.00
 OD2 C:ASP200 2.1 34.9 1.0
OE2 C:GLU279 2.1 37.3 1.0
O C:ASP277 2.1 38.1 1.0
OD1 C:ASP277 2.1 35.3 1.0
O C:HOH688 2.4 24.8 1.0
CD C:GLU279 3.0 37.4 1.0
CG C:ASP200 3.0 32.9 1.0
ZN C:ZN501 3.0 36.0 1.0
C C:ASP277 3.1 36.4 1.0
CG C:ASP277 3.2 35.1 1.0
OE1 C:GLU279 3.2 39.1 1.0
OD1 C:ASP200 3.3 33.6 1.0
O C:HOH681 3.4 26.9 1.0
CA C:ASP277 3.6 36.0 1.0
CB C:ASP277 4.0 36.1 1.0
NZ C:LYS207 4.1 37.8 1.0
OD2 C:ASP277 4.1 34.1 1.0
CE C:LYS207 4.3 37.0 1.0
N C:GLU279 4.3 36.1 1.0
N C:ALA278 4.3 37.8 1.0
CB C:ASP200 4.4 32.0 1.0
CG C:GLU279 4.4 36.4 1.0
OD2 C:ASP218 4.5 37.2 1.0
CA C:ALA278 4.7 37.8 1.0
ND2 C:ASN250 4.7 32.2 1.0
CB C:GLU279 4.9 36.0 1.0
NZ C:LYS195 5.0 37.9 1.0
CA C:GLY202 5.0 33.0 1.0

Manganese binding site 4 out of 6 in 6ov8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:34.8
occ:1.00
 OD2 D:ASP200 2.1 35.3 1.0
OD1 D:ASP277 2.1 36.8 1.0
O D:ASP277 2.1 38.6 1.0
OE2 D:GLU279 2.1 37.5 1.0
O D:HOH700 2.7 29.5 1.0
CD D:GLU279 3.0 37.2 1.0
ZN D:ZN501 3.0 38.9 1.0
CG D:ASP200 3.0 33.0 1.0
C D:ASP277 3.2 36.5 1.0
OE1 D:GLU279 3.2 39.3 1.0
OD1 D:ASP200 3.3 33.0 1.0
CG D:ASP277 3.3 35.8 1.0
CA D:ASP277 3.6 36.0 1.0
NZ D:LYS207 3.8 38.0 1.0
CB D:ASP277 4.0 36.0 1.0
CE D:LYS207 4.1 38.3 1.0
OD2 D:ASP277 4.3 36.5 1.0
N D:ALA278 4.3 37.8 1.0
N D:GLU279 4.4 37.3 1.0
CB D:ASP200 4.4 33.4 1.0
CG D:GLU279 4.4 38.1 1.0
OD2 D:ASP218 4.5 38.7 1.0
ND2 D:ASN250 4.6 33.6 1.0
CA D:ALA278 4.8 37.4 1.0
CA D:GLY202 4.8 34.7 1.0
NZ D:LYS195 4.9 38.8 1.0
N D:ASP277 5.0 35.8 1.0

Manganese binding site 5 out of 6 in 6ov8

Go back to Manganese Binding Sites List in 6ov8
Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:33.6
occ:1.00
 O E:ASP277 2.1 37.3 1.0
OD2 E:ASP200 2.1 35.4 1.0
OD1 E:ASP277 2.1 37.6 1.0
OE2 E:GLU279 2.1 35.5 1.0
O E:HOH693 2.5 20.2 1.0
CD E:GLU279 3.0 34.9 1.0
ZN E:ZN501 3.1 40.0 1.0
CG E:ASP200 3.1 33.2 1.0
C E:ASP277 3.2 35.9 1.0
OE1 E:GLU279 3.2 37.5 1.0
CG E:ASP277 3.2 38.4 1.0
OD1 E:ASP200 3.5 32.6 1.0
O E:HOH643 3.6 27.6 1.0
CA E:ASP277 3.6 36.1 1.0
CB E:ASP277 4.0 37.1 1.0
NZ E:LYS207 4.0 35.0 1.0
CE E:LYS207 4.2 35.0 1.0
OD2 E:ASP277 4.2 39.2 1.0
N E:ALA278 4.4 36.0 1.0
N E:GLU279 4.4 34.9 1.0
CG E:GLU279 4.4 34.3 1.0
CB E:ASP200 4.5 32.8 1.0
OD2 E:ASP218 4.5 39.9 1.0
ND2 E:ASN250 4.7 32.7 1.0
CA E:ALA278 4.9 35.0 1.0
CA E:GLY202 4.9 34.2 1.0
NZ E:LYS195 5.0 40.5 1.0
N E:ASP277 5.0 35.6 1.0

Manganese binding site 6 out of 6 in 6ov8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:33.5
occ:1.00
 OD2 F:ASP200 2.1 34.2 1.0
O F:ASP277 2.1 37.5 1.0
OE2 F:GLU279 2.1 39.2 1.0
OD1 F:ASP277 2.2 37.6 1.0
O F:HOH679 2.6 22.9 1.0
ZN F:ZN501 3.0 37.3 1.0
CG F:ASP200 3.0 32.8 1.0
CD F:GLU279 3.1 37.3 1.0
C F:ASP277 3.2 34.5 1.0
CG F:ASP277 3.2 36.1 1.0
OD1 F:ASP200 3.3 33.3 1.0
OE1 F:GLU279 3.4 38.3 1.0
CA F:ASP277 3.6 34.6 1.0
O F:HOH641 3.7 26.0 1.0
NZ F:LYS207 3.8 39.4 1.0
CB F:ASP277 4.0 35.9 1.0
OD2 F:ASP277 4.1 36.0 1.0
CE F:LYS207 4.1 38.6 1.0
N F:ALA278 4.3 34.8 1.0
N F:GLU279 4.4 34.3 1.0
CB F:ASP200 4.4 33.0 1.0
OD2 F:ASP218 4.5 36.1 1.0
CG F:GLU279 4.5 35.8 1.0
CA F:ALA278 4.8 34.7 1.0
ND2 F:ASN250 4.8 30.4 1.0
NZ F:LYS195 4.8 36.8 1.0
CA F:GLY202 4.9 33.9 1.0
CB F:GLU279 5.0 35.4 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 Dec 15 04:58:38 2020

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