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Manganese in PDB 8d1x: Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae

Enzymatic activity of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae

All present enzymatic activity of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae:
3.4.11.1; 3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae, PDB code: 8d1x was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.61, 93.25, 179.47, 90, 101.32, 90
R / Rfree (%) 17 / 20.3

Other elements in 8d1x:

The structure of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae (pdb code 8d1x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae, PDB code: 8d1x:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 8d1x

Go back to Manganese Binding Sites List in 8d1x
Manganese binding site 1 out of 6 in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:59.5
occ:1.00
 O A:ASP324 2.2 53.4 1.0
OD2 A:ASP247 2.2 51.8 1.0
OE1 A:GLU326 2.4 52.2 1.0
OD1 A:ASP324 2.7 46.7 1.0
O A:HOH601 3.1 43.7 1.0
CD A:GLU326 3.2 52.9 1.0
OE2 A:GLU326 3.3 51.0 1.0
CG A:ASP247 3.4 48.5 1.0
C A:ASP324 3.4 46.2 1.0
CG A:ASP324 3.6 50.9 1.0
OD1 A:ASP247 3.9 48.8 1.0
NZ A:LYS254 4.1 43.3 1.0
CA A:ASP324 4.1 46.2 1.0
CE A:LYS254 4.2 44.9 1.0
N A:GLU326 4.3 45.2 1.0
CB A:ASP324 4.4 49.3 1.0
CL A:CL501 4.4 50.4 1.0
N A:ALA325 4.4 47.4 1.0
OD2 A:ASP324 4.4 55.4 1.0
CB A:ASP247 4.5 50.6 1.0
CA A:ALA325 4.6 44.8 1.0
OD2 A:ASP265 4.6 52.2 1.0
CG A:GLU326 4.7 51.1 1.0

Manganese binding site 2 out of 6 in 8d1x

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Manganese binding site 2 out of 6 in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:61.4
occ:1.00
 O B:ASP324 2.2 53.7 1.0
OD2 B:ASP247 2.2 58.2 1.0
OE1 B:GLU326 2.6 53.7 1.0
OD1 B:ASP324 2.7 49.9 1.0
O B:HOH601 2.9 43.9 1.0
CG B:ASP247 3.3 53.9 1.0
CD B:GLU326 3.4 54.3 1.0
OE2 B:GLU326 3.4 54.1 1.0
C B:ASP324 3.4 45.8 1.0
CG B:ASP324 3.6 54.7 1.0
OD1 B:ASP247 3.7 53.8 1.0
CA B:ASP324 4.2 46.0 1.0
CL B:CL501 4.2 57.0 1.0
CE B:LYS254 4.2 55.3 1.0
N B:GLU326 4.3 45.7 1.0
NZ B:LYS254 4.4 55.2 1.0
OD2 B:ASP324 4.4 52.8 1.0
CB B:ASP324 4.4 48.4 1.0
N B:ALA325 4.4 42.3 1.0
CB B:ASP247 4.5 53.2 1.0
OD2 B:ASP265 4.6 53.5 1.0
CA B:ALA325 4.6 41.2 1.0
CG B:GLU326 4.8 52.2 1.0
N B:GLY327 4.9 41.2 1.0
NZ B:LYS242 5.0 48.2 1.0

Manganese binding site 3 out of 6 in 8d1x

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Manganese binding site 3 out of 6 in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn500

b:68.1
occ:1.00
 OD2 C:ASP247 2.2 64.6 1.0
O C:ASP324 2.2 63.6 1.0
OE1 C:GLU326 2.6 59.6 1.0
OD1 C:ASP324 2.7 64.4 1.0
O C:HOH602 2.8 56.7 1.0
O C:HOH631 3.3 43.1 1.0
CG C:ASP247 3.3 61.5 1.0
CD C:GLU326 3.4 62.2 1.0
OE2 C:GLU326 3.4 63.3 1.0
C C:ASP324 3.4 58.1 1.0
CG C:ASP324 3.7 63.8 1.0
OD1 C:ASP247 3.8 62.2 1.0
NZ C:LYS254 3.8 66.2 1.0
CE C:LYS254 4.1 64.7 1.0
CA C:ASP324 4.2 57.5 1.0
OD2 C:ASP324 4.4 65.0 1.0
N C:GLU326 4.4 51.0 1.0
CB C:ASP324 4.4 59.7 1.0
N C:ALA325 4.5 52.3 1.0
CL C:CL501 4.5 61.8 1.0
CB C:ASP247 4.5 58.1 1.0
OD2 C:ASP265 4.6 58.6 1.0
CA C:ALA325 4.7 48.2 1.0
CG C:GLU326 4.9 57.4 1.0

Manganese binding site 4 out of 6 in 8d1x

Go back to Manganese Binding Sites List in 8d1x
Manganese binding site 4 out of 6 in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn500

b:62.7
occ:1.00
 O D:ASP324 2.1 54.3 1.0
OD2 D:ASP247 2.2 53.8 1.0
O D:HOH649 2.5 51.4 1.0
OE1 D:GLU326 2.5 50.1 1.0
OD1 D:ASP324 2.7 56.9 1.0
O D:HOH601 3.2 39.8 1.0
O D:HOH661 3.3 38.2 1.0
C D:ASP324 3.3 51.4 1.0
CD D:GLU326 3.3 54.8 1.0
CG D:ASP247 3.4 48.3 1.0
OE2 D:GLU326 3.4 52.2 1.0
CG D:ASP324 3.6 55.3 1.0
OD1 D:ASP247 3.9 48.6 1.0
CA D:ASP324 4.0 50.9 1.0
NZ D:LYS254 4.1 46.9 1.0
CE D:LYS254 4.2 46.0 1.0
CB D:ASP324 4.3 52.9 1.0
N D:ALA325 4.3 47.6 1.0
OD2 D:ASP324 4.3 55.5 1.0
N D:GLU326 4.4 47.6 1.0
CL D:CL501 4.5 57.0 1.0
CA D:ALA325 4.6 48.5 1.0
CB D:ASP247 4.6 45.4 1.0
CG D:GLU326 4.8 51.6 1.0

Manganese binding site 5 out of 6 in 8d1x

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Manganese binding site 5 out of 6 in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn500

b:62.7
occ:1.00
 O E:ASP324 2.1 59.6 1.0
OD2 E:ASP247 2.2 54.1 1.0
OD1 E:ASP324 2.5 60.9 1.0
OE1 E:GLU326 2.5 46.1 1.0
O E:HOH667 3.1 40.2 1.0
O E:HOH601 3.1 38.1 1.0
CG E:ASP247 3.3 49.1 1.0
C E:ASP324 3.3 55.1 1.0
CD E:GLU326 3.3 48.1 1.0
OE2 E:GLU326 3.4 51.2 1.0
CG E:ASP324 3.5 62.5 1.0
OD1 E:ASP247 3.8 48.8 1.0
CA E:ASP324 4.0 52.7 1.0
NZ E:LYS254 4.1 53.4 1.0
CE E:LYS254 4.1 51.1 1.0
CB E:ASP324 4.3 55.6 1.0
OD2 E:ASP324 4.3 66.1 1.0
N E:ALA325 4.4 47.6 1.0
N E:GLU326 4.4 44.8 1.0
CB E:ASP247 4.5 45.7 1.0
CL E:CL501 4.5 57.6 1.0
CA E:ALA325 4.6 44.0 1.0
OD2 E:ASP265 4.7 52.3 1.0
CG E:GLU326 4.8 45.7 1.0

Manganese binding site 6 out of 6 in 8d1x

Go back to Manganese Binding Sites List in 8d1x
Manganese binding site 6 out of 6 in the Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn500

b:64.2
occ:1.00
 O F:ASP324 2.2 54.6 1.0
OD2 F:ASP247 2.2 58.1 1.0
OE1 F:GLU326 2.5 53.0 1.0
OD1 F:ASP324 2.6 57.9 1.0
O F:HOH603 2.9 45.7 1.0
OE2 F:GLU326 3.0 53.1 1.0
CD F:GLU326 3.1 53.8 1.0
C F:ASP324 3.3 50.6 1.0
CG F:ASP247 3.3 56.6 1.0
CG F:ASP324 3.6 56.9 1.0
OD1 F:ASP247 3.8 56.0 1.0
CA F:ASP324 4.0 49.3 1.0
NZ F:LYS254 4.0 50.5 1.0
CE F:LYS254 4.2 51.6 1.0
N F:GLU326 4.3 44.4 1.0
CB F:ASP324 4.4 52.5 1.0
N F:ALA325 4.4 44.6 1.0
OD2 F:ASP324 4.4 57.9 1.0
CL F:CL501 4.6 52.8 1.0
CB F:ASP247 4.6 48.6 1.0
CG F:GLU326 4.6 50.2 1.0
CA F:ALA325 4.6 42.7 1.0
OD2 F:ASP265 5.0 51.3 1.0

Reference:

J.Abendroth, N.D.Debouver, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Aminopeptidase A From Neisseria Gonorrhoeae To Be Published.
Page generated: Sun Oct 6 11:29:15 2024

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