Atomistry » Manganese » PDB 8awx-8djy » 8d1x
Atomistry »
  Manganese »
    PDB 8awx-8djy »
      8d1x »

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

Go back to Manganese Binding Sites List in 8d1x
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

Go back to Manganese Binding Sites List in 8d1x
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

Go back to Manganese Binding Sites List in 8d1x
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy