Atomistry » Cadmium » PDB 3zr9-4efp » 4dzi
Atomistry »
  Cadmium »
    PDB 3zr9-4efp »
      4dzi »

Cadmium in PDB 4dzi: Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10

Protein crystallography data

The structure of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10, PDB code: 4dzi was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.106, 136.131, 93.229, 90.00, 113.09, 90.00
R / Rfree (%) 16.6 / 20.3

Other elements in 4dzi:

The structure of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 (pdb code 4dzi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10, PDB code: 4dzi:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 1 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:16.0
occ:1.00
 OE2 A:GLU360 2.3 21.8 1.0
ND1 A:HIS358 2.3 13.8 1.0
OD2 A:ASP355 2.3 15.4 1.0
OE1 A:GLU292 2.3 13.5 1.0
O A:HOH659 2.4 13.8 1.0
OE2 A:GLU292 2.5 15.1 1.0
CD A:GLU292 2.7 15.6 1.0
OD1 A:ASP355 2.8 16.6 1.0
CG A:ASP355 2.9 13.5 1.0
CD A:GLU360 3.2 16.6 1.0
CE1 A:HIS358 3.2 16.8 1.0
CG A:HIS358 3.3 15.7 1.0
CG A:GLU360 3.6 20.1 1.0
CB A:HIS358 3.6 16.0 1.0
CD A:CD502 3.8 14.0 1.0
NE2 A:HIS14 4.0 10.3 1.0
O A:HOH1027 4.2 39.7 1.0
O A:HOH756 4.2 35.2 1.0
CG A:GLU292 4.2 13.1 1.0
OE1 A:GLU360 4.3 19.6 1.0
CD2 A:HIS14 4.3 19.4 1.0
CB A:ASP355 4.4 14.3 1.0
NE2 A:HIS358 4.4 14.7 1.0
CD2 A:HIS358 4.4 17.1 1.0
O A:HOH675 4.6 24.6 1.0
O A:ASP355 4.9 16.4 1.0
O A:HOH920 4.9 29.1 1.0
CE1 A:HIS14 4.9 11.7 1.0
CE1 A:HIS229 5.0 14.9 1.0

Cadmium binding site 2 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 2 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:14.0
occ:1.00
 OE2 A:GLU292 2.2 15.1 1.0
NE2 A:HIS14 2.2 10.3 1.0
OD1 A:ASP12 2.3 15.8 1.0
OD1 A:ASP355 2.3 16.6 1.0
NE2 A:HIS229 2.4 11.6 1.0
OD2 A:ASP12 2.5 12.7 1.0
CG A:ASP12 2.7 15.1 1.0
CE1 A:HIS14 3.2 11.7 1.0
CD2 A:HIS14 3.2 19.4 1.0
CE1 A:HIS229 3.2 14.9 1.0
CD A:GLU292 3.3 15.6 1.0
CG A:ASP355 3.3 13.5 1.0
CD2 A:HIS229 3.5 10.6 1.0
CB A:GLU292 3.7 10.6 1.0
CD A:CD501 3.8 16.0 1.0
CG A:GLU292 3.9 13.1 1.0
OD2 A:ASP355 4.1 15.4 1.0
CB A:ASP355 4.1 14.3 1.0
CB A:ASP12 4.2 13.1 1.0
OE1 A:GLU292 4.3 13.5 1.0
ND1 A:HIS14 4.3 14.5 1.0
CA A:ASP355 4.3 15.1 1.0
CG A:HIS14 4.3 16.0 1.0
ND1 A:HIS229 4.4 13.9 1.0
CG A:HIS229 4.6 11.5 1.0
O A:HOH659 4.6 13.8 1.0
ND1 A:HIS358 4.7 13.8 1.0
CG2 A:ILE291 4.7 11.8 1.0
CD1 A:LEU120 4.8 12.4 1.0
CE1 A:HIS358 4.8 16.8 1.0
CA A:ASP12 4.9 14.3 1.0

Cadmium binding site 3 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 3 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:14.5
occ:1.00
 OE2 B:GLU360 2.3 17.7 1.0
OD2 B:ASP355 2.3 16.4 1.0
ND1 B:HIS358 2.3 16.4 1.0
OE2 B:GLU292 2.4 12.9 1.0
O B:HOH659 2.4 14.8 1.0
OE1 B:GLU292 2.5 15.4 1.0
CD B:GLU292 2.7 14.5 1.0
OD1 B:ASP355 2.7 13.9 1.0
CG B:ASP355 2.9 19.0 1.0
CE1 B:HIS358 3.2 10.7 1.0
CD B:GLU360 3.3 19.2 1.0
CG B:HIS358 3.4 14.6 1.0
CB B:HIS358 3.7 12.8 1.0
CG B:GLU360 3.8 20.2 1.0
CD B:CD502 3.8 12.5 1.0
NE2 B:HIS14 4.0 12.1 1.0
O B:HOH886 4.1 34.4 1.0
CG B:GLU292 4.2 16.8 1.0
CD2 B:HIS14 4.3 11.2 1.0
OE1 B:GLU360 4.4 21.7 1.0
NE2 B:HIS358 4.4 15.9 1.0
CB B:ASP355 4.4 10.8 1.0
CD2 B:HIS358 4.5 13.4 1.0
O B:HOH738 4.6 21.5 1.0
O B:HOH805 4.7 24.7 1.0
O B:HOH705 4.8 22.1 1.0
O B:ASP355 4.8 14.3 1.0
CE1 B:HIS229 4.9 13.6 1.0
CE1 B:HIS14 4.9 11.8 1.0

Cadmium binding site 4 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 4 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:12.5
occ:1.00
 NE2 B:HIS14 2.2 12.1 1.0
OD1 B:ASP12 2.3 11.5 1.0
NE2 B:HIS229 2.3 10.9 1.0
OE2 B:GLU292 2.3 12.9 1.0
OD1 B:ASP355 2.4 13.9 1.0
OD2 B:ASP12 2.6 12.1 1.0
CG B:ASP12 2.8 10.1 1.0
CE1 B:HIS229 3.1 13.6 1.0
CE1 B:HIS14 3.2 11.8 1.0
CD2 B:HIS14 3.2 11.2 1.0
CD B:GLU292 3.3 14.5 1.0
CG B:ASP355 3.3 19.0 1.0
CD2 B:HIS229 3.4 13.2 1.0
CB B:GLU292 3.7 14.5 1.0
CD B:CD501 3.8 14.5 1.0
CG B:GLU292 3.9 16.8 1.0
OD2 B:ASP355 4.1 16.4 1.0
CB B:ASP355 4.1 10.8 1.0
CB B:ASP12 4.3 10.5 1.0
ND1 B:HIS14 4.3 13.2 1.0
ND1 B:HIS229 4.3 14.2 1.0
CG B:HIS14 4.3 12.5 1.0
CA B:ASP355 4.4 11.3 1.0
OE1 B:GLU292 4.4 15.4 1.0
CG B:HIS229 4.5 12.6 1.0
O B:HOH659 4.6 14.8 1.0
ND1 B:HIS358 4.8 16.4 1.0
CG2 B:ILE291 4.8 12.9 1.0
CD1 B:LEU120 4.8 17.1 1.0
O B:HOH738 4.9 21.5 1.0
CE1 B:HIS358 5.0 10.7 1.0
CA B:ASP12 5.0 8.2 1.0

Cadmium binding site 5 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 5 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd501

b:14.2
occ:1.00
 OE2 C:GLU360 2.3 15.6 1.0
ND1 C:HIS358 2.3 11.5 1.0
OD2 C:ASP355 2.3 16.4 1.0
OE1 C:GLU292 2.4 14.5 1.0
O C:HOH615 2.5 15.8 1.0
OE2 C:GLU292 2.5 12.2 1.0
OD1 C:ASP355 2.7 14.7 1.0
CD C:GLU292 2.7 19.0 1.0
CG C:ASP355 2.9 11.9 1.0
CD C:GLU360 3.2 16.5 1.0
CE1 C:HIS358 3.3 11.4 1.0
CG C:HIS358 3.3 11.6 1.0
CB C:HIS358 3.6 12.2 1.0
CG C:GLU360 3.7 15.3 1.0
CD C:CD502 3.8 12.1 1.0
NE2 C:HIS14 4.1 11.3 1.0
CG C:GLU292 4.2 12.1 1.0
O C:HOH849 4.3 31.7 1.0
OE1 C:GLU360 4.3 18.9 1.0
O C:HOH879 4.3 38.4 1.0
CB C:ASP355 4.4 15.0 1.0
CD2 C:HIS14 4.4 13.7 1.0
NE2 C:HIS358 4.4 14.5 1.0
CD2 C:HIS358 4.5 11.9 1.0
O C:HOH816 4.6 22.4 1.0
O C:HOH812 4.7 23.6 1.0
O C:HOH707 4.8 28.8 1.0
O C:ASP355 4.9 14.9 1.0
CE1 C:HIS14 5.0 8.3 1.0
CE1 C:HIS229 5.0 11.7 1.0

Cadmium binding site 6 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 6 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd502

b:12.1
occ:1.00
 NE2 C:HIS14 2.2 11.3 1.0
OE2 C:GLU292 2.2 12.2 1.0
OD1 C:ASP12 2.2 11.9 1.0
OD1 C:ASP355 2.3 14.7 1.0
NE2 C:HIS229 2.4 14.0 1.0
OD2 C:ASP12 2.6 13.5 1.0
CG C:ASP12 2.7 12.1 1.0
CD2 C:HIS14 3.2 13.7 1.0
CE1 C:HIS14 3.2 8.3 1.0
CE1 C:HIS229 3.3 11.7 1.0
CD C:GLU292 3.3 19.0 1.0
CG C:ASP355 3.3 11.9 1.0
CD2 C:HIS229 3.4 12.2 1.0
CB C:GLU292 3.7 9.6 1.0
CD C:CD501 3.8 14.2 1.0
CG C:GLU292 3.9 12.1 1.0
OD2 C:ASP355 4.1 16.4 1.0
CB C:ASP355 4.1 15.0 1.0
CB C:ASP12 4.2 9.2 1.0
CA C:ASP355 4.3 11.4 1.0
OE1 C:GLU292 4.3 14.5 1.0
ND1 C:HIS14 4.3 13.3 1.0
CG C:HIS14 4.3 11.9 1.0
ND1 C:HIS229 4.5 10.8 1.0
CG C:HIS229 4.5 8.8 1.0
ND1 C:HIS358 4.6 11.5 1.0
O C:HOH615 4.7 15.8 1.0
CG2 C:ILE291 4.7 11.1 1.0
CE1 C:HIS358 4.9 11.4 1.0
CD1 C:LEU120 4.9 15.0 1.0
CA C:ASP12 4.9 10.9 1.0

Cadmium binding site 7 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 7 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd501

b:16.2
occ:1.00
 OE2 D:GLU360 2.3 21.3 1.0
ND1 D:HIS358 2.3 12.1 1.0
OD2 D:ASP355 2.3 19.3 1.0
OE1 D:GLU292 2.4 17.6 1.0
OE2 D:GLU292 2.4 12.1 1.0
O D:HOH605 2.5 16.2 1.0
CD D:GLU292 2.7 15.4 1.0
OD1 D:ASP355 2.8 16.3 1.0
CG D:ASP355 2.9 17.4 1.0
CE1 D:HIS358 3.2 14.5 1.0
CD D:GLU360 3.2 17.7 1.0
CG D:HIS358 3.3 14.8 1.0
CB D:HIS358 3.6 13.6 1.0
CG D:GLU360 3.7 24.1 1.0
CD D:CD502 3.8 14.5 1.0
O D:HOH952 4.0 42.9 1.0
NE2 D:HIS14 4.0 11.1 1.0
CG D:GLU292 4.2 12.5 1.0
OE1 D:GLU360 4.3 24.0 1.0
NE2 D:HIS358 4.4 13.2 1.0
CD2 D:HIS14 4.4 11.7 1.0
CB D:ASP355 4.4 12.5 1.0
CD2 D:HIS358 4.4 18.4 1.0
O D:HOH801 4.7 25.1 1.0
O D:HOH705 4.7 26.5 1.0
O D:ASP355 4.9 16.2 1.0
O D:HOH709 4.9 29.2 1.0
CE1 D:HIS14 4.9 14.8 1.0
CE1 D:HIS229 4.9 13.6 1.0

Cadmium binding site 8 out of 8 in 4dzi

Go back to Cadmium Binding Sites List in 4dzi
Cadmium binding site 8 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd502

b:14.5
occ:1.00
 NE2 D:HIS14 2.2 11.1 1.0
OD1 D:ASP355 2.2 16.3 1.0
OE2 D:GLU292 2.2 12.1 1.0
OD1 D:ASP12 2.3 15.5 1.0
NE2 D:HIS229 2.3 15.6 1.0
OD2 D:ASP12 2.5 15.2 1.0
CG D:ASP12 2.7 16.9 1.0
CD2 D:HIS14 3.2 11.7 1.0
CE1 D:HIS14 3.2 14.8 1.0
CE1 D:HIS229 3.2 13.6 1.0
CG D:ASP355 3.3 17.4 1.0
CD D:GLU292 3.4 15.4 1.0
CD2 D:HIS229 3.4 11.0 1.0
CB D:GLU292 3.7 14.7 1.0
CD D:CD501 3.8 16.2 1.0
CG D:GLU292 3.9 12.5 1.0
OD2 D:ASP355 4.1 19.3 1.0
CB D:ASP355 4.1 12.5 1.0
CB D:ASP12 4.2 13.4 1.0
CA D:ASP355 4.3 12.2 1.0
ND1 D:HIS14 4.3 14.6 1.0
CG D:HIS14 4.3 10.1 1.0
OE1 D:GLU292 4.4 17.6 1.0
ND1 D:HIS229 4.4 13.4 1.0
CG D:HIS229 4.5 11.5 1.0
ND1 D:HIS358 4.6 12.1 1.0
O D:HOH605 4.6 16.2 1.0
CG2 D:ILE291 4.7 15.7 1.0
CD1 D:LEU120 4.8 13.9 1.0
CE1 D:HIS358 4.8 14.5 1.0
CA D:ASP12 4.9 11.2 1.0
O D:HOH705 4.9 26.5 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo. Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium To Be Published.
Page generated: Fri Jul 19 17:12:44 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy