Atomistry » Sodium » PDB 6nib-6nxy » 6nic
Atomistry »
  Sodium »
    PDB 6nib-6nxy »
      6nic »

Sodium in PDB 6nic: Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide

Enzymatic activity of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide

All present enzymatic activity of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide:
3.5.3.12;

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide, PDB code: 6nic was solved by B.Sekula, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.19 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.445, 142.445, 345.429, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide (pdb code 6nic). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide, PDB code: 6nic:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6nic

Go back to Sodium Binding Sites List in 6nic
Sodium binding site 1 out of 4 in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:33.2
occ:1.00
 O A:ASP220 2.6 41.8 1.0
O A:TRP125 2.7 29.5 1.0
OD1 A:ASN222 2.9 25.8 1.0
O A:ASP130 3.0 61.2 1.0
O A:ASP219 3.3 42.8 1.0
C A:ASP220 3.6 39.1 1.0
CG A:ASN222 3.7 25.9 1.0
C A:TRP125 3.9 30.0 1.0
ND2 A:ASN222 4.0 24.4 1.0
ND2 A:ASN185 4.1 28.6 1.0
C A:ASP130 4.3 62.7 1.0
C A:ASP219 4.3 37.9 1.0
CA A:ASP220 4.3 43.3 1.0
CB A:TRP125 4.4 26.6 1.0
N A:THR221 4.4 33.0 1.0
N A:ASN222 4.6 24.3 1.0
OD2 A:ASP130 4.6 53.8 1.0
OD1 A:ASP130 4.6 52.1 1.0
CG A:ASP130 4.6 56.5 1.0
C A:THR221 4.6 26.8 1.0
CA A:THR221 4.7 29.2 1.0
CA A:GLY126 4.7 36.3 1.0
NH1 A:ARG186 4.8 22.9 1.0
N A:ASP220 4.8 41.3 1.0
N A:GLY126 4.8 32.3 1.0
CA A:GLY131 4.8 58.4 1.0
CA A:TRP125 4.8 28.2 1.0
CB A:ASN222 5.0 24.6 1.0

Sodium binding site 2 out of 4 in 6nic

Go back to Sodium Binding Sites List in 6nic
Sodium binding site 2 out of 4 in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:36.0
occ:1.00
 O B:ASP220 2.5 47.7 1.0
O B:HOH546 2.6 49.8 1.0
O B:ASP130 2.7 58.9 1.0
O B:TRP125 2.8 31.9 1.0
OD1 B:ASN222 2.9 43.9 1.0
O B:ASP219 3.2 66.1 1.0
C B:ASP220 3.5 51.8 1.0
CG B:ASN222 3.6 39.6 1.0
ND2 B:ASN222 3.8 36.8 1.0
C B:ASP130 3.9 62.4 1.0
C B:TRP125 4.0 32.4 1.0
ND2 B:ASN185 4.1 33.3 1.0
C B:ASP219 4.2 59.4 1.0
CA B:ASP220 4.2 55.4 1.0
N B:THR221 4.4 50.3 1.0
CB B:TRP125 4.5 31.4 1.0
N B:ASN222 4.5 42.6 1.0
CA B:GLY131 4.5 60.5 1.0
N B:ASP220 4.7 55.4 1.0
C B:THR221 4.7 44.4 1.0
N B:GLY131 4.7 58.6 1.0
NH1 B:ARG186 4.7 30.2 1.0
CG B:ASP130 4.8 67.5 1.0
CA B:THR221 4.8 46.0 1.0
C B:GLY131 4.9 60.6 1.0
OD1 B:ASP130 4.9 64.0 1.0
CB B:ASN222 4.9 38.8 1.0
CA B:GLY126 4.9 36.3 1.0
N B:GLY126 4.9 32.9 1.0
CA B:TRP125 4.9 32.7 1.0
OD2 B:ASP130 5.0 63.3 1.0

Sodium binding site 3 out of 4 in 6nic

Go back to Sodium Binding Sites List in 6nic
Sodium binding site 3 out of 4 in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:26.6
occ:1.00
 O C:ASP220 2.6 30.1 1.0
O C:ASP130 2.8 33.6 1.0
O C:TRP125 2.8 18.6 1.0
O C:HOH709 2.9 45.0 1.0
OD1 C:ASN222 3.1 17.8 1.0
O C:ASP219 3.5 38.5 1.0
C C:ASP220 3.6 29.0 1.0
CG C:ASN222 3.8 17.9 1.0
ND2 C:ASN222 4.0 18.1 1.0
ND2 C:ASN185 4.0 15.3 1.0
C C:TRP125 4.0 18.6 1.0
C C:ASP130 4.0 38.0 1.0
CA C:ASP220 4.1 34.5 1.0
C C:ASP219 4.5 33.5 1.0
CG C:ASP130 4.5 42.4 1.0
CB C:TRP125 4.6 17.3 1.0
OD2 C:ASP130 4.6 48.8 1.0
OD1 C:ASP130 4.6 43.7 1.0
N C:THR221 4.6 24.2 1.0
CA C:GLY131 4.7 34.5 1.0
N C:GLY131 4.8 37.0 1.0
N C:ASN222 4.8 19.6 1.0
CA C:GLY126 4.8 21.3 1.0
C C:THR221 4.8 20.7 1.0
N C:ASP220 4.9 32.9 1.0
N C:GLY126 4.9 19.7 1.0
C C:GLY131 4.9 35.8 1.0
CA C:TRP125 4.9 17.6 1.0
CA C:THR221 4.9 21.8 1.0
NH1 C:ARG186 5.0 13.1 1.0

Sodium binding site 4 out of 4 in 6nic

Go back to Sodium Binding Sites List in 6nic
Sodium binding site 4 out of 4 in the Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Medicago Truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-Aminohexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:33.6
occ:1.00
 O D:ASP220 2.6 35.0 1.0
O D:ASP130 2.6 35.0 1.0
O D:HOH632 2.8 43.5 1.0
O D:TRP125 2.8 20.5 1.0
OD1 D:ASN222 3.2 25.5 1.0
O D:ASP219 3.5 44.9 1.0
C D:ASP220 3.6 39.3 1.0
C D:ASP130 3.9 37.9 1.0
CG D:ASN222 4.0 26.0 1.0
C D:TRP125 4.0 21.0 1.0
CA D:ASP220 4.0 44.9 1.0
ND2 D:ASN185 4.1 21.9 1.0
ND2 D:ASN222 4.1 25.3 1.0
CA D:GLY131 4.4 35.6 1.0
CG D:ASP130 4.4 40.7 1.0
C D:ASP219 4.5 43.3 1.0
OD1 D:ASP130 4.5 38.7 1.0
OD2 D:ASP130 4.5 40.2 1.0
CB D:TRP125 4.5 19.7 1.0
N D:THR221 4.6 32.8 1.0
N D:GLY131 4.6 36.0 1.0
C D:GLY131 4.7 35.4 1.0
N D:ASP220 4.8 42.5 1.0
CA D:GLY126 4.8 24.1 1.0
N D:GLY126 4.9 22.3 1.0
N D:ASN222 4.9 27.4 1.0
CB D:ASP130 5.0 40.0 1.0
CA D:TRP125 5.0 20.2 1.0
NH1 D:ARG186 5.0 17.3 1.0
C D:THR221 5.0 28.4 1.0
CA D:ASP130 5.0 40.6 1.0

Reference:

B.Sekula, Z.Dauter. Structural Study of Agmatine Iminohydrolase Frommedicago Truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants. Front Plant Sci V. 10 320 2019.
ISSN: ESSN 1664-462X
PubMed: 30984210
DOI: 10.3389/FPLS.2019.00320
Page generated: Tue Oct 8 12:16:46 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy