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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

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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

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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

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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

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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: Mon Aug 18 06:15:12 2025

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