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Sodium in PDB 4gy9: Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP)

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP), PDB code: 4gy9 was solved by M.Ruszkowski, M.Sikorski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.30 / 2.04
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 96.596, 96.596, 112.031, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP) (pdb code 4gy9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP), PDB code: 4gy9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4gy9

Go back to Sodium Binding Sites List in 4gy9
Sodium binding site 1 out of 6 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP)


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 Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:37.2
occ:1.00
 OG1 A:THR66 2.2 27.1 1.0
O A:SER65 2.3 21.5 1.0
O A:HOH407 2.4 41.4 1.0
O A:HOH416 2.4 41.5 1.0
C A:SER65 3.1 21.4 1.0
CB A:THR66 3.4 22.9 1.0
CA A:THR66 3.6 19.4 1.0
N A:THR66 3.7 20.3 1.0
N A:SER65 3.9 21.1 1.0
CA A:SER65 4.1 23.3 1.0
NA A:NA206 4.2 53.1 1.0
CG2 A:THR66 4.2 26.2 1.0
O A:HOH417 4.3 56.0 1.0
O A:HOH329 4.4 41.3 1.0
CE2 A:PHE59 4.9 25.2 1.0
O A:GLU86 4.9 22.0 1.0
O A:HOH361 4.9 34.7 1.0
C A:GLY64 4.9 23.6 1.0
O A:HOH377 4.9 26.4 1.0

Sodium binding site 2 out of 6 in 4gy9

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Sodium binding site 2 out of 6 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP)


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 Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:27.8
occ:1.00
 O A:HOH302 2.3 24.5 1.0
O A:HOH358 2.4 26.7 0.8
O A:PHE59 2.4 23.8 1.0
O A:HOH366 2.4 31.7 1.0
O A:GLY61 2.5 24.2 1.0
O A:HOH367 2.6 39.6 1.0
N A:GLY61 3.4 27.7 1.0
C A:GLY61 3.5 30.6 1.0
C A:PHE59 3.6 24.2 1.0
C A:VAL60 3.9 22.6 1.0
CA A:GLY61 4.0 30.3 1.0
CA A:VAL60 4.1 23.4 1.0
CG2 A:THR58 4.2 28.6 1.0
N A:VAL60 4.3 23.7 1.0
O A:GLY64 4.4 23.0 1.0
OE1 A:GLU40 4.5 46.2 1.0
N A:PHE59 4.6 21.4 1.0
O A:HOH340 4.6 51.4 1.0
CA A:PHE59 4.7 21.1 1.0
N A:ASP62 4.7 25.0 1.0
O A:VAL60 4.7 25.8 1.0
OE2 A:GLU40 4.8 41.0 1.0
CD A:GLU40 4.8 44.6 1.0
N A:PHE63 4.9 24.1 1.0
N A:GLY64 4.9 22.9 1.0

Sodium binding site 3 out of 6 in 4gy9

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Sodium binding site 3 out of 6 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP)


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 Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:59.5
occ:1.00
 O A:HOH350 2.4 50.4 1.0
O A:HOH319 2.4 36.2 1.0
O A:HOH354 2.4 51.6 1.0
O A:HOH345 2.5 52.6 1.0
O A:ALA34 2.5 31.7 1.0
O A:HOH347 2.6 45.9 1.0
C A:ALA34 3.6 32.3 1.0
O A:HOH432 3.8 61.4 1.0
O A:HOH373 4.0 56.1 1.0
CD A:PRO36 4.3 29.8 1.0
CA A:ALA34 4.4 32.9 1.0
N A:LEU35 4.6 30.6 1.0
O A:LYS33 4.8 33.1 1.0
CA A:LEU35 4.8 28.6 1.0
CB A:ALA147 4.9 29.3 1.0
O A:ALA147 4.9 30.1 1.0
CD2 A:LEU35 4.9 36.9 1.0
O A:HOH425 5.0 26.0 1.0

Sodium binding site 4 out of 6 in 4gy9

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Sodium binding site 4 out of 6 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP)


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 Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:51.5
occ:1.00
 O A:THR0 2.3 22.3 1.0
O A:HOH370 2.5 41.3 1.0
O A:HOH440 2.5 51.6 1.0
O A:HOH404 2.5 44.4 1.0
O A:GLY124 2.6 51.5 1.0
N A:GLY124 3.5 50.3 1.0
C A:GLY124 3.5 57.7 1.0
C A:THR0 3.5 25.2 1.0
N A:THR0 3.9 25.2 1.0
CA A:GLY124 3.9 56.4 1.0
CE1 A:PHE-1 4.0 43.7 1.0
CA A:THR0 4.2 24.4 1.0
O A:HOH365 4.2 60.1 1.0
OD1 A:ASP125 4.3 67.1 1.0
CD1 A:PHE-1 4.3 41.6 1.0
CZ A:PHE-1 4.4 40.4 1.0
C A:LYS123 4.5 52.6 1.0
N A:MET1 4.5 25.4 1.0
N A:ASP125 4.6 53.3 1.0
CB A:THR0 4.6 29.7 1.0
O A:HOH408 4.6 42.4 1.0
CA A:MET1 4.7 24.7 1.0
O A:THR122 4.9 40.9 1.0
CA A:LYS123 4.9 48.6 1.0
O A:HOH433 4.9 48.5 1.0
CA A:ASP125 5.0 57.2 1.0
C A:PHE-1 5.0 27.9 1.0
CG A:PHE-1 5.0 34.6 1.0

Sodium binding site 5 out of 6 in 4gy9

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Sodium binding site 5 out of 6 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:53.1
occ:1.00
 O A:HOH323 2.4 27.4 0.8
O A:HOH329 2.5 41.3 1.0
O A:SER65 2.5 21.5 1.0
OG A:SER65 2.6 29.5 1.0
C A:SER65 3.2 21.4 1.0
CB A:SER65 3.7 26.8 1.0
N A:SER65 3.7 21.1 1.0
O A:HOH332 3.8 56.0 1.0
CA A:SER65 3.8 23.3 1.0
N A:THR66 4.1 20.3 1.0
NA A:NA202 4.2 37.2 1.0
O A:HOH361 4.2 34.7 1.0
O A:HOH407 4.3 41.4 1.0
O A:HOH429 4.3 58.1 1.0
O A:HOH416 4.4 41.5 1.0
CA A:THR66 4.5 19.4 1.0
C A:GLY64 4.9 23.6 1.0

Sodium binding site 6 out of 6 in 4gy9

Go back to Sodium Binding Sites List in 4gy9
Sodium binding site 6 out of 6 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with N6-Isopentenyladenine (2IP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:61.3
occ:1.00
 O A:GLU110 2.3 64.9 1.0
O A:HOH413 2.4 48.5 1.0
O A:HOH435 2.4 55.6 1.0
O A:THR107 2.4 55.8 1.0
O A:GLY111 2.6 34.9 1.0
C A:GLU110 3.3 62.5 1.0
C A:GLY111 3.3 44.7 1.0
CA A:GLY111 3.3 57.0 1.0
C A:THR107 3.6 56.6 1.0
N A:GLY111 3.7 67.3 1.0
O A:HOH318 3.8 38.6 1.0
N A:THR107 4.0 41.4 1.0
O A:PRO108 4.2 73.5 1.0
CG2 A:THR107 4.3 62.0 1.0
CA A:THR107 4.4 50.4 1.0
C A:PRO108 4.5 71.9 1.0
CA A:GLU110 4.6 66.9 1.0
N A:CYS112 4.6 36.6 1.0
N A:PRO108 4.6 61.1 1.0
CA A:PRO108 4.6 66.9 1.0
N A:GLU110 4.7 69.9 1.0
O A:HOH420 4.8 55.1 1.0
C A:PRO106 5.0 41.6 1.0

Reference:

M.Ruszkowski, K.Szpotkowski, M.Sikorski, M.Jaskolski. The Landscape of Cytokinin Binding By A Plant Nodulin. Acta Crystallogr.,Sect.D V. 69 2365 2013.
ISSN: ISSN 0907-4449
PubMed: 24311578
DOI: 10.1107/S0907444913021975
Page generated: Tue Dec 15 06:42:28 2020

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