Atomistry » Sodium » PDB 4gxj-4hfc » 4gy9
Atomistry »
  Sodium »
    PDB 4gxj-4hfc »
      4gy9 »

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

Go back to Sodium Binding Sites List in 4gy9
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

Go back to Sodium Binding Sites List in 4gy9
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

Go back to Sodium Binding Sites List in 4gy9
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

Go back to Sodium Binding Sites List in 4gy9
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: Mon Oct 7 15:41:57 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