Atomistry » Sodium » PDB 8rzk-8ss9 » 8sjj
Atomistry »
  Sodium »
    PDB 8rzk-8ss9 »
      8sjj »

Sodium in PDB 8sjj: X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil

Protein crystallography data

The structure of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil, PDB code: 8sjj was solved by I.A.Cavini, H.M.Pereira, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.29 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.934, 50.811, 91.558, 90, 94.36, 90
R / Rfree (%) 22.1 / 28.6

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil (pdb code 8sjj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil, PDB code: 8sjj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 1 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:52.4
occ:1.00
 O A:GLN41 2.3 29.3 1.0
CG2 A:ILE44 3.2 29.9 1.0
C A:GLN41 3.4 29.2 1.0
CB A:ILE44 3.4 29.2 1.0
N A:ARG45 3.5 29.1 1.0
CA A:GLN41 3.8 29.4 1.0
CB A:ARG45 3.9 33.4 1.0
CB A:GLN41 4.0 32.5 1.0
O A:HOH246 4.1 56.5 1.0
C A:ILE44 4.1 28.8 1.0
CA A:ARG45 4.1 29.8 1.0
CA A:ILE44 4.2 28.4 1.0
N A:GLU42 4.6 28.6 1.0
CG1 A:ILE44 4.6 30.1 1.0
N A:ILE44 4.7 27.8 1.0
CD1 A:ILE44 4.7 31.5 1.0
CG A:GLN41 4.7 37.7 1.0
CG A:ARG45 4.8 39.4 1.0
O A:ILE44 5.0 28.9 1.0

Sodium binding site 2 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 2 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:47.0
occ:1.00
 O A:HOH247 2.6 52.2 1.0
NH1 A:ARG10 3.1 37.6 1.0
O A:HOH244 3.8 60.8 1.0
CD A:ARG10 3.8 35.2 1.0
CZ A:ARG10 4.2 39.5 1.0
O A:HOH224 4.3 32.3 1.0
NE A:ARG10 4.4 37.7 1.0
CD A:ARG14 4.6 36.1 1.0
CB A:ARG10 4.7 29.5 1.0
NH1 A:ARG14 4.8 41.6 1.0
CG A:ARG10 4.9 32.9 1.0

Sodium binding site 3 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 3 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:54.5
occ:1.00
 NZ B:LYS51 3.4 39.9 1.0
CE B:LYS51 4.1 37.1 1.0
CD B:LYS51 4.7 31.6 1.0

Sodium binding site 4 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 4 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na102

b:45.8
occ:1.00
 O C:HOH247 2.4 45.8 1.0
O C:ILE68 2.4 53.8 1.0
C C:ILE68 3.6 53.7 1.0
CA C:LEU69 4.1 53.6 1.0
N C:LEU69 4.3 53.4 1.0
CB C:LEU69 4.6 53.6 1.0
CA C:ILE68 4.8 53.7 1.0
CG2 C:ILE68 4.8 54.9 1.0

Sodium binding site 5 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 5 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na103

b:49.9
occ:1.00
 O C:HOH202 2.2 36.4 1.0
O C:HOH211 3.1 50.0 1.0
CG C:GLU18 3.9 33.2 1.0
CB C:GLN21 4.2 28.8 1.0
CG C:GLN21 4.2 33.5 1.0
O C:GLU18 4.3 25.9 1.0
OE1 C:GLU18 4.4 40.5 1.0
CA C:GLU18 4.5 26.5 1.0
CB C:GLU18 4.6 28.3 1.0
CD C:GLU18 4.6 39.8 1.0
C C:GLU18 4.9 25.7 1.0

Sodium binding site 6 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 6 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:70.7
occ:1.00
 O D:HOH207 2.6 43.2 1.0
NZ D:LYS10 3.1 47.3 1.0
CE D:MET7 3.8 39.7 1.0
CB D:GLU6 3.9 34.5 1.0
O D:GLN3 4.0 35.3 1.0
N D:MET7 4.0 28.5 1.0
OE1 D:GLU6 4.1 57.1 1.0
C D:GLU6 4.3 28.9 1.0
CA D:MET7 4.4 29.1 1.0
CB D:MET7 4.5 31.4 1.0
CE D:LYS10 4.6 44.1 1.0
CA D:GLU6 4.7 29.6 1.0
SD D:MET7 4.8 42.3 1.0
C D:GLN3 4.9 34.7 1.0
CA D:GLN3 4.9 35.6 1.0
O D:GLU6 4.9 28.0 1.0
CG D:GLU6 5.0 43.9 1.0
CD D:GLU6 5.0 55.1 1.0

Sodium binding site 7 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 7 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na102

b:36.8
occ:1.00
 O D:HOH277 2.6 28.9 1.0
O D:HOH236 2.7 35.7 1.0
O D:LYS10 2.9 26.5 1.0
CG D:LYS10 3.6 33.7 1.0
N D:GLN14 3.7 22.3 1.0
C D:LYS10 3.7 25.1 1.0
CA D:LYS10 3.8 25.2 1.0
CG1 D:VAL13 3.8 24.1 1.0
CB D:VAL13 3.8 23.1 1.0
CB D:GLN14 3.9 24.6 1.0
OE1 D:GLN14 4.0 41.0 1.0
CA D:GLN14 4.2 22.8 1.0
CB D:LYS10 4.2 28.1 1.0
C D:VAL13 4.3 23.0 1.0
O D:HOH274 4.5 40.3 1.0
O D:HOH270 4.6 38.9 1.0
CA D:VAL13 4.6 22.4 1.0
CD D:GLN14 4.7 37.8 1.0
CD D:LYS10 4.9 39.0 1.0
CG D:GLN14 4.9 30.9 1.0
CG2 D:VAL13 4.9 23.9 1.0
O D:VAL9 5.0 24.1 1.0

Sodium binding site 8 out of 8 in 8sjj

Go back to Sodium Binding Sites List in 8sjj
Sodium binding site 8 out of 8 in the X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of X-Ray Structure of the Metastable SEPT14-SEPT7 Heterodimeric Coiled Coil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na103

b:42.3
occ:1.00
 O D:ILE61 2.6 20.2 1.0
C D:ILE61 3.7 20.7 1.0
CA D:LEU62 3.9 23.1 1.0
C D:GLN64 3.9 36.6 1.0
O D:LEU62 3.9 25.8 1.0
C D:LEU62 3.9 25.5 1.0
N D:GLN64 4.1 32.4 1.0
N D:LEU62 4.2 20.1 1.0
CA D:GLN64 4.3 35.0 1.0
O D:HOH203 4.4 45.8 1.0
CB D:GLN64 4.4 37.2 1.0
N D:GLU63 4.7 26.2 1.0
CG2 D:ILE61 4.7 21.9 1.0
CA D:ILE61 4.9 20.8 1.0
O D:GLN64 4.9 37.5 1.0

Reference:

I.A.Cavini, A.J.Winter, H.D'muniz Pereira, D.N.Woolfson, M.P.Crump, R.C.Garratt. X-Ray Structure of the Metastable SEPT14-SEPT7 Coiled Coil Reveals A Hendecad Region Crucial For Heterodimerization. Acta Crystallogr D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37712436
DOI: 10.1107/S2059798323006514
Page generated: Wed Oct 9 13:30:26 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