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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

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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

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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

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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

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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

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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

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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

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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

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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: Thu Dec 28 11:45:36 2023

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