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Sodium in PDB 5y7d: Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1

Protein crystallography data

The structure of Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1, PDB code: 5y7d was solved by S.H.Park, M.J.Kim, J.S.Park, H.J.Kim, B.W.Han, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.93 / 1.71
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.765, 49.765, 175.709, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.7

Other elements in 5y7d:

The structure of Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1 also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1 (pdb code 5y7d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1, PDB code: 5y7d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5y7d

Go back to Sodium Binding Sites List in 5y7d
Sodium binding site 1 out of 5 in the Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1


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 Human Endothelial-Overexpressed Lps Associated Factor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:38.1
occ:1.00
 O2 A:GOL201 2.4 35.1 1.0
OE2 A:GLU24 2.4 29.5 1.0
O A:THR25 2.4 22.7 1.0
O A:HOH458 2.6 45.8 1.0
O3 A:GOL201 2.8 35.7 1.0
CD A:GLU24 3.0 30.4 1.0
OE1 A:GLU24 3.2 28.4 1.0
C2 A:GOL201 3.3 39.7 1.0
NH1 A:ARG26 3.3 29.7 1.0
NA A:NA204 3.4 22.4 1.0
O A:HOH306 3.4 36.4 1.0
C3 A:GOL201 3.5 34.9 1.0
C A:THR25 3.6 19.1 1.0
NA A:NA205 3.8 34.1 1.0
O A:HOH342 3.9 42.7 1.0
CG A:ARG26 3.9 22.7 1.0
N A:THR25 4.2 19.8 1.0
CZ A:ARG26 4.2 44.5 1.0
CG A:GLU24 4.3 21.8 1.0
N A:ARG26 4.5 19.8 1.0
CA A:THR25 4.5 20.6 1.0
CA A:ARG26 4.5 21.0 1.0
O A:HOH459 4.6 37.3 1.0
OG1 A:THR25 4.6 20.8 1.0
C1 A:GOL201 4.6 31.9 1.0
CB A:ARG26 4.7 21.8 1.0
CD A:ARG26 4.8 35.5 1.0
NE A:ARG26 4.9 38.4 1.0
CE2 A:PHE8 5.0 24.5 1.0
NH2 A:ARG26 5.0 42.6 1.0
NA A:NA206 5.0 28.8 1.0

Sodium binding site 2 out of 5 in 5y7d

Go back to Sodium Binding Sites List in 5y7d
Sodium binding site 2 out of 5 in the Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1


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 Human Endothelial-Overexpressed Lps Associated Factor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:22.4
occ:1.00
 O3 A:GOL201 2.9 35.7 1.0
NZ A:LYS21 2.9 22.9 1.0
OG1 A:THR25 3.0 20.8 1.0
O A:HOH306 3.3 36.4 1.0
NA A:NA203 3.4 38.1 1.0
OE1 A:GLU24 3.4 28.4 1.0
N A:THR25 3.5 19.8 1.0
O A:THR25 3.5 22.7 1.0
C3 A:GOL201 3.6 34.9 1.0
CE A:LYS21 3.6 20.6 1.0
CD2 A:LEU113 3.7 20.4 1.0
CB A:THR25 3.9 20.0 1.0
CA A:THR25 4.1 20.6 1.0
O2 A:GOL201 4.1 35.1 1.0
CD A:GLU24 4.2 30.4 1.0
C A:THR25 4.2 19.1 1.0
CG2 A:THR25 4.3 20.2 1.0
C A:GLU24 4.5 18.7 1.0
C2 A:GOL201 4.5 39.7 1.0
O A:ALA111 4.6 19.4 1.0
CB A:LEU113 4.6 19.0 1.0
OE2 A:GLU24 4.6 29.5 1.0
CA A:GLU24 4.6 18.7 1.0
CE1 A:TYR12 4.7 20.9 1.0
NZ A:LYS119 4.7 21.1 1.0
CD1 A:TYR12 4.7 19.5 1.0
CG A:LEU113 4.8 19.4 1.0
CD A:LYS21 4.9 18.5 1.0
O A:VAL23 4.9 20.4 1.0

Sodium binding site 3 out of 5 in 5y7d

Go back to Sodium Binding Sites List in 5y7d
Sodium binding site 3 out of 5 in the Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1


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 Human Endothelial-Overexpressed Lps Associated Factor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:34.1
occ:1.00
 O A:HOH458 2.8 45.8 1.0
NZ A:LYS119 2.8 21.1 1.0
O3 A:GOL201 3.0 35.7 1.0
NA A:NA206 3.5 28.8 1.0
O A:THR25 3.7 22.7 1.0
NA A:NA203 3.8 38.1 1.0
CE A:LYS119 3.8 20.4 1.0
CD1 A:TRP27 3.9 22.2 1.0
NE1 A:TRP27 4.0 23.2 1.0
C3 A:GOL201 4.1 34.9 1.0
CA A:ARG26 4.4 21.0 1.0
C2 A:GOL201 4.4 39.7 1.0
CH2 A:TRP48 4.4 30.4 1.0
C A:THR25 4.6 19.1 1.0
OG1 A:THR25 4.6 20.8 1.0
O2 A:GOL201 4.8 35.1 1.0
N A:ARG26 4.9 19.8 1.0
N A:TRP27 4.9 21.9 1.0
CZ3 A:TRP48 4.9 28.9 1.0
CD2 A:LEU113 5.0 20.4 1.0
CG A:TRP27 5.0 20.1 1.0
C A:ARG26 5.0 19.5 1.0

Sodium binding site 4 out of 5 in 5y7d

Go back to Sodium Binding Sites List in 5y7d
Sodium binding site 4 out of 5 in the Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1


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 Human Endothelial-Overexpressed Lps Associated Factor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:28.8
occ:1.00
 O A:HOH458 2.6 45.8 1.0
O A:HOH457 3.2 41.8 1.0
N A:TRP27 3.3 21.9 1.0
NA A:NA205 3.5 34.1 1.0
NA A:NA207 3.5 35.0 1.0
CD1 A:TRP27 3.8 22.2 1.0
CA A:ARG26 3.8 21.0 1.0
CB A:ARG26 3.9 21.8 1.0
C A:ARG26 4.0 19.5 1.0
CB A:TRP27 4.1 27.2 1.0
CG A:TRP27 4.3 20.1 1.0
CA A:TRP27 4.3 23.7 1.0
NH2 A:ARG26 4.3 42.6 1.0
CZ A:ARG26 4.4 44.5 1.0
NE A:ARG26 4.4 38.4 1.0
O A:HOH459 4.6 37.3 1.0
CG A:ARG26 4.6 22.7 1.0
NE1 A:TRP27 4.8 23.2 1.0
O A:THR25 4.9 22.7 1.0
N A:ARG28 5.0 26.0 1.0
NA A:NA203 5.0 38.1 1.0

Sodium binding site 5 out of 5 in 5y7d

Go back to Sodium Binding Sites List in 5y7d
Sodium binding site 5 out of 5 in the Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1


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 Human Endothelial-Overexpressed Lps Associated Factor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:35.0
occ:1.00
 NE A:ARG28 3.1 33.9 1.0
O A:HOH457 3.2 41.8 1.0
N A:ARG28 3.3 26.0 1.0
CB A:ARG28 3.3 27.6 1.0
NH2 A:ARG28 3.4 33.3 1.0
NA A:NA206 3.5 28.8 1.0
CZ A:ARG28 3.6 37.5 1.0
CD1 A:LEU30 3.6 34.0 1.0
NE A:ARG26 3.6 38.4 1.0
CG A:LEU30 3.7 38.4 1.0
CA A:ARG28 3.8 25.9 1.0
O A:ARG28 3.8 25.6 1.0
CB A:ARG26 3.8 21.8 1.0
N A:TRP27 3.9 21.9 1.0
CG A:ARG28 4.0 25.3 1.0
CD A:ARG28 4.1 27.8 1.0
C A:ARG28 4.1 33.6 1.0
C A:TRP27 4.2 27.4 1.0
CD A:ARG26 4.3 35.5 1.0
NH2 A:ARG26 4.4 42.6 1.0
CZ A:ARG26 4.4 44.5 1.0
O A:HOH346 4.5 41.6 1.0
CA A:TRP27 4.5 23.7 1.0
CD2 A:LEU30 4.6 40.3 1.0
CG A:ARG26 4.6 22.7 1.0
C A:ARG26 4.6 19.5 1.0
CA A:ARG26 4.7 21.0 1.0
CB A:LEU30 4.7 27.5 1.0
NH1 A:ARG28 4.8 46.4 1.0
CB A:TRP27 4.9 27.2 1.0

Reference:

S.H.Park, M.J.Kim, J.S.Park, H.J.Kim, B.W.Han. Crystal Structure of Human Endothelial-Overexpressed Lps Associated Factor 1 To Be Published.
Page generated: Tue Oct 8 01:21:19 2024

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