Sodium in PDB 8dq2: X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7

Protein crystallography data

The structure of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7, PDB code: 8dq2 was solved by J.J.Jung, C.-Y.Lin, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.11 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.107, 108.658, 44.697, 90, 90.02, 90
R / Rfree (%) 19 / 20.9

Other elements in 8dq2:

The structure of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 also contains other interesting chemical elements:

Lanthanum (La) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 (pdb code 8dq2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7, PDB code: 8dq2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8dq2

Go back to Sodium Binding Sites List in 8dq2
Sodium binding site 1 out of 4 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:28.0
occ:1.00
O A:LYS113 2.3 35.1 1.0
OD1 A:ASN109 2.3 39.0 1.0
OD1 A:ASP107 2.4 20.3 1.0
OD1 A:ASP111 2.5 23.7 1.0
OE2 A:GLU118 2.5 33.3 1.0
OE1 A:GLU118 2.5 29.8 1.0
O A:HOH322 2.7 28.9 1.0
CD A:GLU118 2.9 30.8 1.0
CG A:ASP111 3.3 25.4 1.0
CG A:ASN109 3.4 37.1 1.0
C A:LYS113 3.5 31.9 1.0
CG A:ASP107 3.6 19.9 1.0
OD2 A:ASP111 3.6 25.9 1.0
ND2 A:ASN109 3.9 39.4 1.0
CA A:ASP107 4.1 18.1 1.0
O A:HOH349 4.2 36.9 1.0
N A:LYS113 4.2 24.8 1.0
N A:ALA108 4.3 29.9 1.0
OD2 A:ASP107 4.4 20.9 1.0
N A:ASN109 4.4 33.4 1.0
N A:ASP111 4.4 24.6 1.0
CG A:GLU118 4.4 25.2 1.0
CA A:LYS113 4.4 25.0 1.0
CB A:ASP107 4.4 18.3 1.0
C A:ASP107 4.4 19.8 1.0
N A:LEU114 4.5 17.9 1.0
N A:LYS110 4.6 42.4 1.0
CA A:LEU114 4.6 17.3 1.0
CB A:ASP111 4.6 25.8 1.0
CD2 A:LEU114 4.7 15.1 1.0
CB A:ASN109 4.7 36.7 1.0
CB A:LYS113 4.8 24.6 1.0
N A:GLY112 4.9 32.4 1.0
CA A:ASN109 4.9 36.5 1.0
CA A:ASP111 4.9 25.1 1.0

Sodium binding site 2 out of 4 in 8dq2

Go back to Sodium Binding Sites List in 8dq2
Sodium binding site 2 out of 4 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:28.0
occ:1.00
OD1 B:ASP111 2.4 30.7 1.0
O B:LYS113 2.4 32.5 1.0
OE1 B:GLU118 2.5 29.6 1.0
OD1 B:ASP107 2.5 21.7 1.0
OE2 B:GLU118 2.6 32.3 1.0
CD B:GLU118 2.9 29.8 1.0
O B:HOH315 3.0 22.1 1.0
CG B:ASP111 3.4 32.0 1.0
CB B:ASN109 3.6 46.0 1.0
N B:ASN109 3.6 43.0 1.0
CG B:ASP107 3.6 21.3 1.0
C B:LYS113 3.7 29.9 1.0
OD2 B:ASP111 3.8 32.8 1.0
CA B:ASN109 4.0 46.5 1.0
CA B:ASP107 4.1 18.9 1.0
N B:ALA108 4.1 23.1 1.0
N B:LYS110 4.1 41.2 1.0
C B:ASP107 4.2 21.6 1.0
N B:ASP111 4.2 28.1 1.0
N B:LYS113 4.3 24.4 1.0
C B:ASN109 4.4 46.3 1.0
CG B:GLU118 4.4 27.4 1.0
CB B:ASP107 4.4 17.4 1.0
CG B:ASN109 4.5 54.6 1.0
OD2 B:ASP107 4.5 22.1 1.0
CA B:LYS113 4.5 24.5 1.0
CB B:ASP111 4.6 28.9 1.0
N B:LEU114 4.6 18.7 1.0
C B:ALA108 4.7 26.5 1.0
CA B:LEU114 4.7 17.0 1.0
CD2 B:LEU114 4.8 15.0 1.0
OD1 B:ASN109 4.9 57.0 1.0
N B:GLY112 4.9 30.7 1.0
CA B:ASP111 4.9 28.4 1.0
CA B:ALA108 4.9 24.0 1.0
CB B:LYS113 4.9 26.3 1.0
O B:ASP107 4.9 21.8 1.0

Sodium binding site 3 out of 4 in 8dq2

Go back to Sodium Binding Sites List in 8dq2
Sodium binding site 3 out of 4 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na204

b:28.0
occ:1.00
O C:LYS113 2.3 27.9 1.0
OD1 C:ASN109 2.4 49.5 1.0
OD1 C:ASP111 2.4 33.4 1.0
OD1 C:ASP107 2.4 32.5 1.0
OE2 C:GLU118 2.4 27.8 1.0
O C:HOH325 2.6 21.3 1.0
OE1 C:GLU118 2.7 30.1 1.0
CD C:GLU118 2.9 28.5 1.0
CG C:ASP111 3.3 33.9 1.0
CG C:ASN109 3.5 45.9 1.0
CG C:ASP107 3.5 33.0 1.0
C C:LYS113 3.5 21.4 1.0
OD2 C:ASP111 3.6 34.2 1.0
ND2 C:ASN109 4.0 43.7 1.0
N C:LYS113 4.2 29.4 1.0
CA C:ASP107 4.2 29.1 1.0
N C:ASP111 4.3 34.4 1.0
OD2 C:ASP107 4.3 34.1 1.0
N C:ALA108 4.3 28.7 1.0
CA C:LYS113 4.4 22.6 1.0
N C:ASN109 4.4 45.2 1.0
CG C:GLU118 4.4 26.0 1.0
CB C:ASP107 4.4 31.9 1.0
N C:LEU114 4.5 22.6 1.0
C C:ASP107 4.5 31.4 1.0
N C:LYS110 4.5 44.4 1.0
CB C:ASP111 4.5 32.9 1.0
CA C:LEU114 4.6 22.8 1.0
CD2 C:LEU114 4.7 18.8 1.0
CB C:ASN109 4.8 45.9 1.0
CB C:LYS113 4.8 25.1 1.0
CA C:ASP111 4.8 32.5 1.0
N C:GLY112 4.9 30.2 1.0
CA C:ASN109 4.9 47.3 1.0
C C:ASN109 5.0 45.5 1.0

Sodium binding site 4 out of 4 in 8dq2

Go back to Sodium Binding Sites List in 8dq2
Sodium binding site 4 out of 4 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na205

b:28.0
occ:1.00
O D:LYS113 2.3 34.1 1.0
OD1 D:ASN109 2.3 37.8 1.0
OD1 D:ASP111 2.4 34.3 1.0
OD1 D:ASP107 2.4 30.9 1.0
OE2 D:GLU118 2.4 29.6 1.0
OE1 D:GLU118 2.7 27.7 1.0
CD D:GLU118 2.9 27.2 1.0
O D:HOH317 2.9 32.7 1.0
CG D:ASP111 3.4 33.2 1.0
CG D:ASN109 3.4 38.9 1.0
C D:LYS113 3.5 28.1 1.0
CG D:ASP107 3.5 29.9 1.0
OD2 D:ASP111 3.8 35.6 1.0
ND2 D:ASN109 4.0 42.8 1.0
CA D:ASP107 4.1 30.0 1.0
N D:LYS113 4.1 33.2 1.0
N D:ALA108 4.1 30.0 1.0
N D:ASN109 4.2 33.8 1.0
N D:ASP111 4.2 36.3 1.0
C D:ASP107 4.3 31.1 1.0
OD2 D:ASP107 4.3 32.5 1.0
CA D:LYS113 4.3 29.9 1.0
CB D:ASP107 4.4 30.6 1.0
CG D:GLU118 4.4 25.1 1.0
N D:LYS110 4.4 43.3 1.0
N D:LEU114 4.5 27.1 1.0
CB D:ASP111 4.6 34.3 1.0
CA D:LEU114 4.6 25.7 1.0
CB D:ASN109 4.7 35.7 1.0
CD2 D:LEU114 4.7 29.3 1.0
CA D:ASN109 4.8 34.4 1.0
CB D:LYS113 4.8 30.9 1.0
N D:GLY112 4.8 31.5 1.0
CA D:ASP111 4.8 34.5 1.0
C D:ASN109 4.8 34.7 1.0

Reference:

J.A.Mattocks, J.J.Jung, C.Y.Lin, Z.Dong, N.H.Yennawar, E.R.Featherston, C.S.Kang-Yun, T.A.Hamilton, D.M.Park, A.K.Boal, J.A.Cotruvo. Enhanced Rare-Earth Separation with A Metal-Sensitive Lanmodulin Dimer Nature V. 618 87 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-05945-5
Page generated: Wed Oct 9 11:32:12 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy