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Sodium in PDB 6ljh: Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+

Protein crystallography data

The structure of Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+, PDB code: 6ljh was solved by X.Feng, S.Fan, M.Li, S.Zou, G.Lv, G.Wu, Y.Jin, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.54 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.446, 54.153, 90.374, 90.00, 101.28, 90.00
R / Rfree (%) 15.2 / 18

Other elements in 6ljh:

The structure of Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+ also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+ (pdb code 6ljh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+, PDB code: 6ljh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6ljh

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Sodium binding site 1 out of 4 in the Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+


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 Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:32.3
occ:1.00
C6N A:NAD401 2.6 41.8 1.0
C5N A:NAD401 2.6 49.2 1.0
N A:HIS49 2.8 13.6 1.0
O A:HOH690 2.9 38.3 1.0
O1N A:NAD401 2.9 16.3 1.0
CB A:HIS49 3.1 17.5 1.0
O3 A:NAD401 3.3 16.5 1.0
PN A:NAD401 3.4 14.9 1.0
O5D A:NAD401 3.5 14.8 1.0
CB A:CYS48 3.5 15.3 1.0
CA A:HIS49 3.5 15.3 1.0
O A:HOH859 3.7 25.6 1.0
C A:CYS48 3.8 15.6 1.0
N1N A:NAD401 3.9 52.5 1.0
C4N A:NAD401 3.9 18.4 1.0
CA A:CYS48 3.9 15.9 1.0
O A:HOH648 4.0 16.8 1.0
O A:HOH549 4.0 15.4 1.0
C3D A:NAD401 4.0 17.2 1.0
SG A:CYS48 4.1 15.0 1.0
C2D A:NAD401 4.4 20.4 1.0
CG A:HIS49 4.5 29.2 1.0
PA A:NAD401 4.6 16.5 1.0
C5D A:NAD401 4.6 15.2 1.0
O2A A:NAD401 4.6 14.1 1.0
C A:HIS49 4.6 16.5 1.0
C1D A:NAD401 4.7 33.2 1.0
N A:THR50 4.7 16.6 1.0
C4D A:NAD401 4.7 16.7 1.0
C2N A:NAD401 4.8 62.9 1.0
C3N A:NAD401 4.8 48.4 1.0
O2N A:NAD401 4.9 14.0 1.0
O A:CYS48 4.9 18.0 1.0
O A:HOH845 4.9 40.7 1.0
O4D A:NAD401 5.0 22.8 1.0
O3D A:NAD401 5.0 20.4 1.0
O A:HOH592 5.0 41.2 1.0
O1A A:NAD401 5.0 16.6 1.0

Sodium binding site 2 out of 4 in 6ljh

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Sodium binding site 2 out of 4 in the Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+


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 Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:33.7
occ:1.00
C2N A:NAD401 2.7 62.9 1.0
O A:ILE297 2.8 15.0 1.0
O A:HOH869 2.8 32.6 1.0
N7N A:NAD401 3.0 47.8 1.0
C3N A:NAD401 3.5 48.4 1.0
N1N A:NAD401 3.5 52.5 1.0
C1D A:NAD401 3.6 33.2 1.0
C7N A:NAD401 3.7 48.3 1.0
N A:ALA299 3.8 14.9 1.0
O4D A:NAD401 3.8 22.8 1.0
O A:HOH715 3.9 15.9 1.0
CB A:ALA299 3.9 24.1 1.0
C A:ILE297 3.9 19.4 1.0
CA A:GLY298 4.0 15.5 1.0
C A:GLY298 4.0 18.8 1.0
N A:GLY298 4.4 18.0 1.0
O A:HOH729 4.4 19.1 1.0
CA A:ALA299 4.4 19.0 1.0
O7N A:NAD401 4.7 63.6 1.0
C4N A:NAD401 4.8 18.4 1.0
O A:GLY298 4.8 15.8 1.0
CG2 A:ILE297 4.8 10.7 1.0
C6N A:NAD401 4.8 41.8 1.0
O A:HOH508 4.9 32.8 1.0
O A:HOH711 5.0 17.2 1.0

Sodium binding site 3 out of 4 in 6ljh

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Sodium binding site 3 out of 4 in the Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+


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 Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:43.3
occ:1.00
OE1 A:GLU380 2.5 75.3 1.0
O A:HOH848 2.7 51.0 1.0
O A:MET42 2.9 16.0 1.0
CD A:GLU380 3.6 73.9 1.0
O A:HOH583 3.8 16.5 1.0
CA A:LEU43 3.8 16.2 1.0
CD2 A:LEU43 3.8 17.4 1.0
CE A:LYS41 3.8 42.2 1.0
O A:HOH519 3.9 31.4 1.0
C A:MET42 3.9 14.0 1.0
NZ A:LYS41 4.1 53.6 1.0
CB A:PHE378 4.1 17.6 1.0
OE2 A:GLU380 4.1 73.1 1.0
O A:LEU43 4.2 19.6 1.0
N A:LEU43 4.3 12.2 1.0
C A:LEU43 4.4 16.3 1.0
O A:HOH530 4.4 26.1 1.0
CG A:LYS41 4.6 21.4 1.0
CB A:LEU43 4.7 16.1 1.0
CG A:GLU380 4.7 55.8 1.0
O A:PHE378 4.7 23.3 1.0
CG A:LEU43 4.7 14.1 1.0
CD A:LYS41 4.8 26.9 1.0
C A:PHE378 4.9 18.4 1.0
O A:LEU379 4.9 31.0 1.0
CG A:PHE378 5.0 12.9 1.0

Sodium binding site 4 out of 4 in 6ljh

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Sodium binding site 4 out of 4 in the Crystal Structure of Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+


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 Alcohol Dehydrogenase 1 From Artemisia Annua in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:40.0
occ:1.00
O A:HOH568 2.8 30.3 1.0
OD1 A:ASP156 3.2 62.0 1.0
O A:SER36 3.4 23.4 1.0
O A:HOH813 3.4 37.3 1.0
O A:ALA35 3.4 22.2 1.0
CB A:SER36 3.5 29.8 1.0
CG A:ASP156 3.6 29.3 1.0
CG A:GLU37 3.7 17.8 1.0
C A:SER36 3.7 20.5 1.0
O A:HOH772 4.0 43.8 1.0
CB A:ASP156 4.1 19.9 1.0
CA A:SER36 4.2 17.9 1.0
OE2 A:GLU37 4.2 19.1 1.0
O A:HOH782 4.3 37.7 1.0
CA A:ASP156 4.3 18.0 1.0
CB A:ASN125 4.3 42.7 1.0
OD2 A:ASP156 4.3 22.3 1.0
N A:GLU37 4.4 16.3 1.0
C A:ALA35 4.5 21.5 1.0
CD A:GLU37 4.5 16.9 1.0
OG A:SER36 4.7 38.0 1.0
N A:SER36 4.8 17.7 1.0
CA A:GLU37 4.9 17.1 1.0
CB A:GLU37 4.9 15.9 1.0

Reference:

Z.Yang, X.Feng, S.Fan, M.Li, S.Zou, G.Lv, G.Wu, Y.Jin, Z.Yang. N/A N/A.
Page generated: Mon Jan 25 15:48:34 2021

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