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Sodium in PDB 1xlt: Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex

Enzymatic activity of Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex

All present enzymatic activity of Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex:
1.6.1.2;

Protein crystallography data

The structure of Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex, PDB code: 1xlt was solved by V.Sundaresan, J.Chartron, M.Yamaguchi, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.68 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.372, 171.082, 203.181, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 31

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex (pdb code 1xlt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex, PDB code: 1xlt:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1xlt

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Sodium binding site 1 out of 3 in the Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex


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 Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:50.7
occ:1.00
 O A:PRO171 2.0 39.7 1.0
O A:ALA159 2.7 41.0 1.0
OD2 B:ASP330 2.7 48.7 1.0
C A:PRO171 3.2 39.8 1.0
OD1 B:ASP330 3.3 51.0 1.0
CG B:ASP330 3.4 48.8 1.0
C A:ALA159 3.9 39.8 1.0
C A:PRO172 4.0 41.1 1.0
CG2 A:VAL170 4.0 39.1 1.0
CB A:ARG158 4.0 39.4 1.0
N A:PRO172 4.0 39.1 1.0
N A:ALA159 4.1 39.1 1.0
CA A:PRO172 4.1 40.0 1.0
CA A:PRO171 4.2 40.7 1.0
O A:PRO172 4.2 41.8 1.0
CD A:ARG158 4.2 40.3 1.0
CG A:PRO171 4.2 40.7 1.0
N A:PRO171 4.2 40.3 1.0
N A:ALA173 4.3 40.2 1.0
CD A:PRO171 4.3 40.1 1.0
CG A:ARG158 4.5 39.5 1.0
CA A:ALA159 4.6 38.9 1.0
NH1 A:ARG158 4.6 41.4 1.0
CB A:PRO171 4.8 40.5 1.0
C A:VAL170 4.8 39.4 1.0
O A:PRO161 4.8 40.4 1.0
O A:PHE160 4.8 39.2 1.0
CA A:ALA173 4.8 39.0 1.0
CB B:ASP330 4.9 45.6 1.0
N A:PHE160 5.0 39.4 1.0
CB A:ALA159 5.0 38.2 1.0
C A:ARG158 5.0 39.1 1.0

Sodium binding site 2 out of 3 in 1xlt

Go back to Sodium Binding Sites List in 1xlt
Sodium binding site 2 out of 3 in the Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex


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 Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:69.7
occ:1.00
 O D:PRO171 2.1 42.2 1.0
O D:ALA159 2.1 42.9 1.0
OD2 E:ASP330 2.7 57.4 1.0
C D:ALA159 3.3 44.7 1.0
C D:PRO171 3.3 42.3 1.0
CG2 D:VAL170 3.6 42.1 1.0
N D:ALA159 3.7 44.3 1.0
CG E:ASP330 3.7 55.9 1.0
OD1 E:ASP330 4.0 55.7 1.0
CA D:ALA159 4.0 43.8 1.0
CB D:ARG158 4.1 43.6 1.0
CG D:PRO171 4.2 42.5 1.0
C D:PRO172 4.2 42.5 1.0
N D:PRO171 4.2 43.4 1.0
N D:PRO172 4.2 42.1 1.0
CA D:PRO171 4.2 42.8 1.0
CA D:PRO172 4.3 42.2 1.0
N D:PHE160 4.3 45.9 1.0
N D:ALA173 4.4 42.1 1.0
O D:PHE160 4.4 46.5 1.0
CB D:ALA159 4.4 42.7 1.0
CD D:PRO171 4.4 43.3 1.0
NH1 D:ARG158 4.5 47.9 1.0
O D:PRO172 4.5 42.8 1.0
C D:ARG158 4.5 43.9 1.0
C D:VAL170 4.6 43.7 1.0
CG D:ARG158 4.6 44.7 1.0
C D:PHE160 4.6 46.3 1.0
CD D:ARG158 4.6 46.3 1.0
CA D:PHE160 4.7 47.1 1.0
O D:PRO161 4.7 47.7 1.0
CB D:PRO171 4.7 43.2 1.0
CA D:ARG158 4.8 43.5 1.0
CA D:ALA173 4.9 42.3 1.0
O D:VAL170 5.0 43.7 1.0

Sodium binding site 3 out of 3 in 1xlt

Go back to Sodium Binding Sites List in 1xlt
Sodium binding site 3 out of 3 in the Crystal Structure of Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex


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 Transhydrogenase [(Domain I)2:Domain III] Heterotrimer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na603

b:48.7
occ:1.00
 O G:ALA159 2.0 43.5 1.0
O G:PRO171 2.2 49.2 1.0
OD2 H:ASP330 2.4 56.2 1.0
C G:ALA159 3.2 43.2 1.0
CG H:ASP330 3.4 55.3 1.0
C G:PRO171 3.4 49.4 1.0
CD G:ARG158 3.7 50.5 1.0
OD1 H:ASP330 3.7 56.0 1.0
CG2 G:VAL170 3.7 49.7 1.0
N G:ALA159 3.8 43.6 1.0
CA G:ALA159 4.0 42.5 1.0
CG G:ARG158 4.0 49.1 1.0
CB G:ARG158 4.3 47.7 1.0
N G:PHE160 4.3 43.2 1.0
CG G:PRO171 4.3 50.8 1.0
N G:PRO172 4.3 47.9 1.0
C G:PRO172 4.3 47.5 1.0
CA G:PRO171 4.3 50.3 1.0
N G:PRO171 4.4 50.8 1.0
N G:ALA173 4.4 47.2 1.0
CA G:PRO172 4.4 47.3 1.0
O G:PHE160 4.4 46.2 1.0
CB G:ALA159 4.5 42.5 1.0
C G:ARG158 4.5 45.7 1.0
O G:PRO161 4.6 48.8 1.0
CD G:PRO171 4.6 50.8 1.0
C G:PHE160 4.6 45.3 1.0
CA G:PHE160 4.6 44.2 1.0
CB H:ASP330 4.7 52.7 1.0
O G:PRO172 4.7 48.1 1.0
C G:VAL170 4.7 51.1 1.0
CB G:PRO171 4.8 50.6 1.0
NE G:ARG158 4.9 51.1 1.0
CA G:ALA173 5.0 46.5 1.0
CE2 G:PHE156 5.0 45.1 1.0

Reference:

V.Sundaresan, J.Chartron, M.Yamaguchi, C.D.Stout. Conformational Diversity in Nad(H) and Transhydrogenase Nicotinamide Nucleotide Binding Domains J.Mol.Biol. V. 346 617 2005.
ISSN: ISSN 0022-2836
PubMed: 15670609
DOI: 10.1016/J.JMB.2004.11.070
Page generated: Tue Dec 15 05:41:45 2020

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