Atomistry » Sodium » PDB 1nnh-1oan » 1nzw
Atomistry »
  Sodium »
    PDB 1nnh-1oan »
      1nzw »

Sodium in PDB 1nzw: CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+

Enzymatic activity of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+

All present enzymatic activity of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+:
1.2.1.3;

Protein crystallography data

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+, PDB code: 1nzw was solved by S.J.Perez-Miller, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.65 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.361, 150.494, 176.923, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.2

Other elements in 1nzw:

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ (pdb code 1nzw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+, PDB code: 1nzw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 1 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1601

b:31.2
occ:1.00
 O A:GLN196 2.3 34.1 1.0
OD1 A:ASP109 2.4 31.8 1.0
O A:VAL40 2.4 39.0 1.0
O A:ASP109 2.7 30.2 1.0
OG1 A:THR39 3.4 36.5 1.0
CG A:ASP109 3.4 33.3 1.0
C A:GLN196 3.5 32.6 1.0
C A:VAL40 3.6 38.8 1.0
N A:VAL40 3.7 39.2 1.0
C A:ASP109 3.7 30.1 1.0
CA A:ASP109 4.1 30.2 1.0
CA A:VAL40 4.1 38.9 1.0
OD2 A:ASP109 4.2 34.7 1.0
CA A:GLN196 4.2 32.9 1.0
CB A:ASP109 4.4 31.8 1.0
CD A:PRO42 4.4 36.3 1.0
C A:THR39 4.4 39.2 1.0
N A:THR197 4.5 31.4 1.0
CG2 A:THR197 4.6 26.2 1.0
CB A:THR39 4.6 38.2 1.0
CB A:GLN196 4.7 31.7 1.0
CA A:THR197 4.7 29.9 1.0
N A:ASN41 4.7 38.4 1.0
CA A:THR39 4.7 38.1 1.0
O A:VAL345 4.8 35.1 1.0
CB A:VAL40 4.8 38.3 1.0
N A:ASN110 4.9 29.5 1.0

Sodium binding site 2 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 2 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1602

b:41.9
occ:1.00
 OD1 B:ASP109 2.2 30.5 1.0
O B:GLN196 2.2 24.8 1.0
O B:VAL40 2.5 34.8 1.0
O B:HOH2582 2.5 35.6 1.0
OG1 B:THR39 2.8 33.0 1.0
O B:ASP109 3.0 27.7 1.0
O B:HOH2571 3.1 26.7 1.0
C B:GLN196 3.4 27.7 1.0
CG B:ASP109 3.4 30.8 1.0
N B:VAL40 3.5 34.7 1.0
C B:VAL40 3.6 33.5 1.0
C B:ASP109 4.0 28.6 1.0
CA B:VAL40 4.0 33.8 1.0
C B:THR39 4.1 34.9 1.0
CB B:THR39 4.1 34.9 1.0
CA B:GLN196 4.2 28.5 1.0
CA B:ASP109 4.2 27.8 1.0
OD2 B:ASP109 4.2 30.8 1.0
CA B:THR39 4.3 34.6 1.0
CB B:ASP109 4.4 28.6 1.0
N B:THR197 4.4 28.4 1.0
CG2 B:THR197 4.6 32.1 1.0
CA B:THR197 4.6 30.0 1.0
N B:ASN41 4.7 31.8 1.0
CD B:PRO42 4.8 31.4 1.0
CB B:GLN196 4.8 25.6 1.0
CB B:VAL40 4.8 33.0 1.0
O B:THR39 4.9 32.5 1.0
CD1 B:ILE48 5.0 30.9 1.0
CG2 B:THR39 5.0 34.7 1.0

Sodium binding site 3 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 3 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1603

b:27.4
occ:1.00
 O C:HOH3549 2.1 26.0 1.0
O C:VAL40 2.3 24.8 1.0
O C:GLN196 2.4 22.5 1.0
OD1 C:ASP109 2.4 16.2 1.0
O C:ASP109 2.8 17.9 1.0
OG1 C:THR39 3.4 26.4 1.0
C C:VAL40 3.4 24.6 1.0
O C:HOH3561 3.5 40.8 1.0
N C:VAL40 3.5 23.9 1.0
C C:GLN196 3.5 22.3 1.0
CG C:ASP109 3.6 15.9 1.0
C C:ASP109 3.9 16.7 1.0
CA C:VAL40 3.9 24.7 1.0
CA C:ASP109 4.2 17.3 1.0
CA C:GLN196 4.3 21.7 1.0
CD C:PRO42 4.3 21.6 1.0
C C:THR39 4.3 23.8 1.0
OD2 C:ASP109 4.5 12.4 1.0
CB C:ASP109 4.5 17.1 1.0
N C:ASN41 4.5 24.1 1.0
CB C:THR39 4.6 24.3 1.0
N C:THR197 4.6 22.7 1.0
CG2 C:THR197 4.7 22.0 1.0
CA C:THR39 4.7 23.7 1.0
CB C:VAL40 4.7 25.9 1.0
CB C:GLN196 4.7 22.1 1.0
O C:VAL345 4.7 22.8 1.0
CA C:THR197 4.8 21.3 1.0
CD1 C:ILE48 4.9 24.9 1.0
CA C:ASN41 5.0 22.0 1.0

Sodium binding site 4 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 4 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1604

b:41.6
occ:1.00
 O D:VAL40 2.3 33.6 1.0
OD1 D:ASP109 2.4 34.4 1.0
O D:GLN196 2.4 33.3 1.0
O D:ASP109 2.5 29.8 1.0
OG1 D:THR39 3.3 32.7 1.0
C D:VAL40 3.5 34.1 1.0
C D:ASP109 3.6 30.9 1.0
CG D:ASP109 3.6 35.0 1.0
C D:GLN196 3.6 31.4 1.0
N D:VAL40 3.7 34.1 1.0
CA D:ASP109 4.0 30.6 1.0
CA D:VAL40 4.1 34.7 1.0
CD D:PRO42 4.3 35.6 1.0
CG2 D:THR197 4.3 30.8 1.0
CB D:ASP109 4.4 32.0 1.0
CA D:GLN196 4.4 30.8 1.0
C D:THR39 4.5 33.3 1.0
OD2 D:ASP109 4.5 35.3 1.0
CD1 D:ILE48 4.6 34.8 1.0
N D:ASN41 4.6 33.6 1.0
N D:THR197 4.6 30.4 1.0
CB D:THR39 4.6 32.6 1.0
O D:VAL345 4.7 35.7 1.0
CA D:THR197 4.7 30.4 1.0
N D:ASN110 4.8 30.8 1.0
CB D:GLN196 4.8 31.6 1.0
CA D:THR39 4.8 33.5 1.0
CB D:VAL40 4.9 34.7 1.0
CA D:ASN41 4.9 34.8 1.0

Sodium binding site 5 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 5 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1605

b:40.3
occ:1.00
 O E:GLN196 2.3 32.2 1.0
O E:ASP109 2.4 30.0 1.0
OD1 E:ASP109 2.4 30.1 1.0
O E:VAL40 2.7 34.7 1.0
C E:GLN196 3.4 32.4 1.0
OG1 E:THR39 3.5 29.9 1.0
C E:ASP109 3.5 32.0 1.0
CG E:ASP109 3.5 30.1 1.0
C E:VAL40 3.8 33.8 1.0
CA E:ASP109 4.0 32.2 1.0
N E:VAL40 4.1 33.2 1.0
CG2 E:THR197 4.2 34.9 1.0
CA E:GLN196 4.2 32.2 1.0
CD E:PRO42 4.3 36.2 1.0
CB E:ASP109 4.3 31.7 1.0
OD2 E:ASP109 4.4 32.1 1.0
N E:THR197 4.4 32.5 1.0
O E:VAL345 4.5 32.7 1.0
CA E:VAL40 4.5 33.6 1.0
CA E:THR197 4.6 32.3 1.0
CB E:GLN196 4.6 31.2 1.0
N E:ASN110 4.6 32.1 1.0
CB E:THR39 4.8 33.9 1.0
C E:THR39 4.8 33.9 1.0
CG2 E:VAL345 4.9 28.4 1.0
N E:ASN41 4.9 33.8 1.0

Sodium binding site 6 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 6 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1606

b:27.6
occ:1.00
 O F:GLN196 2.3 22.8 1.0
O F:VAL40 2.4 25.6 1.0
OD1 F:ASP109 2.5 23.9 1.0
O F:ASP109 2.7 21.9 1.0
OG1 F:THR39 3.4 24.1 1.0
C F:GLN196 3.5 21.1 1.0
C F:VAL40 3.5 25.9 1.0
CG F:ASP109 3.7 22.7 1.0
C F:ASP109 3.7 21.3 1.0
N F:VAL40 3.8 25.5 1.0
CA F:VAL40 4.1 25.3 1.0
CA F:ASP109 4.2 20.3 1.0
CA F:GLN196 4.2 19.7 1.0
CD F:PRO42 4.3 22.8 1.0
CG2 F:THR197 4.5 16.6 1.0
O F:VAL345 4.5 28.1 1.0
CB F:ASP109 4.5 21.5 1.0
C F:THR39 4.5 24.0 1.0
N F:THR197 4.5 20.9 1.0
CB F:GLN196 4.5 21.8 1.0
OD2 F:ASP109 4.5 20.8 1.0
O F:HOH6593 4.6 31.6 1.0
N F:ASN41 4.7 26.2 1.0
CB F:THR39 4.7 22.6 1.0
CA F:THR197 4.8 18.4 1.0
CA F:THR39 4.8 22.6 1.0
CB F:VAL40 4.9 23.9 1.0
N F:ASN110 4.9 19.8 1.0

Sodium binding site 7 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 7 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1607

b:34.9
occ:1.00
 O G:VAL40 2.3 30.9 1.0
OD1 G:ASP109 2.4 23.2 1.0
O G:GLN196 2.4 29.5 1.0
O G:ASP109 2.5 25.5 1.0
OG1 G:THR39 3.3 35.0 1.0
C G:VAL40 3.4 31.9 1.0
CG G:ASP109 3.5 22.9 1.0
C G:ASP109 3.6 26.5 1.0
C G:GLN196 3.6 30.5 1.0
N G:VAL40 3.7 33.7 1.0
CA G:ASP109 3.9 25.6 1.0
CA G:VAL40 4.1 32.4 1.0
CD G:PRO42 4.2 28.5 1.0
CB G:ASP109 4.3 24.1 1.0
OD2 G:ASP109 4.4 22.2 1.0
C G:THR39 4.4 33.9 1.0
CG2 G:THR197 4.4 29.5 1.0
CA G:GLN196 4.5 29.8 1.0
N G:ASN41 4.5 29.9 1.0
CB G:THR39 4.6 34.2 1.0
CD1 G:ILE48 4.6 34.3 1.0
N G:THR197 4.6 30.9 1.0
CA G:THR197 4.7 30.1 1.0
CA G:THR39 4.8 33.7 1.0
N G:ASN110 4.8 28.5 1.0
CB G:VAL40 4.8 32.0 1.0
O G:VAL345 4.8 30.3 1.0
CA G:ASN41 4.9 30.2 1.0
CB G:GLN196 4.9 29.0 1.0

Sodium binding site 8 out of 8 in 1nzw

Go back to Sodium Binding Sites List in 1nzw
Sodium binding site 8 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1608

b:34.5
occ:1.00
 O H:GLN196 2.3 36.4 1.0
OD1 H:ASP109 2.4 35.1 1.0
O H:VAL40 2.5 41.4 1.0
O H:ASP109 2.6 29.3 1.0
O H:HOH8543 3.1 28.2 1.0
C H:GLN196 3.5 34.1 1.0
OG1 H:THR39 3.5 38.4 1.0
CG H:ASP109 3.6 34.6 1.0
C H:VAL40 3.6 39.4 1.0
C H:ASP109 3.7 30.8 1.0
N H:VAL40 3.9 38.4 1.0
CA H:ASP109 4.1 31.6 1.0
CA H:GLN196 4.2 32.8 1.0
CA H:VAL40 4.3 38.8 1.0
CD H:PRO42 4.3 38.8 1.0
CB H:ASP109 4.5 32.8 1.0
O H:VAL345 4.5 37.2 1.0
CG2 H:THR197 4.5 31.8 1.0
OD2 H:ASP109 4.5 35.1 1.0
N H:THR197 4.5 34.3 1.0
CB H:GLN196 4.6 29.8 1.0
C H:THR39 4.6 38.1 1.0
CA H:THR197 4.7 33.3 1.0
N H:ASN41 4.8 38.4 1.0
CB H:THR39 4.8 37.9 1.0
N H:ASN110 4.8 30.6 1.0
CA H:THR39 4.9 37.8 1.0
CG2 H:VAL345 4.9 34.4 1.0
CB H:VAL40 4.9 38.7 1.0

Reference:

S.J.Perez-Miller, T.D.Hurley. Coenzyme Isomerization Is Integral to Catalysis in Aldehyde Dehydrogenase Biochemistry V. 42 7100 2003.
ISSN: ISSN 0006-2960
PubMed: 12795606
DOI: 10.1021/BI034182W
Page generated: Tue Dec 15 05:31:45 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy