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Sodium in PDB 6qap: Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group

Enzymatic activity of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group

All present enzymatic activity of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group:
1.2.1.19; 1.2.1.3; 1.2.1.47;

Protein crystallography data

The structure of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group, PDB code: 6qap was solved by S.Morera, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.74 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.290, 160.030, 84.600, 90.00, 91.09, 90.00
R / Rfree (%) 22 / 25.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group (pdb code 6qap). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group, PDB code: 6qap:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6qap

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Sodium binding site 1 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:74.2
occ:1.00
 O C:HOH677 2.9 53.0 1.0
O C:HOH678 3.5 56.1 1.0
CB C:ALA155 4.1 39.3 1.0
O C:HOH693 4.3 72.8 1.0
O C:HOH694 4.4 59.3 1.0
OD1 C:ASN157 4.7 52.6 1.0
ND2 C:ASN157 4.7 50.2 1.0
CG C:ASN157 4.9 60.4 1.0

Sodium binding site 2 out of 8 in 6qap

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Sodium binding site 2 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:71.9
occ:1.00
 NE2 C:GLN10 3.2 69.8 1.0
OE1 C:GLN10 3.2 75.8 1.0
OE2 C:GLU194 3.4 68.4 1.0
CD C:GLN10 3.7 78.2 1.0
OE1 C:GLU194 3.9 65.7 1.0
CD C:GLU194 4.0 75.6 1.0
O C:HOH614 4.4 65.3 1.0
NE C:ARG19 4.6 53.3 1.0
NH1 C:ARG19 4.8 56.2 1.0
CZ C:ARG19 4.9 57.5 1.0

Sodium binding site 3 out of 8 in 6qap

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Sodium binding site 3 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:60.5
occ:1.00
 N C:SER9 3.1 54.8 1.0
OG C:SER9 3.3 68.8 1.0
OE1 C:GLN10 3.5 75.8 1.0
CA C:VAL8 3.8 49.9 1.0
N C:GLN10 3.8 52.7 1.0
C C:VAL8 3.9 56.8 1.0
CA C:SER9 4.0 55.3 1.0
CE1 C:PHE6 4.2 52.0 1.0
CB C:SER9 4.2 58.4 1.0
CG C:GLN10 4.2 60.5 1.0
C C:SER9 4.2 58.5 1.0
CB C:GLN10 4.3 53.3 1.0
CD C:GLN10 4.3 78.2 1.0
CZ C:PHE6 4.3 49.8 1.0
O C:VAL7 4.3 56.8 1.0
CG1 C:VAL8 4.4 50.5 1.0
CB C:VAL8 4.6 51.3 1.0
NH2 C:ARG19 4.7 40.6 1.0
CA C:GLN10 4.7 52.4 1.0
N C:VAL8 4.8 50.4 1.0
CG2 C:VAL8 4.9 50.1 1.0

Sodium binding site 4 out of 8 in 6qap

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Sodium binding site 4 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:47.5
occ:1.00
 O2 D:EDO507 2.5 53.6 1.0
OD1 D:ASN207 2.7 51.9 1.0
N D:GLY17 2.9 42.4 1.0
N D:GLY204 3.0 38.2 1.0
N D:GLY16 3.2 44.8 1.0
C1 D:EDO507 3.3 51.9 1.0
C2 D:EDO507 3.3 51.7 1.0
CE1 D:TYR14 3.4 44.5 1.0
CA D:GLY204 3.5 36.6 1.0
O D:PHE206 3.5 40.0 1.0
CD1 D:TYR14 3.5 42.1 1.0
C D:ARG15 3.7 46.1 1.0
CA D:GLY17 3.8 42.7 1.0
CA D:GLY16 3.8 45.2 1.0
C D:GLY16 3.9 48.3 1.0
CA D:ARG15 3.9 40.0 1.0
CG D:ASN207 3.9 58.0 1.0
C D:GLY204 4.0 39.2 1.0
C D:PRO203 4.1 46.5 1.0
C D:PHE206 4.2 40.4 1.0
N D:ARG15 4.3 39.5 1.0
OD1 D:ASN57 4.3 37.0 1.0
N D:LEU205 4.4 38.3 1.0
CA D:PRO203 4.4 45.1 1.0
O D:ARG15 4.5 46.2 1.0
O D:HOH603 4.5 35.1 1.0
N D:PHE206 4.6 37.8 1.0
CA D:ASN207 4.6 38.9 1.0
O D:GLY204 4.6 38.2 1.0
N D:ASN207 4.6 37.8 1.0
CZ D:TYR14 4.7 51.4 1.0
O D:TYR14 4.7 38.5 1.0
C D:TYR14 4.7 40.3 1.0
O1 D:EDO507 4.7 48.2 1.0
ND2 D:ASN207 4.8 39.6 1.0
CG D:TYR14 4.8 40.7 1.0
C D:GLY17 4.8 46.3 1.0
CB D:ASN207 4.9 43.6 1.0
N D:ALA18 4.9 43.9 1.0

Sodium binding site 5 out of 8 in 6qap

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Sodium binding site 5 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:65.3
occ:1.00
 OE1 D:GLU118 3.2 50.2 1.0
CB D:GLU118 3.4 41.4 1.0
C2 D:EDO506 3.5 46.9 1.0
O D:GLN115 3.7 45.9 1.0
SG A:CYS74 3.9 44.5 1.0
CD D:GLU118 4.1 63.0 1.0
O D:HOH650 4.1 43.6 1.0
O2 D:EDO506 4.2 46.9 1.0
N D:TYR119 4.2 36.8 1.0
CG D:GLU118 4.3 45.4 1.0
CB A:ALA125 4.3 47.3 1.0
C D:GLU118 4.5 42.4 1.0
CA D:GLU118 4.5 38.6 1.0
CA D:GLN115 4.5 41.1 1.0
SD A:MET71 4.5 71.1 1.0
C D:GLN115 4.5 44.7 1.0
O A:HOH629 4.6 44.2 1.0
C1 D:EDO506 4.7 48.5 1.0
CG D:GLN115 4.9 50.4 1.0
CA D:TYR119 4.9 35.7 1.0
CD1 A:LEU78 4.9 53.4 1.0

Sodium binding site 6 out of 8 in 6qap

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Sodium binding site 6 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:48.4
occ:1.00
 O D:ALA155 2.8 43.9 1.0
N D:SER182 3.0 35.2 1.0
OG1 D:THR185 3.4 36.7 1.0
N D:ALA155 3.6 35.6 1.0
CA D:PRO181 3.6 30.4 1.0
C D:ALA155 3.6 42.6 1.0
CB D:PRO181 3.7 31.4 1.0
CB D:SER182 3.8 37.1 1.0
CA D:GLY154 3.8 34.7 1.0
C D:PRO181 3.8 38.0 1.0
C D:GLY154 3.8 36.7 1.0
O D:THR185 3.9 41.6 1.0
CA D:PRO159 3.9 39.6 1.0
CA D:SER182 4.0 34.4 1.0
CB D:PRO159 4.1 40.8 1.0
O D:HOH621 4.2 34.8 1.0
CA D:ALA155 4.2 36.3 1.0
O D:PRO159 4.4 36.0 1.0
N D:TRP156 4.5 39.2 1.0
O D:SER182 4.6 37.0 1.0
CB D:THR185 4.6 35.1 1.0
CE2 D:PHE179 4.6 35.9 1.0
CZ D:PHE179 4.6 34.0 1.0
O D:GLY154 4.6 36.1 1.0
C D:PRO159 4.6 39.7 1.0
CG D:PRO159 4.7 46.6 1.0
CA D:TRP156 4.7 39.4 1.0
C D:THR185 4.8 42.4 1.0
C D:SER182 4.8 36.6 1.0
N D:PRO159 5.0 41.5 1.0
N D:PRO181 5.0 31.2 1.0

Sodium binding site 7 out of 8 in 6qap

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Sodium binding site 7 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na504

b:56.0
occ:1.00
 N D:SER9 3.1 50.7 1.0
OE1 D:GLN10 3.4 78.3 1.0
OG D:SER9 3.5 64.6 1.0
N D:GLN10 3.7 52.4 1.0
CA D:VAL8 3.8 45.5 1.0
C D:VAL8 3.9 52.5 1.0
CA D:SER9 4.0 51.8 1.0
CB D:GLN10 4.1 52.6 1.0
CG D:GLN10 4.1 62.6 1.0
CD D:GLN10 4.2 81.2 1.0
C D:SER9 4.2 57.5 1.0
CG1 D:VAL8 4.3 46.7 1.0
CE1 D:PHE6 4.3 52.6 1.0
CZ D:PHE6 4.3 51.4 1.0
CB D:SER9 4.3 55.0 1.0
NH2 D:ARG19 4.4 45.4 1.0
O D:VAL7 4.4 54.7 1.0
CB D:VAL8 4.5 47.2 1.0
CA D:GLN10 4.5 51.9 1.0
CG2 D:VAL8 4.8 45.5 1.0
N D:VAL8 4.9 46.0 1.0
CZ D:ARG19 5.0 63.1 1.0

Sodium binding site 8 out of 8 in 6qap

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Sodium binding site 8 out of 8 in the Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Human Aldehyde Dehydrogenase 9A1 in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na505

b:72.2
occ:1.00
 OE1 D:GLN10 3.5 78.3 1.0
OE2 D:GLU194 3.6 67.7 1.0
NE2 D:GLN10 3.7 71.3 1.0
OE1 D:GLU194 3.8 64.1 1.0
CD D:GLU194 4.0 76.2 1.0
CD D:GLN10 4.0 81.2 1.0
O D:HOH633 4.3 63.3 1.0
NE D:ARG19 4.8 55.6 1.0
NH1 D:ARG19 4.9 57.0 1.0

Reference:

R.Koncitikova, A.Vigouroux, M.Kopecna, M.Sebela, S.Morera, D.Kopecny. Kinetic and Structural Analysis of Human ALDH9A1. Biosci.Rep. V. 39 2019.
ISSN: ISSN 0144-8463
PubMed: 30914451
DOI: 10.1042/BSR20190558
Page generated: Tue Dec 15 12:48:11 2020

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