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Sodium in PDB 9dk4: Ancestral Hydroxynitrile Lyase with Fifteen Substitutions

Protein crystallography data

The structure of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions, PDB code: 9dk4 was solved by S.C.Sarak, P.Tan, R.L.Evans Iii, K.Shi, R.J.Kazlauskas, H.Aihara, C.T.Pierce, M.E.Walsh, L.R.Greenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.41 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.244, 80.385, 92.823, 90, 90.62, 90
R / Rfree (%) 18.6 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions (pdb code 9dk4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions, PDB code: 9dk4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 9dk4

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Sodium binding site 1 out of 7 in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:28.4
occ:1.00
 O B:MET171 2.6 13.3 1.0
OD2 A:ASP37 2.7 13.5 1.0
O A:HOH457 2.9 26.2 1.0
O A:HOH445 3.1 12.6 1.0
CG A:ASP37 3.3 16.3 1.0
C B:MET171 3.5 15.0 1.0
OD1 A:ASP37 3.6 12.9 1.0
CA B:MET171 3.8 12.7 1.0
CG1 A:ILE43 3.8 16.0 1.0
CB A:ALA16 3.8 11.4 1.0
CB B:MET171 4.1 13.7 1.0
CD1 A:ILE43 4.2 15.7 1.0
CB A:ASP37 4.5 14.3 1.0
CG B:MET171 4.6 12.4 1.0
N B:LEU172 4.7 11.5 1.0
N A:ILE43 4.8 11.6 1.0
CD2 B:LEU172 5.0 13.3 1.0

Sodium binding site 2 out of 7 in 9dk4

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Sodium binding site 2 out of 7 in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:31.8
occ:1.00
 OE1 B:GLU167 2.4 16.8 1.0
O A:HOH461 2.8 24.7 1.0
O B:ILE163 3.3 12.0 1.0
CD B:GLU167 3.4 20.8 1.0
CB B:GLU167 3.5 14.0 1.0
CD2 B:TYR166 3.5 17.8 1.0
CG1 B:ILE163 3.6 18.5 1.0
CA B:GLU167 3.6 12.7 1.0
N B:GLU167 3.6 11.3 1.0
O A:HOH402 3.9 25.7 1.0
CG B:GLU167 4.0 15.6 1.0
CE B:LYS170 4.1 18.7 1.0
CE2 B:TYR166 4.1 17.5 1.0
CB A:PRO24 4.2 18.7 1.0
CD1 B:ILE163 4.3 23.2 1.0
C B:ILE163 4.3 14.4 1.0
C B:TYR166 4.3 12.9 1.0
OE2 B:GLU167 4.4 22.4 1.0
CG B:TYR166 4.4 14.6 1.0
NZ B:LYS170 4.5 21.4 1.0
CB B:TYR166 4.6 13.0 1.0
CG A:PRO24 4.7 16.3 1.0
CB B:ILE163 4.8 18.4 1.0
OE1 A:GLU27 4.8 20.6 1.0
CA B:ILE163 4.9 13.2 1.0
O B:TYR166 4.9 10.9 1.0

Sodium binding site 3 out of 7 in 9dk4

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Sodium binding site 3 out of 7 in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:27.7
occ:1.00
 OE2 B:GLU206 2.5 21.8 1.0
CD B:GLU206 3.3 21.3 1.0
O B:HOH413 3.4 19.1 1.0
OE1 B:GLU206 3.5 16.9 1.0
CA B:GLY232 4.0 13.4 1.0
O B:GLY232 4.6 13.4 1.0
ND2 B:ASN160 4.7 12.5 1.0
CG B:GLU206 4.7 19.8 1.0
C B:GLY232 4.9 14.9 1.0

Sodium binding site 4 out of 7 in 9dk4

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Sodium binding site 4 out of 7 in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:33.4
occ:1.00
 OG1 C:THR110 2.5 16.9 1.0
OH C:TYR222 3.2 20.6 1.0
O C:HOH458 3.2 39.0 1.0
CG2 C:THR110 3.3 21.6 1.0
CB C:THR110 3.5 18.9 1.0
CB C:GLU191 3.8 27.2 1.0
CE1 C:TYR222 3.8 23.4 1.0
CZ C:TYR222 3.9 25.2 1.0
CA C:GLU191 4.0 24.8 1.0
CA C:GLY195 4.1 20.6 1.0
N C:GLU191 4.6 21.1 1.0
CA C:THR110 4.7 22.1 1.0
O C:HOH439 4.7 19.8 1.0
N C:THR110 4.8 16.8 1.0
N C:GLY195 4.9 21.1 1.0

Sodium binding site 5 out of 7 in 9dk4

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Sodium binding site 5 out of 7 in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:28.3
occ:0.73
 OD1 C:ASN221 2.5 18.4 1.0
OH C:TYR116 2.9 21.1 1.0
CG C:ASN221 3.6 21.6 1.0
CZ2 C:TRP217 3.8 21.7 1.0
CZ C:TYR116 3.9 19.4 1.0
CE2 C:TYR116 3.9 18.3 1.0
CE1 C:HIS112 4.2 24.9 1.0
CB C:ASN221 4.3 18.9 1.0
NE1 C:TRP217 4.4 31.9 1.0
CE2 C:TRP217 4.4 23.9 1.0
ND2 C:ASN221 4.6 17.3 1.0
NE2 C:HIS112 4.7 20.1 1.0
CH2 C:TRP217 4.8 23.8 1.0
CA C:ASN221 4.8 15.6 1.0

Sodium binding site 6 out of 7 in 9dk4

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Sodium binding site 6 out of 7 in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:26.6
occ:1.00
 O D:HOH435 2.6 16.1 1.0
OD1 D:ASP109 2.8 20.3 1.0
O D:SER113 2.8 19.5 1.0
N D:ASP109 3.1 16.7 1.0
CG D:ASP109 3.5 23.9 1.0
O D:HIS112 3.6 20.7 1.0
C D:SER113 3.7 19.1 1.0
CB D:TYR116 3.7 21.5 1.0
O D:ASP109 3.7 16.1 1.0
CB D:PRO108 3.8 16.6 1.0
O D:HOH442 3.9 21.9 1.0
CA D:PRO108 3.9 15.7 1.0
CA D:ASP109 3.9 20.0 1.0
C D:HIS112 3.9 23.5 1.0
C D:PRO108 4.0 18.0 1.0
CA D:PRO114 4.0 18.0 1.0
C D:ASP109 4.0 22.8 1.0
CB D:HIS112 4.1 22.8 1.0
OD2 D:ASP109 4.1 25.4 1.0
N D:PRO114 4.2 21.4 1.0
CB D:ASP109 4.2 20.1 1.0
C D:PRO114 4.3 22.9 1.0
O D:PRO114 4.3 20.8 1.0
N D:TYR116 4.4 16.0 1.0
CA D:HIS112 4.4 25.5 1.0
N D:SER113 4.5 20.4 1.0
N D:HIS112 4.5 22.5 1.0
CG D:TYR116 4.6 23.2 1.0
CD2 D:TYR116 4.6 19.8 1.0
CA D:TYR116 4.6 17.8 1.0
CA D:SER113 4.8 22.2 1.0
N D:VAL117 4.8 16.4 1.0
CG1 D:VAL117 5.0 14.9 1.0

Sodium binding site 7 out of 7 in 9dk4

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Sodium binding site 7 out of 7 in the Ancestral Hydroxynitrile Lyase with Fifteen Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ancestral Hydroxynitrile Lyase with Fifteen Substitutions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:29.0
occ:1.00
 OE2 D:GLU206 2.4 21.1 1.0
O A:HOH424 2.8 21.5 1.0
O A:SER240 2.9 15.8 1.0
O D:HOH440 3.2 19.9 1.0
O D:HOH431 3.3 19.4 1.0
CD D:GLU206 3.3 21.3 1.0
OE1 D:GLU206 3.6 19.3 1.0
C A:SER240 3.7 15.7 1.0
CA A:LYS241 3.9 14.0 1.0
CA D:GLY232 3.9 15.3 1.0
N A:LYS241 4.1 15.3 1.0
N A:THR242 4.1 12.2 1.0
C A:LYS241 4.4 14.5 1.0
O D:GLY232 4.6 13.8 1.0
CD A:LYS241 4.6 23.3 1.0
CG D:GLU206 4.7 18.0 1.0
ND2 D:ASN160 4.7 14.6 1.0
NZ A:LYS241 4.8 20.4 1.0
C D:GLY232 4.8 15.0 1.0
CA A:SER240 4.9 13.7 1.0
N D:GLY232 5.0 15.2 1.0

Reference:

P.Tan, S.Sarak. To Be Published To Be Published.
Page generated: Thu Oct 31 23:05:58 2024

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