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Sodium in PDB 2wm2: Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride

Enzymatic activity of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride

All present enzymatic activity of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride:
1.13.11.48;

Protein crystallography data

The structure of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride, PDB code: 2wm2 was solved by R.A.Steiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.38 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.770, 167.000, 166.940, 90.00, 90.00, 90.00
R / Rfree (%) 21.094 / 24.569

Other elements in 2wm2:

The structure of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride also contains other interesting chemical elements:

Potassium (K) 4 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride (pdb code 2wm2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride, PDB code: 2wm2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 2wm2

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Sodium binding site 1 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


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 the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1280

b:16.0
occ:1.00
 O A:HIS164 2.8 33.8 1.0
NH2 A:ARG170 3.3 35.2 1.0
CD1 A:LEU161 3.6 30.7 1.0
CE1 C:HIS264 3.7 32.8 1.0
C A:HIS164 3.8 33.5 1.0
CB C:ALA244 3.8 32.8 1.0
CD A:ARG170 4.2 34.4 1.0
CB A:LEU161 4.3 31.0 1.0
O C:TYR243 4.3 32.2 1.0
CA A:ASP165 4.3 34.6 1.0
CZ A:ARG170 4.4 35.1 1.0
N A:ASP165 4.4 34.2 1.0
CG A:LEU161 4.5 31.1 1.0
N A:HIS164 4.5 33.1 1.0
ND1 C:HIS264 4.5 32.2 1.0
NE2 C:HIS264 4.6 33.2 1.0
CA C:ALA244 4.6 32.8 1.0
CG A:ARG170 4.6 34.1 1.0
NE A:ARG170 4.7 35.2 1.0
NH1 C:ARG216 4.8 34.2 1.0
CA A:HIS164 4.8 33.2 1.0
CD2 A:LEU161 4.9 31.1 1.0

Sodium binding site 2 out of 12 in 2wm2

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Sodium binding site 2 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


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 the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1279

b:27.5
occ:1.00
 O B:HOH2019 2.9 13.4 1.0
NE B:ARG121 3.8 41.2 1.0
CB B:PRO120 4.0 38.9 1.0
CG B:ARG121 4.3 38.9 1.0
O B:PRO120 4.3 39.2 1.0
NH2 B:ARG121 4.5 42.7 1.0
CD B:ARG121 4.6 39.9 1.0
CZ B:ARG121 4.7 42.6 1.0
CG B:PRO214 4.7 36.8 1.0
CD B:PRO214 4.7 37.1 1.0
C B:PRO120 4.8 38.9 1.0
CA B:PRO120 4.9 39.0 1.0
C B:GLY275 4.9 50.7 1.0
O B:GLY275 4.9 50.5 1.0
CG B:PRO120 5.0 38.9 1.0

Sodium binding site 3 out of 12 in 2wm2

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Sodium binding site 3 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


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 the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1280

b:24.4
occ:1.00
 OD2 B:ASP53 3.7 48.6 1.0
CD B:ARG266 3.8 39.6 1.0
CE2 B:PHE54 3.9 43.9 1.0
CB B:ASP53 4.0 45.5 1.0
CZ B:PHE54 4.0 43.6 1.0
CG B:ASP53 4.1 47.0 1.0
CG B:ARG266 4.4 38.2 1.0
NE B:ARG266 4.5 41.0 1.0
O B:HOH2009 4.6 16.4 1.0
CB B:ARG266 4.9 36.6 1.0
CD2 B:PHE54 5.0 44.2 1.0

Sodium binding site 4 out of 12 in 2wm2

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Sodium binding site 4 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


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 the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1281

b:21.0
occ:1.00
 O3 B:SRT1284 3.1 62.5 1.0
O11 B:SRT1284 3.3 62.7 1.0
CA B:GLY247 3.4 33.1 1.0
C1 B:SRT1284 3.8 62.6 1.0
N B:GLY247 3.9 33.3 1.0
C2 B:SRT1284 4.1 62.8 1.0
C3 B:SRT1284 4.1 62.5 1.0
O B:HOH2041 4.3 24.5 1.0
C B:LEU246 4.5 33.4 1.0
O1 B:SRT1284 4.7 62.0 1.0
C B:GLY247 4.7 33.1 1.0
O B:LYS245 4.7 34.1 1.0
C4 B:SRT1284 4.8 62.2 1.0
O B:LEU246 4.9 33.6 1.0
O B:GLY247 4.9 33.0 1.0

Sodium binding site 5 out of 12 in 2wm2

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Sodium binding site 5 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1278

b:19.9
occ:1.00
 OD1 C:ASP256 2.8 33.9 1.0
O C:THR250 2.8 30.9 1.0
OG C:SER220 2.8 33.3 1.0
OD2 C:ASP256 3.0 34.9 1.0
CB C:SER220 3.2 33.2 1.0
CG C:ASP256 3.3 34.2 1.0
CA C:PRO253 3.4 31.5 1.0
N C:PRO253 3.5 31.3 1.0
CD C:PRO253 3.7 31.2 1.0
C C:THR250 3.7 31.1 1.0
CB C:PRO253 3.8 31.5 1.0
N C:THR250 3.8 31.3 1.0
CA C:GLY248 3.8 32.5 1.0
C C:GLY248 3.8 32.2 1.0
C C:PHE252 3.9 31.2 1.0
CG2 C:VAL257 4.0 33.7 1.0
O C:GLY248 4.0 32.0 1.0
CG C:PRO253 4.1 31.6 1.0
N C:PRO249 4.2 32.1 1.0
O C:PHE252 4.2 31.1 1.0
CA C:THR250 4.3 31.0 1.0
N C:PHE252 4.3 31.3 1.0
OG1 C:THR250 4.4 30.4 1.0
CD C:PRO249 4.4 31.7 1.0
N C:GLY248 4.4 32.9 1.0
CA C:SER220 4.6 33.1 1.0
C C:PRO249 4.7 31.7 1.0
CA C:PHE252 4.7 31.0 1.0
CB C:ASP256 4.8 33.6 1.0
N C:HIS251 4.8 31.4 1.0
C C:PRO253 4.8 31.5 1.0
C C:HIS251 4.9 31.5 1.0
CB C:THR250 5.0 30.8 1.0

Sodium binding site 6 out of 12 in 2wm2

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Sodium binding site 6 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1279

b:19.4
occ:1.00
 O C:TYR180 2.8 40.1 1.0
O C:MET177 2.8 39.4 1.0
NE1 C:TRP185 3.3 37.1 1.0
O C:HOH2023 3.3 32.5 1.0
O C:ALA178 3.7 40.0 1.0
C C:TYR180 3.8 39.5 1.0
C C:MET177 3.9 39.3 1.0
CD1 C:TRP185 4.1 37.7 1.0
C C:ALA178 4.1 39.8 1.0
N C:TYR180 4.2 39.4 1.0
CA C:ALA178 4.2 39.5 1.0
CE2 C:TRP185 4.2 37.6 1.0
CB C:TYR180 4.2 38.9 1.0
CZ3 C:TRP149 4.3 40.7 1.0
CA C:TYR180 4.3 39.2 1.0
N C:ALA178 4.5 39.4 1.0
CH2 C:TRP149 4.6 40.9 1.0
CZ2 C:TRP185 4.6 37.3 1.0
CB C:MET177 4.9 39.2 1.0
N C:ASP179 5.0 39.9 1.0

Sodium binding site 7 out of 12 in 2wm2

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Sodium binding site 7 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1280

b:27.5
occ:1.00
 O C:GLU112 2.7 42.5 1.0
NH2 C:ARG213 3.5 38.7 1.0
C C:GLU112 3.6 42.2 1.0
CA C:GLY115 3.7 42.9 1.0
CA C:GLU112 3.8 41.9 1.0
OE2 C:GLU112 3.9 47.6 1.0
O C:LEU111 3.9 40.5 1.0
CD C:GLU112 4.1 45.4 1.0
N C:GLY115 4.2 43.0 1.0
CD C:PRO116 4.3 43.1 1.0
CB C:LYS211 4.3 41.7 1.0
OE1 C:GLU112 4.4 46.5 1.0
CG C:LYS211 4.4 43.1 1.0
N C:LYS211 4.6 41.8 1.0
CG C:GLU112 4.6 43.4 1.0
CB C:THR210 4.7 42.2 1.0
CZ C:ARG213 4.7 38.1 1.0
C C:LEU111 4.7 40.6 1.0
N C:GLU112 4.7 41.1 1.0
CB C:GLU112 4.8 42.1 1.0
N C:GLN113 4.8 42.6 1.0
C C:GLY115 4.8 43.0 1.0
N C:PRO116 4.9 43.2 1.0

Sodium binding site 8 out of 12 in 2wm2

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Sodium binding site 8 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1281

b:51.7
occ:1.00
 O C:GLY247 3.2 33.1 1.0
N C:PRO249 3.5 32.1 1.0
CA C:PRO249 3.7 31.8 1.0
C C:GLY248 3.7 32.2 1.0
CD C:PRO249 4.0 31.7 1.0
CB C:PRO249 4.1 31.9 1.0
O C:GLY248 4.2 32.0 1.0
CA C:GLY248 4.2 32.5 1.0
C C:GLY247 4.3 33.1 1.0
CG C:PRO249 4.6 31.5 1.0
CE1 C:HIS164 4.6 34.1 1.0
N C:GLY248 4.7 32.9 1.0
NE2 C:HIS164 4.9 34.4 1.0

Sodium binding site 9 out of 12 in 2wm2

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Sodium binding site 9 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1278

b:14.4
occ:1.00
 O D:MET177 2.5 39.4 1.0
O D:TYR180 2.7 40.1 1.0
NE1 D:TRP185 3.3 37.3 1.0
O D:ALA178 3.5 39.9 1.0
C D:MET177 3.6 39.4 1.0
C D:TYR180 3.7 39.6 1.0
C D:ALA178 3.9 39.8 1.0
N D:TYR180 3.9 39.4 1.0
CB D:TYR180 4.0 38.9 1.0
CA D:ALA178 4.1 39.6 1.0
CA D:TYR180 4.1 39.2 1.0
CD1 D:TRP185 4.2 37.9 1.0
CE2 D:TRP185 4.3 37.8 1.0
N D:ALA178 4.3 39.5 1.0
CZ3 D:TRP149 4.5 40.8 1.0
CZ2 D:TRP185 4.6 37.4 1.0
CB D:MET177 4.7 39.2 1.0
N D:ASP179 4.7 39.8 1.0
CA D:MET177 4.8 39.2 1.0
CH2 D:TRP149 4.8 40.9 1.0
C D:ASP179 4.9 39.8 1.0
N D:GLY181 4.9 39.8 1.0

Sodium binding site 10 out of 12 in 2wm2

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Sodium binding site 10 out of 12 in the Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Cofactor-Devoid 1-H-3-Hydroxy-4- Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter Nitroguajacolicus RU61A in Complex with Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1279

b:21.1
occ:1.00
 OG D:SER220 2.7 33.2 1.0
OD1 D:ASP256 2.7 33.9 1.0
O D:THR250 2.9 30.9 1.0
OD2 D:ASP256 2.9 34.9 1.0
CB D:SER220 3.2 33.2 1.0
CG D:ASP256 3.2 34.2 1.0
CA D:GLY248 3.5 32.5 1.0
C D:GLY248 3.5 32.2 1.0
CA D:PRO253 3.6 31.4 1.0
N D:PRO253 3.7 31.2 1.0
N D:THR250 3.8 31.4 1.0
O D:GLY248 3.8 32.1 1.0
C D:THR250 3.9 31.2 1.0
CB D:PRO253 3.9 31.4 1.0
CG2 D:VAL257 3.9 33.7 1.0
CD D:PRO253 3.9 31.2 1.0
N D:PRO249 3.9 32.0 1.0
C D:PHE252 4.1 31.2 1.0
N D:GLY248 4.2 32.8 1.0
CD D:PRO249 4.2 31.8 1.0
CG D:PRO253 4.3 31.6 1.0
CA D:THR250 4.3 31.0 1.0
O D:PHE252 4.4 31.0 1.0
OG1 D:THR250 4.5 30.4 1.0
N D:PHE252 4.5 31.3 1.0
C D:PRO249 4.6 31.7 1.0
CA D:SER220 4.6 33.1 1.0
CB D:ASP256 4.7 33.5 1.0
CA D:PRO249 4.8 31.7 1.0
C D:PRO253 5.0 31.6 1.0
N D:HIS251 5.0 31.5 1.0
CA D:PHE252 5.0 31.0 1.0

Reference:

R.A.Steiner, H.J.Janssen, P.Roversi, A.J.Oakley, S.Fetzner. Structural Basis For Cofactor-Independent Dioxygenation of N-Heteroaromatic Compounds at the {Alpha}/{Beta}-Hydrolase Fold. Proc.Natl.Acad.Sci.Usa V. 107 657 2010.
ISSN: ISSN 0027-8424
PubMed: 20080731
DOI: 10.1073/PNAS.0909033107
Page generated: Mon Oct 7 04:42:37 2024

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