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Chlorine in PDB 3kbo: 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp

Enzymatic activity of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp

All present enzymatic activity of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp:
1.1.1.79; 1.1.1.81;

Protein crystallography data

The structure of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp, PDB code: 3kbo was solved by G.Minasov, Z.Wawrzak, T.Skarina, O.Onopriyenko, L.Papazisi, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 2.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 279.621, 45.585, 112.335, 90.00, 101.58, 90.00
R / Rfree (%) 21.1 / 26.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp (pdb code 3kbo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp, PDB code: 3kbo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3kbo

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Chlorine binding site 1 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl315

b:52.5
occ:1.00
 NH2 A:ARG227 3.1 30.5 1.0
C5N A:NDP313 3.3 17.0 1.0
N A:GLY66 3.4 30.2 1.0
C6N A:NDP313 3.5 21.4 1.0
CH2 A:TRP45 3.6 35.3 1.0
C4N A:NDP313 3.6 14.1 1.0
N A:ALA65 3.8 29.6 1.0
NH1 A:ARG227 3.9 33.9 1.0
CZ A:ARG227 3.9 33.3 1.0
N1N A:NDP313 4.0 17.6 1.0
C3N A:NDP313 4.1 12.0 1.0
CA A:GLY66 4.1 32.6 1.0
C2N A:NDP313 4.2 17.5 1.0
CZ2 A:TRP45 4.3 36.5 1.0
C2D A:NDP313 4.3 17.7 1.0
CB A:ALA65 4.4 29.2 1.0
C A:ALA65 4.4 29.1 1.0
CA A:ALA65 4.4 29.8 1.0
CZ3 A:TRP45 4.6 39.1 1.0
C A:GLY64 4.7 29.6 1.0
CA A:GLY64 4.7 28.7 1.0
C1D A:NDP313 4.8 16.5 1.0
O A:GLY66 4.8 35.7 1.0
O A:HOH539 4.9 37.4 1.0

Chlorine binding site 2 out of 8 in 3kbo

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Chlorine binding site 2 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl316

b:62.1
occ:1.00
 O A:HOH369 2.9 28.7 1.0
N A:ASN11 3.7 32.1 1.0
NE1 A:TRP15 3.8 27.9 1.0
CB A:PHE10 3.9 35.2 1.0
CD1 A:PHE10 4.0 41.4 1.0
CG A:PHE10 4.1 37.0 1.0
CA A:PHE10 4.1 32.9 1.0
CB A:ASN11 4.4 33.5 1.0
CD1 A:TRP15 4.4 32.5 1.0
C A:PHE10 4.4 32.1 1.0
CA A:ASN11 4.6 32.3 1.0
CE1 A:PHE10 4.8 38.0 1.0
CG A:PRO282 4.8 27.6 1.0
CD2 A:PHE10 4.9 39.3 1.0
CE2 A:TRP15 4.9 26.2 1.0
O A:ASN11 5.0 30.5 1.0

Chlorine binding site 3 out of 8 in 3kbo

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Chlorine binding site 3 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl315

b:55.0
occ:1.00
 O B:HOH375 2.8 32.8 1.0
C5N B:NDP313 3.3 20.3 1.0
N B:GLY66 3.5 31.4 1.0
C6N B:NDP313 3.5 25.9 1.0
NH2 B:ARG227 3.6 31.7 1.0
CH2 B:TRP45 3.7 45.6 1.0
C4N B:NDP313 3.7 26.0 1.0
N B:ALA65 3.7 30.4 1.0
N1N B:NDP313 4.0 27.1 1.0
C3N B:NDP313 4.2 27.5 1.0
CA B:GLY66 4.2 31.9 1.0
NH1 B:ARG227 4.2 35.7 1.0
C2N B:NDP313 4.3 26.5 1.0
CZ3 B:TRP45 4.3 45.8 1.0
CA B:ALA65 4.4 30.5 1.0
CB B:ALA65 4.4 28.7 1.0
C B:ALA65 4.4 30.5 1.0
CZ B:ARG227 4.4 34.0 1.0
CZ2 B:TRP45 4.5 45.5 1.0
CA B:GLY64 4.5 32.0 1.0
C B:GLY64 4.6 31.1 1.0
C2D B:NDP313 4.6 27.6 1.0
C1D B:NDP313 4.8 27.7 1.0
SE B:MSE95 4.9 29.1 1.0
O B:GLY66 4.9 32.8 1.0

Chlorine binding site 4 out of 8 in 3kbo

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Chlorine binding site 4 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl316

b:61.3
occ:1.00
 O B:HOH542 2.8 45.5 1.0
N B:ASN11 3.4 40.0 1.0
NE1 B:TRP15 3.6 36.6 1.0
CB B:PHE10 3.7 42.2 1.0
CD1 B:PHE10 3.7 44.0 1.0
CG B:PHE10 3.8 43.6 1.0
CA B:PHE10 3.8 41.6 1.0
C B:PHE10 4.1 41.0 1.0
CD1 B:TRP15 4.1 35.0 1.0
CB B:ASN11 4.3 41.6 1.0
CA B:ASN11 4.4 39.9 1.0
CE1 B:PHE10 4.5 44.7 1.0
CD2 B:PHE10 4.6 43.4 1.0
CE2 B:TRP15 4.8 36.5 1.0
CG B:PRO282 4.9 28.4 1.0
O B:ASN11 4.9 36.0 1.0

Chlorine binding site 5 out of 8 in 3kbo

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Chlorine binding site 5 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl314

b:44.8
occ:1.00
 O C:HOH379 3.0 31.1 1.0
N C:ARG56 3.3 27.4 1.0
CA C:ARG55 3.7 27.0 1.0
C C:ARG55 4.1 27.4 1.0
CG C:ARG55 4.1 28.1 1.0
CB C:ARG55 4.1 26.3 1.0
CB C:ARG56 4.2 30.6 1.0
CA C:ARG56 4.3 30.3 1.0
O C:ARG56 4.3 28.7 1.0
NH1 C:ARG55 4.3 25.2 1.0
CG C:ARG56 4.6 37.7 1.0
O C:GLY54 4.6 26.5 1.0
C C:ARG56 4.6 29.1 1.0
CA C:PRO38 4.8 29.6 1.0
N C:ARG55 4.9 26.9 1.0
O C:HOH383 4.9 22.2 1.0
CD C:ARG55 5.0 23.9 1.0

Chlorine binding site 6 out of 8 in 3kbo

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Chlorine binding site 6 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl315

b:63.5
occ:1.00
 O C:HOH323 2.6 43.0 1.0
NE1 C:TRP15 3.3 22.1 1.0
N C:ASN11 3.5 28.6 1.0
CD1 C:TRP15 4.0 29.3 1.0
CG C:PHE10 4.1 35.7 1.0
CA C:PHE10 4.1 31.8 1.0
CB C:PHE10 4.1 32.6 1.0
CB C:ASN11 4.2 30.6 1.0
C C:PHE10 4.3 29.8 1.0
CD1 C:PHE10 4.3 37.9 1.0
CA C:ASN11 4.4 29.3 1.0
CE2 C:TRP15 4.4 25.5 1.0
CG C:PRO282 4.5 28.2 1.0
CD2 C:PHE10 4.6 37.3 1.0
O C:ASN11 4.8 27.9 1.0
CZ2 C:TRP15 4.9 26.2 1.0
CE1 C:PHE10 5.0 39.1 1.0

Chlorine binding site 7 out of 8 in 3kbo

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Chlorine binding site 7 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl315

b:56.0
occ:1.00
 O D:HOH379 2.8 31.6 1.0
N D:GLY66 3.0 28.6 1.0
N D:ALA65 3.2 30.5 1.0
C5N D:NDP313 3.6 30.0 1.0
NH2 D:ARG227 3.7 53.0 1.0
C6N D:NDP313 3.7 25.8 1.0
CB D:ALA65 3.8 27.8 1.0
CA D:ALA65 3.8 28.3 1.0
C D:ALA65 3.9 28.6 1.0
CA D:GLY66 3.9 31.7 1.0
CH2 D:TRP45 4.0 51.7 1.0
C4N D:NDP313 4.0 25.3 1.0
C D:GLY64 4.1 33.0 1.0
CA D:GLY64 4.2 33.9 1.0
NH1 D:ARG227 4.2 52.1 1.0
N1N D:NDP313 4.2 29.5 1.0
CZ D:ARG227 4.4 48.9 1.0
C3N D:NDP313 4.5 30.0 1.0
CZ3 D:TRP45 4.5 51.0 1.0
C2N D:NDP313 4.6 30.2 1.0
C2D D:NDP313 4.6 28.6 1.0
O D:GLY66 4.7 35.8 1.0
C D:GLY66 4.8 34.0 1.0
CZ2 D:TRP45 4.8 50.6 1.0
SE D:MSE95 4.9 30.7 1.0
C1D D:NDP313 5.0 24.9 1.0

Chlorine binding site 8 out of 8 in 3kbo

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Chlorine binding site 8 out of 8 in the 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl316

b:62.5
occ:1.00
 CD1 D:PHE10 3.3 54.9 1.0
N D:ASN11 3.5 48.4 1.0
NE1 D:TRP15 3.6 36.4 1.0
CB D:PHE10 3.6 51.1 1.0
CG D:PHE10 3.6 52.4 1.0
CA D:PHE10 3.8 51.2 1.0
CE1 D:PHE10 4.1 57.5 1.0
C D:PHE10 4.2 50.1 1.0
CD1 D:TRP15 4.2 35.0 1.0
CB D:ASN11 4.4 48.9 1.0
CA D:ASN11 4.5 47.7 1.0
CD2 D:PHE10 4.6 56.1 1.0
CE2 D:TRP15 4.7 37.7 1.0
O D:ASN11 4.9 45.0 1.0
CZ D:PHE10 5.0 57.9 1.0
CG D:PRO282 5.0 26.3 1.0

Reference:

G.Minasov, Z.Wawrzak, T.Skarina, O.Onopriyenko, L.Papazisi, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (Ycdw) From Salmonella Typhimurium in Complex with Nadp. To Be Published.
Page generated: Sat Dec 12 09:50:49 2020

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