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Tungsten in PDB 1xdy: Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor

Protein crystallography data

The structure of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor, PDB code: 1xdy was solved by L.Loschi, S.J.Brokx, T.L.Hills, G.Zhang, M.G.Bertero, A.L.Lovering, J.H.Weiner, N.C.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.96 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.842, 177.513, 104.214, 90.00, 109.73, 90.00
R / Rfree (%) 22.6 / 25.8

Tungsten Binding Sites:

The binding sites of Tungsten atom in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor (pdb code 1xdy). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 10 binding sites of Tungsten where determined in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor, PDB code: 1xdy:
Jump to Tungsten binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tungsten binding site 1 out of 10 in 1xdy

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Tungsten binding site 1 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W401

b:28.9
occ:1.00
 S2' A:MTE301 2.3 25.9 1.0
S1' A:MTE301 2.5 20.2 1.0
SG A:CYS102 2.5 23.2 1.0
C1' A:MTE301 3.2 18.6 1.0
C2' A:MTE301 3.3 19.7 1.0
CB A:CYS102 3.5 13.9 1.0
N A:VAL103 3.7 31.0 1.0
ND2 A:ASN45 3.8 39.1 1.0
CA A:CYS102 3.8 27.1 1.0
N A:PHE203 3.9 21.9 1.0
CG1 A:VAL103 4.2 30.0 1.0
C A:CYS102 4.2 36.4 1.0
C A:GLY202 4.3 14.3 1.0
CA A:GLY202 4.3 24.7 1.0
CA A:PHE203 4.6 21.8 1.0
CB A:PHE203 4.6 26.0 1.0
CG A:ASN45 4.7 44.5 1.0
C6 A:MTE301 4.7 26.7 1.0
N A:GLY202 4.7 24.5 1.0
CB A:VAL103 4.7 32.1 1.0
CA A:VAL103 4.8 32.5 1.0
C3' A:MTE301 4.8 28.2 1.0
CG A:GLU104 4.9 36.1 1.0
N A:GLU104 4.9 33.6 1.0
CB A:ASN45 4.9 36.7 1.0
CD A:GLU104 5.0 38.9 1.0

Tungsten binding site 2 out of 10 in 1xdy

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Tungsten binding site 2 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:W402

b:43.8
occ:1.00
 S2' B:MTE302 2.3 37.0 1.0
S1' B:MTE302 2.4 37.5 1.0
SG B:CYS102 2.5 48.1 1.0
C1' B:MTE302 3.3 44.1 1.0
C2' B:MTE302 3.4 43.9 1.0
CB B:CYS102 3.5 45.0 1.0
N B:VAL103 3.7 38.7 1.0
CA B:CYS102 3.9 44.9 1.0
N B:PHE203 3.9 38.2 1.0
ND2 B:ASN45 4.0 71.9 1.0
CG1 B:VAL103 4.0 43.6 1.0
C B:CYS102 4.3 44.8 1.0
C B:GLY202 4.4 28.5 1.0
CA B:GLY202 4.4 33.6 1.0
CB B:PHE203 4.6 33.9 1.0
CA B:PHE203 4.6 40.5 1.0
CG B:ASN45 4.6 68.8 1.0
C6 B:MTE302 4.7 32.1 1.0
CB B:VAL103 4.7 41.9 1.0
N B:GLY202 4.8 35.1 1.0
CA B:VAL103 4.8 33.8 1.0
N B:GLU104 4.8 42.6 1.0
O B:HOH411 4.9 43.1 1.0
CB B:ASN45 4.9 64.7 1.0
C3' B:MTE302 4.9 44.7 1.0
CG B:GLU104 5.0 59.2 1.0

Tungsten binding site 3 out of 10 in 1xdy

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Tungsten binding site 3 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:W403

b:32.3
occ:1.00
 S2' C:MTE303 2.4 30.9 1.0
S1' C:MTE303 2.4 28.9 1.0
SG C:CYS102 2.4 25.0 1.0
C1' C:MTE303 3.2 15.5 1.0
C2' C:MTE303 3.4 36.3 1.0
CB C:CYS102 3.4 8.0 1.0
N C:VAL103 3.8 29.4 1.0
CA C:CYS102 3.8 22.2 1.0
ND2 C:ASN45 3.8 46.6 1.0
N C:PHE203 4.0 35.2 1.0
CG1 C:VAL103 4.0 24.0 1.0
C C:CYS102 4.3 30.4 1.0
C C:GLY202 4.3 31.6 1.0
CA C:GLY202 4.4 28.2 1.0
CB C:PHE203 4.6 28.9 1.0
CA C:PHE203 4.6 32.4 1.0
C6 C:MTE303 4.6 39.0 1.0
CG C:ASN45 4.7 38.0 1.0
N C:GLY202 4.7 22.5 1.0
CB C:VAL103 4.7 31.0 1.0
CA C:VAL103 4.8 32.7 1.0
O C:HOH433 4.8 46.6 1.0
CD C:GLU104 4.9 50.9 1.0
C3' C:MTE303 4.9 24.9 1.0
CD2 C:PHE203 4.9 30.8 1.0
CB C:ASN45 4.9 35.4 1.0
N C:GLU104 4.9 26.8 1.0
CG C:GLU104 4.9 36.5 1.0
OE1 C:GLU104 5.0 49.6 1.0

Tungsten binding site 4 out of 10 in 1xdy

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Tungsten binding site 4 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:W404

b:32.7
occ:1.00
 S1' D:MTE304 2.3 27.1 1.0
S2' D:MTE304 2.4 28.7 1.0
SG D:CYS102 2.5 29.2 1.0
C1' D:MTE304 3.2 28.8 1.0
ND2 D:ASN45 3.4 43.5 1.0
C2' D:MTE304 3.4 30.7 1.0
CB D:CYS102 3.4 18.7 1.0
N D:VAL103 3.8 26.9 1.0
CA D:CYS102 3.8 20.2 1.0
N D:PHE203 4.0 32.6 1.0
CG1 D:VAL103 4.0 32.8 1.0
C D:CYS102 4.3 25.9 1.0
C D:GLY202 4.4 25.5 1.0
CG D:ASN45 4.4 39.1 1.0
CA D:GLY202 4.5 26.8 1.0
CB D:PHE203 4.6 33.4 1.0
CA D:PHE203 4.6 30.8 1.0
C6 D:MTE304 4.6 38.3 1.0
N D:GLY202 4.7 30.7 1.0
CG D:GLU104 4.8 46.1 1.0
CB D:VAL103 4.8 32.5 1.0
CB D:ASN45 4.8 33.3 1.0
CA D:VAL103 4.8 36.7 1.0
N D:GLU104 4.9 30.1 1.0
C3' D:MTE304 4.9 37.5 1.0
CD D:GLU104 4.9 48.0 1.0

Tungsten binding site 5 out of 10 in 1xdy

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Tungsten binding site 5 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 5 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W405

b:32.6
occ:1.00
 S1' E:MTE305 2.1 18.6 1.0
S2' E:MTE305 2.5 21.2 1.0
SG E:CYS102 2.5 34.3 1.0
C1' E:MTE305 3.0 33.7 1.0
C2' E:MTE305 3.3 8.4 1.0
CB E:CYS102 3.5 43.3 1.0
N E:VAL103 3.7 33.1 1.0
ND2 E:ASN45 3.8 50.0 1.0
CA E:CYS102 3.9 35.2 1.0
N E:PHE203 4.0 23.4 1.0
CG1 E:VAL103 4.2 40.8 1.0
C E:CYS102 4.3 29.0 1.0
C E:GLY202 4.4 28.2 1.0
CA E:GLY202 4.4 26.1 1.0
CB E:PHE203 4.5 30.2 1.0
C6 E:MTE305 4.5 23.9 1.0
CA E:PHE203 4.5 13.7 1.0
CB E:VAL103 4.7 34.6 1.0
N E:GLY202 4.7 31.2 1.0
CA E:VAL103 4.7 38.0 1.0
CG E:ASN45 4.7 44.3 1.0
C3' E:MTE305 4.8 27.9 1.0
CD E:GLU104 4.9 51.7 1.0
N E:GLU104 4.9 38.4 1.0
OE1 E:GLU104 4.9 49.6 1.0
CG E:GLU104 4.9 41.5 1.0
CB E:ASN45 5.0 41.9 1.0

Tungsten binding site 6 out of 10 in 1xdy

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Tungsten binding site 6 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 6 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:W406

b:41.5
occ:1.00
 S1' F:MTE306 2.2 36.7 1.0
S2' F:MTE306 2.4 38.8 1.0
SG F:CYS102 2.5 35.6 1.0
C1' F:MTE306 3.1 39.3 1.0
ND2 F:ASN45 3.3 48.9 1.0
C2' F:MTE306 3.3 33.6 1.0
CB F:CYS102 3.5 41.7 0.0
N F:VAL103 3.8 41.2 1.0
N F:PHE203 3.9 41.4 1.0
CG1 F:VAL103 3.9 54.2 1.0
CA F:CYS102 3.9 46.7 1.0
C F:CYS102 4.3 39.2 1.0
C F:GLY202 4.4 38.0 1.0
CB F:PHE203 4.4 44.5 1.0
CA F:PHE203 4.5 34.1 1.0
CG F:ASN45 4.5 55.4 1.0
C6 F:MTE306 4.5 35.6 1.0
CA F:GLY202 4.5 32.7 1.0
N F:GLU104 4.8 41.1 1.0
N F:GLY202 4.8 39.6 1.0
CB F:VAL103 4.8 46.3 1.0
CA F:VAL103 4.9 42.1 1.0
CB F:ASN45 4.9 45.6 1.0
CG F:GLU104 4.9 43.9 1.0
C3' F:MTE306 4.9 39.1 1.0
CD F:GLU104 5.0 58.8 1.0

Tungsten binding site 7 out of 10 in 1xdy

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Tungsten binding site 7 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 7 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:W407

b:29.7
occ:1.00
 S1' G:MTE307 2.4 26.1 1.0
S2' G:MTE307 2.4 22.9 1.0
SG G:CYS102 2.5 28.6 1.0
O G:HOH426 2.5 28.9 1.0
C1' G:MTE307 3.2 19.0 1.0
C2' G:MTE307 3.4 17.6 1.0
CB G:CYS102 3.4 20.7 1.0
CA G:CYS102 3.7 23.9 1.0
N G:VAL103 3.7 25.5 1.0
ND2 G:ASN45 3.9 45.0 1.0
N G:PHE203 4.0 16.4 1.0
CG1 G:VAL103 4.1 26.8 1.0
C G:CYS102 4.2 24.9 1.0
C G:GLY202 4.3 17.0 1.0
CA G:GLY202 4.5 24.1 1.0
CG G:ASN45 4.6 47.2 1.0
CA G:PHE203 4.6 18.1 1.0
CB G:PHE203 4.7 33.8 1.0
C6 G:MTE307 4.7 31.6 1.0
N G:GLY202 4.7 19.4 1.0
CB G:VAL103 4.8 35.6 1.0
CA G:VAL103 4.8 37.0 1.0
CB G:ASN45 4.9 38.3 1.0
N G:GLU104 4.9 31.2 1.0
C3' G:MTE307 4.9 28.7 1.0
CG G:GLU104 4.9 35.3 1.0
O G:HOH425 4.9 49.6 1.0
CD G:GLU104 4.9 47.0 1.0
CD2 G:PHE203 5.0 25.3 1.0

Tungsten binding site 8 out of 10 in 1xdy

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Tungsten binding site 8 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 8 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:W408

b:41.7
occ:1.00
 S2' H:MTE308 2.3 37.0 1.0
S1' H:MTE308 2.4 37.5 1.0
SG H:CYS102 2.5 38.3 1.0
C1' H:MTE308 3.2 41.0 1.0
C2' H:MTE308 3.3 43.7 1.0
CB H:CYS102 3.5 27.2 1.0
N H:VAL103 3.7 48.9 1.0
CA H:CYS102 3.8 46.3 1.0
ND2 H:ASN45 4.0 58.4 1.0
N H:PHE203 4.0 45.2 1.0
C H:CYS102 4.2 48.8 1.0
CG1 H:VAL103 4.3 40.9 1.0
CA H:GLY202 4.4 39.0 1.0
C H:GLY202 4.4 41.1 1.0
CG H:ASN45 4.6 56.0 1.0
CB H:PHE203 4.6 43.7 1.0
C6 H:MTE308 4.7 44.2 1.0
N H:GLY202 4.7 36.0 1.0
CA H:PHE203 4.7 47.5 1.0
CA H:VAL103 4.7 43.3 1.0
N H:GLU104 4.7 41.5 1.0
CB H:VAL103 4.7 34.7 1.0
C3' H:MTE308 4.8 45.0 1.0
CB H:ASN45 4.9 49.8 1.0
CD2 H:PHE203 5.0 32.2 1.0

Tungsten binding site 9 out of 10 in 1xdy

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Tungsten binding site 9 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 9 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:W409

b:42.9
occ:1.00
 S1' I:MTE309 2.3 39.6 1.0
S2' I:MTE309 2.5 33.6 1.0
SG I:CYS102 2.5 32.0 1.0
C1' I:MTE309 3.3 41.2 1.0
C2' I:MTE309 3.4 39.8 1.0
CB I:CYS102 3.5 46.1 1.0
ND2 I:ASN45 3.5 60.5 1.0
N I:VAL103 3.8 45.6 1.0
CA I:CYS102 3.9 43.8 1.0
N I:PHE203 3.9 38.2 1.0
CG1 I:VAL103 4.0 39.6 1.0
CA I:GLY202 4.3 28.9 1.0
C I:CYS102 4.3 47.9 1.0
C I:GLY202 4.4 39.3 1.0
CG I:ASN45 4.5 60.9 1.0
CA I:PHE203 4.6 33.3 1.0
CB I:PHE203 4.6 36.4 1.0
N I:GLY202 4.6 30.4 1.0
C6 I:MTE309 4.7 50.2 1.0
CB I:VAL103 4.7 43.8 1.0
CA I:VAL103 4.8 44.3 1.0
CB I:ASN45 4.9 54.0 1.0
N I:GLU104 4.9 52.6 1.0
C3' I:MTE309 5.0 42.5 1.0

Tungsten binding site 10 out of 10 in 1xdy

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Tungsten binding site 10 out of 10 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 10 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, W-Containing Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:W410

b:30.7
occ:1.00
 S1' J:MTE310 2.3 27.5 1.0
S2' J:MTE310 2.5 24.4 1.0
SG J:CYS102 2.5 28.8 1.0
C1' J:MTE310 3.2 25.9 1.0
C2' J:MTE310 3.3 8.9 1.0
ND2 J:ASN45 3.4 39.2 1.0
CB J:CYS102 3.4 36.6 1.0
N J:VAL103 3.7 26.0 1.0
CA J:CYS102 3.7 24.3 1.0
CG1 J:VAL103 3.9 40.2 1.0
N J:PHE203 4.0 18.5 1.0
C J:CYS102 4.2 30.5 1.0
CA J:GLY202 4.3 22.4 1.0
C J:GLY202 4.4 25.7 1.0
CG J:ASN45 4.5 30.7 1.0
N J:GLY202 4.6 18.6 1.0
C6 J:MTE310 4.6 28.3 1.0
CB J:PHE203 4.6 28.3 1.0
CA J:PHE203 4.6 25.0 1.0
CB J:VAL103 4.7 31.3 1.0
CG J:GLU104 4.7 35.6 1.0
CA J:VAL103 4.8 31.6 1.0
CB J:ASN45 4.8 28.7 1.0
N J:GLU104 4.9 35.6 1.0
C3' J:MTE310 4.9 17.9 1.0
CD J:GLU104 5.0 38.9 1.0

Reference:

L.Loschi, S.J.Brokx, T.L.Hills, G.Zhang, M.G.Bertero, A.L.Lovering, J.H.Weiner, N.C.Strynadka. Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase. J.Biol.Chem. V. 279 50391 2004.
ISSN: ISSN 0021-9258
PubMed: 15355966
DOI: 10.1074/JBC.M408876200
Page generated: Sat Oct 12 03:46:25 2024

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