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Molybdenum in PDB 1xdq: Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase

Protein crystallography data

The structure of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, PDB code: 1xdq 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) 39.75 / 2.55
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.345, 165.064, 181.447, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27.4

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase (pdb code 1xdq). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 5 binding sites of Molybdenum where determined in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, PDB code: 1xdq:
Jump to Molybdenum binding site number: 1; 2; 3; 4; 5;

Molybdenum binding site 1 out of 5 in 1xdq

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Molybdenum binding site 1 out of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo501

b:40.7
occ:1.00
O A:O601 1.7 35.3 1.0
O A:HOH645 2.2 13.8 1.0
S2' A:MTE301 2.4 44.4 1.0
S1' A:MTE301 2.4 36.7 1.0
SG A:CYS102 2.5 39.8 1.0
C1' A:MTE301 3.2 41.8 1.0
C2' A:MTE301 3.4 42.9 1.0
CB A:CYS102 3.5 39.0 1.0
ND2 A:ASN45 3.6 46.6 1.0
N A:VAL103 3.8 49.0 1.0
N A:PHE203 3.9 41.1 1.0
CA A:CYS102 3.9 41.7 1.0
CG1 A:VAL103 4.3 37.8 1.0
CA A:GLY202 4.3 37.4 1.0
C A:GLY202 4.3 40.5 1.0
C A:CYS102 4.3 47.9 1.0
CA A:PHE203 4.6 41.4 1.0
CB A:PHE203 4.6 36.6 1.0
N A:GLY202 4.7 40.2 1.0
C6 A:MTE301 4.7 41.0 1.0
CG A:ASN45 4.7 46.2 1.0
N A:GLU104 4.7 39.4 1.0
CA A:VAL103 4.8 46.3 1.0
CD2 A:PHE203 4.8 40.8 1.0
CB A:VAL103 4.9 45.9 1.0

Molybdenum binding site 2 out of 5 in 1xdq

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Molybdenum binding site 2 out of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo502

b:41.2
occ:1.00
O B:O602 1.7 32.2 1.0
S1' B:MTE302 2.3 40.1 1.0
S2' B:MTE302 2.4 44.2 1.0
SG B:CYS102 2.5 47.1 1.0
O B:HOH628 2.5 17.1 1.0
C1' B:MTE302 3.2 46.0 1.0
CB B:CYS102 3.4 50.0 1.0
C2' B:MTE302 3.4 42.6 1.0
ND2 B:ASN45 3.6 63.4 1.0
N B:VAL103 3.8 46.1 1.0
CA B:CYS102 3.9 45.9 1.0
N B:PHE203 3.9 40.8 1.0
CG1 B:VAL103 4.2 34.3 1.0
C B:CYS102 4.3 47.0 1.0
CA B:GLY202 4.4 44.9 1.0
C B:GLY202 4.4 42.1 1.0
C6 B:MTE302 4.6 33.6 1.0
CA B:PHE203 4.6 42.5 1.0
CB B:PHE203 4.7 41.7 1.0
N B:GLY202 4.7 42.6 1.0
CG B:ASN45 4.7 61.2 1.0
N B:GLU104 4.8 44.7 1.0
CA B:VAL103 4.8 46.7 1.0
CD2 B:PHE203 4.8 35.8 1.0
CB B:VAL103 4.8 42.7 1.0
CG B:GLU104 5.0 45.5 1.0

Molybdenum binding site 3 out of 5 in 1xdq

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Molybdenum binding site 3 out of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo503

b:41.4
occ:1.00
O C:O603 1.7 42.6 1.0
O C:HOH621 2.2 15.9 1.0
S2' C:MTE303 2.3 45.3 1.0
S1' C:MTE303 2.3 43.5 1.0
SG C:CYS102 2.4 44.0 1.0
C1' C:MTE303 3.2 49.8 1.0
CB C:CYS102 3.4 43.3 1.0
C2' C:MTE303 3.4 47.3 1.0
ND2 C:ASN45 3.8 51.4 1.0
N C:VAL103 3.8 46.7 1.0
CA C:CYS102 3.9 46.2 1.0
N C:PHE203 3.9 46.2 1.0
CG1 C:VAL103 4.2 28.8 1.0
C C:GLY202 4.3 44.8 1.0
C C:CYS102 4.3 47.2 1.0
CA C:GLY202 4.3 41.5 1.0
CB C:PHE203 4.6 43.5 1.0
CA C:PHE203 4.6 45.2 1.0
N C:GLY202 4.6 44.8 1.0
C6 C:MTE303 4.6 45.2 1.0
CD2 C:PHE203 4.7 40.2 1.0
N C:GLU104 4.8 47.4 1.0
CA C:VAL103 4.8 42.0 1.0
CG C:ASN45 4.8 46.0 1.0
CB C:VAL103 4.9 43.7 1.0

Molybdenum binding site 4 out of 5 in 1xdq

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Molybdenum binding site 4 out of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mo504

b:41.9
occ:1.00
O D:O604 1.7 31.2 1.0
O D:HOH629 2.3 19.8 1.0
S2' D:MTE304 2.3 47.4 1.0
S1' D:MTE304 2.4 46.9 1.0
SG D:CYS102 2.4 45.0 1.0
C1' D:MTE304 3.2 50.6 1.0
C2' D:MTE304 3.4 50.4 1.0
CB D:CYS102 3.5 44.4 1.0
ND2 D:ASN45 3.7 51.2 1.0
N D:VAL103 3.7 43.2 1.0
N D:PHE203 3.8 45.0 1.0
CA D:CYS102 3.8 44.8 1.0
CA D:GLY202 4.2 46.0 1.0
C D:GLY202 4.3 46.9 1.0
C D:CYS102 4.3 46.0 1.0
CG1 D:VAL103 4.3 44.6 1.0
N D:GLY202 4.5 39.1 1.0
CA D:PHE203 4.6 46.0 1.0
CB D:PHE203 4.6 43.0 1.0
C6 D:MTE304 4.7 47.0 1.0
CA D:VAL103 4.8 43.3 1.0
CB D:VAL103 4.8 41.2 1.0
N D:GLU104 4.8 42.3 1.0
CG D:ASN45 4.8 56.9 1.0
CD2 D:PHE203 4.9 45.3 1.0

Molybdenum binding site 5 out of 5 in 1xdq

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Molybdenum binding site 5 out of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mo505

b:49.0
occ:1.00
O E:O605 1.7 32.2 1.0
S2' E:MTE305 2.3 49.2 1.0
S1' E:MTE305 2.3 43.3 1.0
O E:HOH630 2.4 29.2 1.0
SG E:CYS102 2.5 53.4 1.0
C1' E:MTE305 3.2 50.5 1.0
C2' E:MTE305 3.4 49.3 1.0
CB E:CYS102 3.5 51.2 1.0
ND2 E:ASN45 3.6 47.1 1.0
N E:VAL103 3.8 52.4 1.0
CA E:CYS102 3.9 53.8 1.0
N E:PHE203 3.9 40.6 1.0
CA E:GLY202 4.2 43.2 1.0
C E:GLY202 4.3 45.8 1.0
CG1 E:VAL103 4.3 46.1 1.0
C E:CYS102 4.3 55.9 1.0
N E:GLY202 4.6 45.8 1.0
CA E:PHE203 4.6 41.4 1.0
C6 E:MTE305 4.7 45.9 1.0
CB E:PHE203 4.7 45.2 1.0
N E:GLU104 4.7 47.8 1.0
CG E:ASN45 4.7 52.7 1.0
CA E:VAL103 4.8 46.7 1.0
CD2 E:PHE203 4.8 46.6 1.0
CB E:VAL103 4.8 45.7 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: Wed Sep 23 13:32:18 2020
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