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Vanadium in PDB 1uzi: C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form

Enzymatic activity of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form

All present enzymatic activity of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form:
2.4.2.30;

Protein crystallography data

The structure of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form, PDB code: 1uzi was solved by H.R.Evans, D.E.Holloway, J.M.Sutton, J.Ayriss, C.C.Shone, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.89
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 73.293, 73.293, 218.233, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.3

Vanadium Binding Sites:

The binding sites of Vanadium atom in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form (pdb code 1uzi). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 7 binding sites of Vanadium where determined in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form, PDB code: 1uzi:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6; 7;

Vanadium binding site 1 out of 7 in 1uzi

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Vanadium binding site 1 out of 7 in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:69.4
occ:1.00
 V1 A:V4O1001 0.0 69.4 1.0
O1 A:V4O1001 1.6 71.9 1.0
O0 A:V4O1001 1.7 71.7 1.0
O3 A:V4O1001 1.8 71.5 1.0
O9 A:V4O1001 1.8 73.2 1.0
V2 A:V4O1001 3.2 70.6 1.0
V4 A:V4O1001 3.3 72.5 1.0
O11 A:V4O1001 3.4 72.9 1.0
O2 A:V4O1001 3.6 66.4 1.0
ND2 B:ASN151 4.0 61.4 1.0
O6 A:V4O1001 4.0 70.4 1.0
CD A:LYS152 4.2 56.7 1.0
CE A:LYS152 4.4 56.5 1.0
O10 A:V4O1001 4.4 74.2 1.0
ND2 B:ASN145 4.4 52.8 1.0
O8 A:V4O1001 4.5 72.7 1.0
O4 A:V4O1001 4.5 69.8 1.0
OD1 B:ASN145 4.7 54.8 1.0
CB A:LYS152 4.8 57.1 1.0
CG B:ASN145 4.9 56.4 1.0
V3 A:V4O1001 4.9 66.7 1.0
CG A:LYS152 5.0 56.3 1.0

Vanadium binding site 2 out of 7 in 1uzi

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Vanadium binding site 2 out of 7 in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:70.6
occ:1.00
 V2 A:V4O1001 0.0 70.6 1.0
O4 A:V4O1001 1.7 69.8 1.0
O2 A:V4O1001 1.7 66.4 1.0
O3 A:V4O1001 1.8 71.5 1.0
O6 A:V4O1001 1.8 70.4 1.0
V1 A:V4O1001 3.2 69.4 1.0
V3 A:V4O1001 3.3 66.7 1.0
O9 A:V4O1001 3.5 73.2 1.0
O7 A:V4O1001 3.7 68.3 1.0
ND2 A:ASN145 3.8 52.4 1.0
N A:LYS152 3.9 58.3 1.0
ND2 A:ASN151 3.9 61.6 1.0
CB A:LYS152 4.0 57.1 1.0
O1 A:V4O1001 4.1 71.9 1.0
O8 A:V4O1001 4.2 72.7 1.0
CD A:LYS152 4.2 56.7 1.0
V4 A:V4O1001 4.3 72.5 1.0
O0 A:V4O1001 4.4 71.7 1.0
O11 A:V4O1001 4.5 72.9 1.0
CG A:ASN151 4.5 62.3 1.0
CA A:LYS152 4.6 56.8 1.0
O5 A:V4O1001 4.6 69.2 1.0
CA A:ASN151 4.7 59.3 1.0
C A:ASN151 4.7 58.9 1.0
CG A:LYS152 4.8 56.3 1.0
CG A:ASN145 4.8 55.6 1.0
OD1 A:ASN145 4.9 56.0 1.0
OD1 A:ASN151 5.0 64.4 1.0
N A:THR153 5.0 54.0 1.0

Vanadium binding site 3 out of 7 in 1uzi

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Vanadium binding site 3 out of 7 in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:66.7
occ:1.00
 V3 A:V4O1001 0.0 66.7 1.0
O5 A:V4O1001 1.6 69.2 1.0
O7 A:V4O1001 1.7 68.3 1.0
O8 A:V4O1001 1.8 72.7 1.0
O6 A:V4O1001 1.8 70.4 1.0
V4 A:V4O1001 3.3 72.5 1.0
V2 A:V4O1001 3.3 70.6 1.0
O2 A:V4O1001 3.5 66.4 1.0
O9 A:V4O1001 3.8 73.2 1.0
CD B:LYS152 3.9 57.2 1.0
O11 A:V4O1001 3.9 72.9 1.0
ND2 A:ASN151 4.0 61.6 1.0
O3 A:V4O1001 4.4 71.5 1.0
O4 A:V4O1001 4.5 69.8 1.0
O10 A:V4O1001 4.5 74.2 1.0
CB B:LYS152 4.8 57.5 1.0
CE B:LYS152 4.8 57.9 1.0
OD1 A:ASN145 4.9 56.0 1.0
CG B:LYS152 4.9 58.7 1.0
V1 A:V4O1001 4.9 69.4 1.0

Vanadium binding site 4 out of 7 in 1uzi

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Vanadium binding site 4 out of 7 in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:72.5
occ:1.00
 V4 A:V4O1001 0.0 72.5 1.0
O10 A:V4O1001 1.6 74.2 1.0
O11 A:V4O1001 1.7 72.9 1.0
O8 A:V4O1001 1.8 72.7 1.0
O9 A:V4O1001 1.8 73.2 1.0
V3 A:V4O1001 3.3 66.7 1.0
V1 A:V4O1001 3.3 69.4 1.0
ND2 B:ASN145 3.4 52.8 1.0
O6 A:V4O1001 3.6 70.4 1.0
O0 A:V4O1001 3.8 71.7 1.0
N B:LYS152 3.9 58.1 1.0
O3 A:V4O1001 4.0 71.5 1.0
ND2 B:ASN151 4.1 61.4 1.0
CB B:LYS152 4.1 57.5 1.0
O7 A:V4O1001 4.2 68.3 1.0
V2 A:V4O1001 4.3 70.6 1.0
CD B:LYS152 4.3 57.2 1.0
CG B:LYS152 4.4 58.7 1.0
O5 A:V4O1001 4.5 69.2 1.0
CG B:ASN145 4.5 56.4 1.0
O1 A:V4O1001 4.6 71.9 1.0
O2 A:V4O1001 4.6 66.4 1.0
CA B:LYS152 4.6 56.8 1.0
CA B:ASN151 4.7 58.3 1.0
C B:ASN151 4.7 58.4 1.0
CG B:ASN151 4.7 61.3 1.0
OD1 B:ASN145 4.9 54.8 1.0
N B:THR153 5.0 53.9 1.0

Vanadium binding site 5 out of 7 in 1uzi

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Vanadium binding site 5 out of 7 in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 5 of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1002

b:46.3
occ:1.00
 V A:VO41002 0.0 46.3 1.0
O1 A:VO41002 1.7 34.8 1.0
O3 A:VO41002 1.7 42.7 1.0
O4 A:VO41002 1.7 46.8 1.0
O2 A:VO41002 1.7 47.9 1.0
O A:HOH2153 3.5 30.0 1.0
O A:HOH2155 3.9 23.7 1.0
N A:SER102 4.0 18.7 1.0
O A:HOH2154 4.2 33.8 1.0
CB A:SER102 4.3 22.8 1.0
OG A:SER102 4.5 29.2 1.0
CA A:PRO101 4.6 19.0 1.0
CA A:SER102 4.9 20.9 1.0
C A:PRO101 4.9 20.3 1.0
CB A:PRO101 4.9 18.1 1.0

Vanadium binding site 6 out of 7 in 1uzi

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Vanadium binding site 6 out of 7 in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 6 of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1003

b:54.7
occ:1.00
 V A:VO41003 0.0 54.7 1.0
O1 A:VO41003 1.7 53.9 1.0
O2 A:VO41003 1.7 39.4 1.0
O4 A:VO41003 1.7 48.3 1.0
O3 A:VO41003 1.7 52.8 1.0
O1 A:GOL1004 3.0 37.8 1.0
OG A:SER71 3.5 32.1 1.0
O1 A:GOL1005 3.7 38.4 1.0
CB A:SER71 4.1 24.1 1.0
C1 A:GOL1004 4.1 22.6 1.0
N A:SER71 4.2 23.6 1.0
CB A:SER69 4.2 25.5 1.0
O2 A:GOL1004 4.3 41.5 1.0
C2 A:GOL1004 4.4 36.3 1.0
OG A:SER69 4.4 21.9 1.0
N A:LYS70 4.6 24.6 1.0
C1 A:GOL1005 4.6 26.8 1.0
CB A:LYS70 4.7 26.0 1.0
CA A:SER71 4.7 23.1 1.0
O2 A:GOL1005 5.0 42.3 1.0
C2 A:GOL1005 5.0 40.0 1.0

Vanadium binding site 7 out of 7 in 1uzi

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Vanadium binding site 7 out of 7 in the C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 7 of C3 Exoenzyme From Clostridium Botulinum, Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V1002

b:47.5
occ:1.00
 V B:VO41002 0.0 47.5 1.0
O1 B:VO41002 1.7 35.5 1.0
O2 B:VO41002 1.7 40.2 1.0
O4 B:VO41002 1.7 47.7 1.0
O3 B:VO41002 1.8 47.5 1.0
O B:HOH2150 3.5 28.3 1.0
O B:HOH2152 3.8 23.2 1.0
N B:SER102 4.0 18.4 1.0
O B:HOH2151 4.1 31.0 1.0
CB B:SER102 4.3 23.1 1.0
OG B:SER102 4.4 32.8 1.0
CA B:PRO101 4.6 18.7 1.0
CA B:SER102 4.8 20.7 1.0
C B:PRO101 4.8 21.2 1.0
CB B:PRO101 4.9 19.0 1.0

Reference:

H.R.Evans, D.E.Holloway, J.M.Sutton, J.Ayriss, C.C.Shone, K.R.Acharya. C3 Exoenzyme From Clostridium Botulinum: Structure of A Tetragonal Crystal Form and A Reassessment of Nad-Induced Flexure Acta Crystallogr.,Sect.D V. 60 1502 2004.
ISSN: ISSN 0907-4449
PubMed: 15272191
DOI: 10.1107/S0907444904011680
Page generated: Fri Oct 11 11:34:06 2024

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