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Arsenic in PDB 3od5: Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho

Enzymatic activity of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho

All present enzymatic activity of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho:
3.4.22.59;

Protein crystallography data

The structure of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho, PDB code: 3od5 was solved by X.-J.Wang, X.Liu, K.-T.Wang, Q.Cao, X.-D.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.18 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.464, 89.589, 61.145, 90.00, 111.67, 90.00
R / Rfree (%) 15.5 / 18.9

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho (pdb code 3od5). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 8 binding sites of Arsenic where determined in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho, PDB code: 3od5:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Arsenic binding site 1 out of 8 in 3od5

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Arsenic binding site 1 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1

b:22.0
occ:1.00
 AS A:CAC1 0.0 22.0 1.0
C1 A:CAC1 2.0 17.0 1.0
C2 A:CAC1 2.0 21.4 1.0
SG A:CYS264 2.3 19.9 1.0
O C:VAL301 3.2 19.5 1.0
CB A:CYS264 3.2 22.7 1.0
CA A:CYS264 3.7 16.6 1.0
O C:HOH438 3.8 27.4 1.0
O A:HOH465 3.9 23.7 1.0
O A:PHE263 4.1 16.9 1.0
O A:HOH326 4.2 24.3 1.0
C C:VAL301 4.2 20.4 1.0
CG1 A:VAL261 4.3 13.8 1.0
CB C:VAL301 4.5 17.0 1.0
N A:LYS265 4.5 19.2 1.0
C A:CYS264 4.6 19.8 1.0
N A:CYS264 4.8 18.8 1.0
CA C:VAL301 4.9 15.3 1.0
C A:PHE263 4.9 17.9 1.0
N C:VAL301 4.9 16.7 1.0

Arsenic binding site 2 out of 8 in 3od5

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Arsenic binding site 2 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As3

b:18.6
occ:1.00
 AS A:CAC3 0.0 18.6 1.0
C1 A:CAC3 2.0 24.4 1.0
C2 A:CAC3 2.0 21.6 1.0
SG A:CYS277 2.3 13.2 1.0
O A:HOH464 3.1 23.3 1.0
CB A:CYS277 3.2 9.8 1.0
NH1 A:ARG164 3.6 13.7 1.0
O A:HOH481 3.6 14.8 1.0
CG A:GLU214 4.3 18.4 1.0
O A:CYS277 4.3 14.0 1.0
CD2 A:TYR210 4.3 17.0 1.0
C A:CYS277 4.4 12.1 1.0
NH2 A:ARG164 4.4 13.8 1.0
CB B:ALA279 4.4 11.1 1.0
CA A:CYS277 4.4 8.7 1.0
CZ A:ARG164 4.5 12.6 1.0
OE2 A:GLU214 4.5 24.7 1.0
N A:GLU214 4.7 14.0 1.0
CD A:GLU214 4.8 25.2 1.0
CA A:ALA213 4.9 12.5 1.0
CG A:TYR210 4.9 12.1 1.0
CE2 A:TYR210 5.0 14.3 1.0
N A:PHE278 5.0 9.9 1.0
CB A:TYR210 5.0 12.6 1.0

Arsenic binding site 3 out of 8 in 3od5

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Arsenic binding site 3 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As7

b:21.3
occ:1.00
 AS A:CAC7 0.0 21.3 1.0
C2 A:CAC7 2.0 13.5 1.0
C1 A:CAC7 2.0 19.2 1.0
SG A:CYS68 2.3 18.8 1.0
CB A:CYS68 3.2 13.7 1.0
O A:HOH517 3.4 21.0 1.0
NH2 A:ARG71 3.9 14.2 1.0
OD2 A:ASP72 3.9 19.8 1.0
C A:CYS68 4.1 16.0 1.0
O A:HOH410 4.1 30.8 1.0
CA A:CYS68 4.2 12.7 1.0
O A:CYS68 4.3 13.7 1.0
O A:HOH820 4.5 72.9 1.0
O A:HOH493 4.5 22.6 1.0
N A:ALA69 4.5 15.9 1.0
CG A:ASP72 4.9 16.7 1.0

Arsenic binding site 4 out of 8 in 3od5

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Arsenic binding site 4 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As8

b:32.2
occ:1.00
 AS A:CAC8 0.0 32.2 1.0
C2 A:CAC8 2.0 31.8 1.0
C1 A:CAC8 2.0 27.7 1.0
SG A:CYS87 2.4 17.8 1.0
O A:HOH665 3.0 50.7 1.0
CB A:CYS87 3.0 15.3 1.0
O A:HOH498 3.6 21.6 1.0
O A:HOH407 3.7 18.9 1.0
N A:CYS87 3.9 15.4 1.0
CA A:CYS87 4.0 14.2 1.0
OG1 A:THR75 4.2 13.2 1.0
O A:HOH454 4.3 26.2 1.0
O A:HOH519 4.3 41.4 1.0
CG2 A:THR75 4.7 15.4 1.0
CD A:ARG71 4.8 13.2 1.0
C A:LYS86 4.8 15.2 1.0
O A:HOH686 4.8 39.0 1.0
C A:CYS87 5.0 14.4 1.0

Arsenic binding site 5 out of 8 in 3od5

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Arsenic binding site 5 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As2

b:21.1
occ:1.00
 AS B:CAC2 0.0 21.1 1.0
C2 B:CAC2 2.0 17.4 1.0
C1 B:CAC2 2.0 19.0 1.0
SG B:CYS264 2.3 17.7 1.0
O D:VAL301 3.2 20.9 1.0
CB B:CYS264 3.2 18.9 1.0
CA B:CYS264 3.7 15.5 1.0
O B:HOH409 3.8 21.9 1.0
O B:HOH556 3.8 26.8 1.0
O B:PHE263 4.1 15.7 1.0
O B:HOH345 4.1 24.6 1.0
C D:VAL301 4.2 17.6 1.0
CG1 B:VAL261 4.4 14.1 1.0
N B:LYS265 4.4 17.8 1.0
C B:CYS264 4.6 18.1 1.0
CB D:VAL301 4.6 17.7 1.0
O B:HOH469 4.8 42.2 1.0
N B:CYS264 4.8 18.2 1.0
C B:PHE263 4.9 19.6 1.0
CA D:VAL301 4.9 11.3 1.0

Arsenic binding site 6 out of 8 in 3od5

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Arsenic binding site 6 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As4

b:25.0
occ:1.00
 AS B:CAC4 0.0 25.0 1.0
C2 B:CAC4 2.0 21.1 1.0
C1 B:CAC4 2.0 21.6 1.0
SG B:CYS68 2.2 15.9 1.0
CB B:CYS68 3.1 14.6 1.0
OD1 B:ASN51 3.6 17.4 1.0
NH1 B:ARG71 3.7 18.6 1.0
CZ B:ARG71 3.8 21.6 1.0
NH2 B:ARG71 3.9 18.5 1.0
CA B:CYS68 3.9 12.9 1.0
OD1 B:ASN89 4.1 19.3 1.0
ND2 B:ASN89 4.3 24.0 1.0
NE B:ARG71 4.3 16.6 1.0
CG B:ASN89 4.5 25.2 1.0
O B:HOH503 4.7 18.6 1.0
CD B:ARG71 4.8 18.7 1.0
N B:CYS68 4.8 13.2 1.0
OE2 B:GLU53 4.8 30.8 1.0
CG B:ASN51 4.8 13.7 1.0

Arsenic binding site 7 out of 8 in 3od5

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Arsenic binding site 7 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As5

b:18.5
occ:1.00
 AS B:CAC5 0.0 18.5 1.0
C2 B:CAC5 2.0 21.6 1.0
C1 B:CAC5 2.0 17.9 1.0
SG B:CYS277 2.3 13.5 1.0
O B:HOH476 3.1 21.1 1.0
CB B:CYS277 3.2 11.8 1.0
O B:HOH492 3.4 17.8 1.0
NH1 B:ARG164 3.5 15.6 1.0
O B:CYS277 4.2 11.4 1.0
CG B:GLU214 4.2 17.6 1.0
C B:CYS277 4.3 12.1 1.0
CD2 B:TYR210 4.3 15.3 1.0
CA B:CYS277 4.4 7.9 1.0
CB A:ALA279 4.4 8.8 1.0
CZ B:ARG164 4.4 12.8 1.0
NH2 B:ARG164 4.5 11.9 1.0
OE2 B:GLU214 4.7 24.7 1.0
N B:GLU214 4.7 12.4 1.0
CD B:GLU214 4.9 24.3 1.0
CE2 B:TYR210 4.9 13.9 1.0
CA B:ALA213 4.9 13.6 1.0
N B:PHE278 5.0 11.2 1.0
CG B:TYR210 5.0 13.0 1.0

Arsenic binding site 8 out of 8 in 3od5

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Arsenic binding site 8 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As6

b:25.8
occ:1.00
 AS B:CAC6 0.0 25.8 1.0
C1 B:CAC6 2.0 20.3 1.0
C2 B:CAC6 2.0 20.5 1.0
SG B:CYS87 2.3 20.8 1.0
CB B:CYS87 3.2 15.5 1.0
N B:CYS87 3.6 13.5 1.0
CA B:CYS87 4.0 12.0 1.0
CG2 B:THR75 4.1 6.9 1.0
C B:LYS86 4.1 16.9 1.0
O B:VAL85 4.1 16.1 1.0
O B:HOH351 4.2 36.4 1.0
CG1 B:VAL85 4.3 13.2 1.0
O B:HOH555 4.4 21.4 1.0
CA B:LYS86 4.4 13.8 1.0
C B:VAL85 4.5 13.8 1.0
OG1 B:THR75 4.6 20.9 1.0
CB B:THR75 4.6 28.9 1.0
N B:LYS86 4.7 12.1 1.0
O B:HOH750 4.8 56.9 1.0
O B:LYS86 4.8 16.7 1.0
O B:HOH386 4.8 31.5 1.0
CB B:VAL85 4.9 13.1 1.0
C B:CYS87 5.0 14.4 1.0

Reference:

X.-J.Wang, Q.Cao, X.Liu, K.-T.Wang, W.Mi, Y.Zhang, L.-F.Li, A.C.Leblanc, X.-D.Su. Crystal Structures of Human Caspase 6 Reveal A New Mechanism For Intramolecular Cleavage Self-Activation Embo Rep. V. 11 841 2010.
ISSN: ISSN 1469-221X
PubMed: 20890311
DOI: 10.1038/EMBOR.2010.141
Page generated: Wed Jul 10 11:51:01 2024

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