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Arsenic in PDB 3s70: Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad

Enzymatic activity of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad

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

Protein crystallography data

The structure of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad, PDB code: 3s70 was solved by X.-D.Su, X.Liu, X.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.48 / 1.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.390, 89.450, 61.130, 90.00, 111.70, 90.00
R / Rfree (%) 16.4 / 19.4

Other elements in 3s70:

The structure of Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad (pdb code 3s70). 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 Solved By As-Sad, PDB code: 3s70:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Arsenic binding site 1 out of 8 in 3s70

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


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2

b:14.1
occ:0.90
AS A:CAC2 0.0 14.1 0.9
C2 A:CAC2 2.0 13.8 0.9
C1 A:CAC2 2.0 10.4 0.9
SG A:CYS264 2.3 14.1 1.0
O B:VAL1 3.1 13.1 1.0
CB A:CYS264 3.2 19.0 1.0
CA A:CYS264 3.7 13.9 1.0
O B:HOH203 3.7 19.8 1.0
O A:HOH341 3.7 17.3 1.0
O A:PHE263 4.0 11.1 1.0
O A:HOH407 4.1 17.7 1.0
C B:VAL1 4.2 13.0 1.0
CG1 A:VAL261 4.3 10.5 1.0
N A:LYS265 4.5 12.4 1.0
C A:CYS264 4.6 14.3 1.0
CB B:VAL1 4.6 13.0 1.0
O A:HOH374 4.7 36.4 1.0
N A:CYS264 4.7 11.7 1.0
C A:PHE263 4.8 13.7 1.0
CA B:VAL1 4.9 6.9 1.0

Arsenic binding site 2 out of 8 in 3s70

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


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As3

b:10.7
occ:0.90
AS A:CAC3 0.0 10.7 0.9
C2 A:CAC3 2.0 19.6 0.9
C1 A:CAC3 2.0 13.4 0.9
SG A:CYS277 2.3 8.9 1.0
O A:HOH464 3.1 14.8 1.0
CB A:CYS277 3.2 5.3 1.0
NH1 A:ARG164 3.5 8.0 1.0
O A:HOH352 3.6 11.9 1.0
O A:CYS277 4.2 6.0 1.0
CG A:GLU214 4.2 10.2 1.0
CD1 A:TYR210 4.3 12.1 1.0
C A:CYS277 4.3 5.1 1.0
CA A:CYS277 4.4 5.2 1.0
CZ A:ARG164 4.4 8.4 1.0
CB C:ALA279 4.4 4.1 1.0
NH2 A:ARG164 4.4 8.6 1.0
OE2 A:GLU214 4.6 20.4 1.0
N A:GLU214 4.7 8.9 1.0
CD A:GLU214 4.8 18.4 1.0
CE1 A:TYR210 4.8 11.4 1.0
CG A:TYR210 4.9 5.8 1.0
CA A:ALA213 4.9 9.6 1.0
N A:PHE278 4.9 4.9 1.0

Arsenic binding site 3 out of 8 in 3s70

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


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As6

b:17.0
occ:0.80
AS A:CAC6 0.0 17.0 0.8
C1 A:CAC6 2.0 36.8 0.8
C2 A:CAC6 2.0 11.1 0.8
SG A:CYS87 2.4 17.4 1.0
CB A:CYS87 3.3 12.6 1.0
N A:CYS87 3.6 9.3 1.0
OG1 A:THR75 4.0 6.0 1.0
CA A:CYS87 4.1 7.9 1.0
O A:VAL85 4.1 9.9 1.0
O A:HOH509 4.1 21.8 1.0
C A:LYS86 4.1 10.9 1.0
CG1 A:VAL85 4.2 10.1 1.0
O A:HOH437 4.2 15.9 1.0
CA A:LYS86 4.4 8.9 1.0
CG2 A:THR75 4.4 7.6 1.0
C A:VAL85 4.5 8.2 1.0
O A:ACT1 4.5 15.6 1.0
O A:HOH316 4.6 23.6 1.0
N A:LYS86 4.6 6.3 1.0
O A:LYS86 4.8 11.7 1.0
CB A:THR75 4.9 4.2 1.0
CB A:VAL85 4.9 7.3 1.0
C A:ACT1 4.9 16.2 1.0
O A:HOH572 4.9 48.7 1.0
CH3 A:ACT1 5.0 13.7 1.0

Arsenic binding site 4 out of 8 in 3s70

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


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As7

b:13.6
occ:0.70
AS A:CAC7 0.0 13.6 0.7
C1 A:CAC7 2.0 11.3 0.7
C2 A:CAC7 2.0 14.8 0.7
SG A:CYS68 2.3 10.9 1.0
CB A:CYS68 3.1 6.8 1.0
NH1 A:ARG71 3.6 12.9 1.0
OD1 A:ASN51 3.6 13.5 1.0
CZ A:ARG71 3.7 15.6 1.0
CA A:CYS68 4.0 6.4 1.0
NH2 A:ARG71 4.0 12.6 1.0
OD1 A:ASN89 4.0 13.4 1.0
ND2 A:ASN89 4.2 6.0 0.6
NE A:ARG71 4.2 13.1 1.0
CG A:ASN89 4.4 14.8 0.8
CD A:ARG71 4.7 12.8 1.0
O A:HOH429 4.8 13.5 1.0
CG A:ASN51 4.8 5.1 1.0
N A:CYS68 4.8 8.9 1.0
OE1 A:GLU53 4.9 25.1 1.0

Arsenic binding site 5 out of 8 in 3s70

Go back to Arsenic Binding Sites List in 3s70
Arsenic binding site 5 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As1

b:9.6
occ:0.80
AS C:CAC1 0.0 9.6 0.8
C1 C:CAC1 2.0 20.0 0.8
C2 C:CAC1 2.0 14.4 0.8
SG C:CYS277 2.3 8.1 1.0
O C:HOH410 3.1 19.0 1.0
CB C:CYS277 3.2 6.0 1.0
NH1 C:ARG164 3.5 7.3 1.0
O C:HOH21 3.6 11.6 1.0
CG C:GLU214 4.2 13.5 1.0
O C:CYS277 4.3 6.7 1.0
NH2 C:ARG164 4.3 8.0 1.0
CD1 C:TYR210 4.3 10.3 1.0
C C:CYS277 4.4 6.6 1.0
CB A:ALA279 4.4 5.8 1.0
CZ C:ARG164 4.4 9.6 1.0
CA C:CYS277 4.4 4.9 1.0
OE2 C:GLU214 4.6 21.5 1.0
N C:GLU214 4.7 7.6 1.0
CD C:GLU214 4.8 17.9 1.0
CG C:TYR210 4.9 4.9 1.0
CA C:ALA213 4.9 9.6 1.0
CE1 C:TYR210 4.9 8.7 1.0
CB C:TYR210 4.9 5.9 1.0
N C:PHE278 5.0 6.7 1.0

Arsenic binding site 6 out of 8 in 3s70

Go back to Arsenic Binding Sites List in 3s70
Arsenic binding site 6 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As4

b:13.0
occ:0.80
AS C:CAC4 0.0 13.0 0.8
C1 C:CAC4 2.0 7.7 0.8
C2 C:CAC4 2.0 10.3 0.8
SG C:CYS264 2.4 14.1 1.0
O D:VAL1 3.1 13.8 1.0
CB C:CYS264 3.2 17.6 1.0
CA C:CYS264 3.7 12.6 1.0
O C:HOH392 3.8 17.8 1.0
O D:HOH305 3.8 19.6 1.0
O C:PHE263 4.1 11.9 1.0
C D:VAL1 4.2 14.8 1.0
O D:HOH194 4.3 17.3 1.0
CG1 C:VAL261 4.3 6.8 1.0
CB D:VAL1 4.5 13.2 1.0
N C:LYS265 4.5 16.0 1.0
C C:CYS264 4.6 16.5 1.0
N C:CYS264 4.8 13.8 1.0
CA D:VAL1 4.8 12.1 1.0
C C:PHE263 4.9 12.4 1.0
N D:VAL1 5.0 11.8 1.0

Arsenic binding site 7 out of 8 in 3s70

Go back to Arsenic Binding Sites List in 3s70
Arsenic binding site 7 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As5

b:12.3
occ:0.80
AS C:CAC5 0.0 12.3 0.8
C2 C:CAC5 2.0 9.4 0.8
C1 C:CAC5 2.0 8.2 0.8
SG C:CYS68 2.4 13.5 1.0
CB C:CYS68 3.2 8.6 1.0
NH2 C:ARG71 3.8 8.1 1.0
OD2 C:ASP72 3.9 11.9 1.0
C C:CYS68 4.1 11.3 1.0
O C:HOH455 4.2 26.6 1.0
CA C:CYS68 4.2 8.3 1.0
O C:CYS68 4.3 7.3 1.0
N C:ALA69 4.5 8.5 1.0
O C:HOH395 4.5 15.8 1.0
CG C:ASP72 4.8 12.2 1.0
O C:HOH436 5.0 22.2 1.0
CZ C:ARG71 5.0 8.0 1.0

Arsenic binding site 8 out of 8 in 3s70

Go back to Arsenic Binding Sites List in 3s70
Arsenic binding site 8 out of 8 in the Crystal Structure of Active Caspase-6 Bound with Ac-Veid-Cho Solved By As-Sad


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 Solved By As-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As8

b:14.0
occ:0.50
AS C:CAC8 0.0 14.0 0.5
C1 C:CAC8 2.0 9.7 0.5
C2 C:CAC8 2.0 10.7 0.5
SG C:CYS87 2.5 12.8 1.0
CB C:CYS87 3.0 8.8 1.0
O C:HOH382 3.6 14.9 1.0
O C:HOH423 3.7 12.9 1.0
N C:CYS87 3.9 9.5 1.0
CA C:CYS87 4.0 9.5 1.0
OG1 C:THR75 4.2 8.7 1.0
O C:HOH637 4.2 33.4 1.0
O C:HOH351 4.4 22.1 1.0
O C:HOH548 4.7 35.4 1.0
CG2 C:THR75 4.7 8.7 1.0
CD C:ARG71 4.8 7.2 1.0
C C:LYS86 4.8 9.6 1.0

Reference:

X.Liu, H.Zhang, X.-J.Wang, L.-F.Li, X.-D.Su. Get Phases From Arsenic Anomalous Scattering: De Novo Sad Phasing of Two Protein Structures Crystallized in Cacodylate Buffer Plos One V. 6 24227 2011.
ISSN: ESSN 1932-6203
PubMed: 21912678
DOI: 10.1371/JOURNAL.PONE.0024227
Page generated: Tue Oct 27 16:51:40 2020

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