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Mercury in PDB 3i34: Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf

Enzymatic activity of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf

All present enzymatic activity of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf:
3.4.21.64;

Protein crystallography data

The structure of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf, PDB code: 3i34 was solved by E.Pechkova, S.K.Tripathi, R.Ravelli, S.Mcsweeney, C.Nicolini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.99 / 1.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.865, 67.865, 102.335, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 22

Other elements in 3i34:

The structure of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf (pdb code 3i34). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 3 binding sites of Mercury where determined in the Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf, PDB code: 3i34:
Jump to Mercury binding site number: 1; 2; 3;

Mercury binding site 1 out of 3 in 3i34

Go back to Mercury Binding Sites List in 3i34
Mercury binding site 1 out of 3 in the Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg280

b:0.0
occ:1.00
 ND1 X:HIS69 2.4 12.8 1.0
O X:HIS69 2.7 3.9 1.0
CE X:MET225 2.9 7.3 1.0
CA X:HIS69 3.0 4.8 1.0
C X:HIS69 3.2 3.8 1.0
CD1 X:ILE220 3.2 6.8 1.0
CG X:HIS69 3.3 11.7 1.0
CB X:HIS72 3.3 3.7 1.0
CE1 X:HIS69 3.4 14.3 1.0
CB X:HIS69 3.5 7.2 1.0
SG X:CYS73 3.6 6.5 1.0
O X:HOH610 3.9 91.7 1.0
CG X:HIS72 3.9 3.8 1.0
ND1 X:HIS72 4.0 4.3 1.0
N X:CYS73 4.1 3.0 1.0
OG X:SER224 4.1 11.2 0.7
N X:HIS69 4.3 4.8 1.0
SD X:MET225 4.4 6.4 1.0
CG1 X:ILE220 4.4 6.4 1.0
CA X:HIS72 4.4 3.1 1.0
CZ3 X:TRP212 4.5 4.7 1.0
CD2 X:HIS69 4.5 13.2 1.0
N X:GLY70 4.5 3.7 1.0
O X:GLY68 4.5 4.2 1.0
NE2 X:HIS69 4.5 14.0 1.0
C X:HIS72 4.6 3.1 1.0
N X:HIS72 4.7 3.0 1.0
CB X:CYS73 4.8 3.8 1.0
C X:GLY68 4.8 4.6 1.0
O X:HOH562 4.8 16.5 1.0
CA X:CYS73 4.9 3.5 1.0
HG X:HG282 5.0 16.6 0.2
CD2 X:HIS72 5.0 3.5 1.0

Mercury binding site 2 out of 3 in 3i34

Go back to Mercury Binding Sites List in 3i34
Mercury binding site 2 out of 3 in the Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg282

b:0.0
occ:0.30
 HG X:HG282 0.0 0.0 0.3
HG X:HG282 1.1 16.6 0.2
OG1 X:THR76 2.4 3.4 1.0
ND1 X:HIS72 3.1 4.3 1.0
CE1 X:HIS72 3.2 4.2 1.0
CB X:THR76 3.3 3.4 1.0
CG X:MET225 3.3 5.3 1.0
CG2 X:ILE208 3.4 4.4 1.0
CB X:MET225 3.5 4.9 1.0
CA X:MET225 3.5 4.4 1.0
O X:MET225 3.8 3.9 1.0
CG2 X:THR76 3.9 3.5 1.0
O X:HIS72 3.9 3.1 1.0
CG X:PRO228 4.1 3.8 1.0
CB X:ILE208 4.2 4.1 1.0
C X:MET225 4.2 4.0 1.0
CE X:MET225 4.2 7.3 1.0
CG X:HIS72 4.4 3.8 1.0
C X:HIS72 4.4 3.1 1.0
CB X:SER210 4.4 3.7 1.0
CA X:CYS73 4.5 3.5 1.0
NE2 X:HIS72 4.5 4.1 1.0
O X:HOH329 4.6 4.1 1.0
SD X:MET225 4.6 6.4 1.0
N X:CYS73 4.7 3.0 1.0
CA X:THR76 4.7 3.4 1.0
N X:MET225 4.8 4.6 1.0
OG X:SER210 4.8 3.9 1.0
O X:SER224 4.8 4.5 1.0
CG1 X:ILE208 4.9 4.1 1.0
N X:THR76 4.9 2.6 1.0
NE2 X:HIS229 5.0 4.9 1.0

Mercury binding site 3 out of 3 in 3i34

Go back to Mercury Binding Sites List in 3i34
Mercury binding site 3 out of 3 in the Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline at Esrf within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg282

b:16.6
occ:0.25
 HG X:HG282 0.0 16.6 0.2
HG X:HG282 1.1 0.0 0.3
OG1 X:THR76 2.9 3.4 1.0
ND1 X:HIS72 2.9 4.3 1.0
O X:HIS72 3.5 3.1 1.0
CE1 X:HIS72 3.5 4.2 1.0
CA X:CYS73 3.5 3.5 1.0
CA X:MET225 3.5 4.4 1.0
CG X:MET225 3.5 5.3 1.0
CB X:THR76 3.6 3.4 1.0
CE X:MET225 3.6 7.3 1.0
CG X:PRO228 3.7 3.8 1.0
C X:HIS72 3.7 3.1 1.0
N X:CYS73 3.7 3.0 1.0
CB X:MET225 3.8 4.9 1.0
O X:MET225 4.1 3.9 1.0
CG X:HIS72 4.1 3.8 1.0
O X:SER224 4.2 4.5 1.0
SG X:CYS73 4.2 6.5 1.0
CG2 X:THR76 4.3 3.5 1.0
C X:MET225 4.3 4.0 1.0
CB X:CYS73 4.4 3.8 1.0
C X:CYS73 4.4 2.9 1.0
O X:CYS73 4.5 3.1 1.0
SD X:MET225 4.5 6.4 1.0
CG2 X:ILE208 4.5 4.4 1.0
N X:MET225 4.5 4.6 1.0
CB X:HIS72 4.6 3.7 1.0
C X:SER224 4.7 5.1 1.0
CD X:PRO228 4.7 3.5 1.0
NE2 X:HIS72 4.7 4.1 1.0
CB X:PRO228 4.7 3.7 1.0
CB X:SER210 4.8 3.7 1.0
CA X:HIS72 4.8 3.1 1.0
CA X:THR76 4.8 3.4 1.0
N X:THR76 4.9 2.6 1.0
OG X:SER210 5.0 3.9 1.0
HG X:HG280 5.0 0.0 1.0

Reference:

E.Pechkova, S.K.Tripathi, R.Ravelli, S.Mcsweeney, C.Nicolini. Radiation Damage Study of Proteinase K at ID14-2 Beamline at Esrf To Be Published.
Page generated: Wed Oct 28 18:42:38 2020

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