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Mercury in PDB 3w1b: Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)

Enzymatic activity of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)

All present enzymatic activity of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative):
6.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative), PDB code: 3w1b was solved by T.Ochi, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.82 / 2.40
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.630, 105.210, 122.040, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.5

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) (pdb code 3w1b). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative), PDB code: 3w1b:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Mercury binding site 1 out of 9 in 3w1b

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Mercury binding site 1 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg712

b:69.3
occ:0.61
 O A:HOH1016 2.8 34.1 1.0
SG A:CYS137 2.9 62.4 1.0
CB A:CYS137 3.1 36.8 1.0
NE2 A:GLN139 3.2 29.9 1.0
CD A:GLN139 3.5 38.4 1.0
OE1 A:GLN139 3.6 46.6 1.0
NE2 A:GLN183 4.0 27.9 1.0
CD2 A:LEU97 4.1 39.0 1.0
CA A:CYS137 4.1 36.6 1.0
CG A:GLN139 4.4 36.9 1.0
O A:ILE175 4.6 36.1 1.0
CD2 A:LEU133 4.6 26.8 1.0
CG2 A:ILE175 4.9 28.8 1.0

Mercury binding site 2 out of 9 in 3w1b

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Mercury binding site 2 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg713

b:69.2
occ:0.50
 SG A:CYS225 2.7 38.1 1.0
O A:LEU221 3.3 25.8 1.0
N A:CYS225 3.4 21.8 1.0
CB A:CYS225 3.5 20.3 1.0
CG A:MET68 3.5 26.2 1.0
CE A:MET68 3.5 31.8 1.0
CA A:CYS225 3.5 21.4 1.0
CG1 A:VAL224 3.8 22.9 1.0
CB A:MET68 4.0 17.4 1.0
C A:VAL224 4.1 27.1 1.0
CB A:VAL224 4.1 30.9 1.0
CE2 A:PHE207 4.1 27.2 1.0
CZ A:PHE207 4.2 21.6 1.0
C A:LEU221 4.2 22.2 1.0
SD A:MET68 4.3 35.0 1.0
CD2 A:LEU221 4.4 23.7 1.0
CA A:LEU221 4.4 20.1 1.0
CD2 A:PHE207 4.5 30.5 1.0
CB A:LEU221 4.6 23.2 1.0
CE1 A:PHE207 4.6 21.0 1.0
O A:VAL224 4.6 29.6 1.0
CA A:VAL224 4.7 23.3 1.0
CG A:PHE207 4.9 31.7 1.0
CD1 A:PHE207 4.9 28.2 1.0

Mercury binding site 3 out of 9 in 3w1b

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Mercury binding site 3 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg714

b:58.3
occ:0.81
 SG A:CYS363 2.6 39.1 1.0
SG A:CYS365 2.6 41.1 1.0
CZ A:PHE342 3.3 27.4 1.0
N A:CYS365 3.4 25.3 1.0
CB A:CYS363 3.4 23.6 1.0
CB A:CYS365 3.5 43.9 1.0
CA A:CYS365 3.5 23.8 1.0
C A:TYR364 3.6 26.4 1.0
CE2 A:PHE342 3.6 24.6 1.0
OE1 A:GLU401 3.7 44.7 1.0
O A:TYR364 3.7 27.1 1.0
O A:CYS363 3.7 22.6 1.0
C A:CYS363 3.7 23.0 1.0
CD A:GLU401 3.9 39.8 1.0
CB A:GLU401 4.0 31.5 1.0
N A:TYR364 4.1 25.9 1.0
CG A:MET333 4.1 27.0 1.0
CA A:CYS363 4.2 23.4 1.0
CE1 A:PHE342 4.3 32.9 1.0
CG A:GLU401 4.3 34.3 1.0
CA A:TYR364 4.4 26.9 1.0
CB A:MET333 4.4 27.9 1.0
OE2 A:GLU401 4.5 47.6 1.0
N A:GLU401 4.7 30.7 1.0
CD2 A:PHE342 4.7 26.0 1.0
CA A:GLU401 5.0 31.2 1.0

Mercury binding site 4 out of 9 in 3w1b

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Mercury binding site 4 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg715

b:70.4
occ:0.40
 O A:CYS510 2.7 30.9 1.0
CB A:CYS510 3.0 28.1 1.0
CE A:MET343 3.2 27.4 1.0
C A:CYS510 3.5 29.7 1.0
SD A:MET343 3.6 33.8 1.0
SG A:CYS510 3.6 62.8 1.0
CA A:CYS510 3.8 41.2 1.0
CB A:TYR516 3.9 29.8 1.0
OG1 A:THR339 3.9 28.9 1.0
OG1 A:THR341 4.1 41.6 1.0
ND2 A:ASN336 4.1 29.0 1.0
O A:MET512 4.3 32.2 1.0
CD1 A:TYR516 4.3 33.2 1.0
CG A:TYR516 4.4 32.5 1.0
CG2 A:THR339 4.4 31.2 1.0
C A:MET512 4.5 31.2 1.0
CB A:THR339 4.6 34.5 1.0
CA A:LYS513 4.6 35.6 1.0
N A:THR511 4.6 37.9 1.0
N A:LYS513 4.7 33.3 1.0
N A:MET512 4.7 31.6 1.0
CG A:ASN336 4.9 35.5 1.0
O A:HOH849 4.9 37.1 1.0
CA A:TYR516 5.0 33.6 1.0
CB A:ASN336 5.0 27.3 1.0

Mercury binding site 5 out of 9 in 3w1b

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Mercury binding site 5 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg716

b:65.4
occ:0.49
 SG A:CYS510 3.0 62.8 1.0
HG A:HG720 3.1 0.1 0.4
CB A:CYS510 3.2 28.1 1.0
SD A:MET479 3.3 80.1 1.0
N A:CYS510 3.5 27.5 1.0
CB A:MET479 3.7 46.1 1.0
CG A:MET479 3.7 46.9 1.0
CA A:CYS510 4.0 41.2 1.0
O A:SER508 4.2 30.9 1.0
CE A:MET479 4.2 45.8 1.0
O A:MET480 4.4 41.5 1.0
C A:GLY509 4.5 37.2 1.0
CA A:GLY509 4.8 35.6 1.0
CG2 A:THR339 4.9 31.2 1.0
CB A:THR339 5.0 34.5 1.0

Mercury binding site 6 out of 9 in 3w1b

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Mercury binding site 6 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg717

b:79.6
occ:0.58
 SG A:CYS552 2.9 50.5 1.0
OD1 A:ASN553 3.0 43.9 1.0
CB A:CYS552 3.2 42.7 1.0
O A:CYS552 3.6 39.4 1.0
C A:CYS552 3.7 38.0 1.0
CG A:ASN553 3.9 35.6 1.0
CA A:CYS552 4.1 39.1 1.0
N A:ASN553 4.1 34.3 1.0
ND2 A:ASN553 4.5 32.5 1.0
CA A:ASN553 4.5 36.4 1.0
CB A:ASN553 4.8 35.4 1.0

Mercury binding site 7 out of 9 in 3w1b

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Mercury binding site 7 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg718

b:0.8
occ:0.59
 SG A:CYS540 3.0 44.1 1.0
O A:ILE538 3.2 53.9 1.0
CB A:CYS540 3.3 35.0 1.0
N A:CYS540 3.5 47.9 1.0
CZ A:PHE529 3.6 40.6 1.0
CE1 A:PHE529 3.6 38.2 1.0
CA A:CYS540 4.0 31.7 1.0
CB A:PRO534 4.1 58.5 1.0
C A:ILE538 4.2 47.4 1.0
C A:LEU539 4.2 32.9 1.0
CA A:LEU539 4.3 34.4 1.0
O A:HOH1014 4.5 47.9 1.0
N A:LEU539 4.6 44.2 1.0
NZ A:LYS544 4.8 37.5 1.0
CG A:PRO534 4.9 58.5 1.0
CE2 A:PHE529 4.9 35.7 1.0
CD1 A:PHE529 4.9 38.6 1.0
CD A:LYS544 5.0 36.7 1.0

Mercury binding site 8 out of 9 in 3w1b

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Mercury binding site 8 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg719

b:75.1
occ:0.80
 SG A:CYS574 2.7 42.4 1.0
NH1 A:ARG603 3.3 83.2 1.0
CB A:CYS574 3.5 45.3 1.0
CD2 A:LEU599 3.5 39.0 1.0
O A:THR572 3.6 40.0 1.0
CZ A:ARG603 3.7 83.2 1.0
CG A:LEU599 3.9 46.9 1.0
O A:HOH876 3.9 46.5 1.0
NE A:ARG603 4.0 82.0 1.0
CB A:THR572 4.0 36.3 1.0
CD A:ARG603 4.1 81.2 1.0
OG1 A:THR572 4.3 34.7 1.0
NH2 A:ARG603 4.3 80.3 1.0
C A:THR572 4.4 38.1 1.0
N A:CYS574 4.6 36.7 1.0
CD1 A:LEU599 4.6 47.4 1.0
CA A:CYS574 4.6 43.5 1.0
CG2 A:ILE564 4.7 41.2 1.0
CA A:THR572 4.8 36.9 1.0
CG A:ARG603 5.0 82.5 1.0

Mercury binding site 9 out of 9 in 3w1b

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Mercury binding site 9 out of 9 in the Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of Human Dna Ligase IV-Artemis Complex (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg720

b:0.1
occ:0.41
 SG A:CYS510 2.9 62.8 1.0
HG A:HG716 3.1 65.4 0.5
O A:SER508 3.3 30.9 1.0
O A:LEU515 3.5 27.1 1.0
C A:LEU515 4.0 25.7 1.0
CB A:CYS510 4.1 28.1 1.0
N A:TYR516 4.3 26.6 1.0
CA A:TYR516 4.3 33.6 1.0
N A:CYS510 4.3 27.5 1.0
CA A:CYS510 4.4 41.2 1.0
O A:MET480 4.4 41.5 1.0
CG A:MET479 4.5 46.9 1.0
C A:SER508 4.5 37.0 1.0
CB A:LEU515 4.6 26.2 1.0
CB A:MET479 4.8 46.1 1.0
C A:GLY509 4.9 37.2 1.0
SD A:MET479 4.9 80.1 1.0
CA A:LEU515 4.9 31.8 1.0
CB A:SER508 4.9 38.0 1.0

Reference:

T.Ochi, X.Gu, T.L.Blundell. Structure of the Catalytic Region of Dna Ligase IV in Complex with An Artemis Fragment Sheds Light on Double-Strand Break Repair Structure V. 21 672 2013.
ISSN: ISSN 0969-2126
PubMed: 23523427
DOI: 10.1016/J.STR.2013.02.014
Page generated: Sun Dec 13 19:10:29 2020

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