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Samarium in PDB 1bix: The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites

Enzymatic activity of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites

All present enzymatic activity of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites:
4.2.99.18;

Protein crystallography data

The structure of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites, PDB code: 1bix was solved by M.A.Gorman, S.Morera, D.G.Rothwell, E.De La Fortelle, C.D.Mol, J.A.Tainer, I.D.Hickson, P.S.Freemont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.260, 44.701, 78.778, 90.00, 103.45, 90.00
R / Rfree (%) 18.4 / 26.9

Other elements in 1bix:

The structure of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites also contains other interesting chemical elements:

Platinum (Pt) 1 atom

Samarium Binding Sites:

The binding sites of Samarium atom in the The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites (pdb code 1bix). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 4 binding sites of Samarium where determined in the The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites, PDB code: 1bix:
Jump to Samarium binding site number: 1; 2; 3; 4;

Samarium binding site 1 out of 4 in 1bix

Go back to Samarium Binding Sites List in 1bix
Samarium binding site 1 out of 4 in the The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm400

b:24.6
occ:1.00
 OE1 A:GLU217 2.3 16.5 1.0
OE2 A:GLU217 2.7 14.9 1.0
OE1 A:GLU216 2.7 20.7 1.0
CD A:GLU217 2.9 15.1 1.0
OE2 A:GLU216 3.0 19.6 1.0
CD A:GLU216 3.2 19.4 1.0
NH2 A:ARG237 4.2 12.7 1.0
CG A:GLU217 4.4 14.5 1.0
O A:HOH525 4.5 12.7 1.0
CG A:GLU216 4.7 16.8 1.0
O A:HOH505 4.8 19.2 1.0
O A:HOH554 4.9 26.0 1.0
N A:GLU217 5.0 14.9 1.0

Samarium binding site 2 out of 4 in 1bix

Go back to Samarium Binding Sites List in 1bix
Samarium binding site 2 out of 4 in the The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm401

b:24.2
occ:1.00
 OE2 A:GLU96 2.3 25.0 1.0
OD1 A:ASP70 2.5 18.3 1.0
OE1 A:GLU96 2.8 24.0 1.0
O A:HOH563 2.8 13.8 1.0
CD A:GLU96 2.9 20.8 1.0
CG A:ASP70 3.5 16.0 1.0
O A:HOH644 4.1 55.3 1.0
CB A:ASP70 4.3 14.4 1.0
O A:HOH649 4.3 19.7 1.0
OD2 A:ASP70 4.3 14.6 1.0
CG A:GLU96 4.4 19.1 1.0
OD2 A:ASP308 4.4 15.7 1.0
OD1 A:ASP308 4.5 15.1 1.0
NZ A:LYS98 4.5 17.9 1.0
CA A:ASP70 4.5 15.1 1.0
OH A:TYR171 4.5 11.5 1.0
OD1 A:ASN68 4.7 13.6 1.0
CG A:ASP308 4.9 13.1 1.0
ND2 A:ASN68 5.0 11.9 1.0

Samarium binding site 3 out of 4 in 1bix

Go back to Samarium Binding Sites List in 1bix
Samarium binding site 3 out of 4 in the The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm402

b:43.3
occ:1.00
 OD1 A:ASP148 2.4 32.4 1.0
OE2 A:GLU150 2.6 33.0 1.0
OE1 A:GLU150 2.7 34.4 1.0
CD A:GLU150 3.0 32.8 1.0
CG A:ASP148 3.4 33.1 1.0
OD2 A:ASP148 3.7 33.5 1.0
CG A:GLU150 4.6 30.9 1.0
CB A:ASP148 4.7 32.6 1.0
CA A:ASP148 4.9 31.9 1.0

Samarium binding site 4 out of 4 in 1bix

Go back to Samarium Binding Sites List in 1bix
Samarium binding site 4 out of 4 in the The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm403

b:66.8
occ:1.00
 OXT A:LEU318 2.6 26.0 1.0
O A:LEU318 2.6 26.7 1.0
C A:LEU318 2.9 23.9 1.0
O A:HOH590 3.5 49.5 1.0
CA A:LEU318 4.5 22.4 1.0
CE A:LYS58 4.8 22.6 1.0

Reference:

M.A.Gorman, S.Morera, D.G.Rothwell, E.De La Fortelle, C.D.Mol, J.A.Tainer, I.D.Hickson, P.S.Freemont. The Crystal Structure of the Human Dna Repair Endonuclease HAP1 Suggests the Recognition of Extra-Helical Deoxyribose at Dna Abasic Sites. Embo J. V. 16 6548 1997.
ISSN: ISSN 0261-4189
PubMed: 9351835
DOI: 10.1093/EMBOJ/16.21.6548
Page generated: Thu Oct 10 13:47:27 2024

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