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Zinc in PDB 6lae: Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna

Protein crystallography data

The structure of Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna, PDB code: 6lae was solved by F.M.Lian, X.Yang, Y.L.Jiang, F.Yang, C.Li, W.Yang, C.Qian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.70 / 2.81
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 69.112, 69.112, 63.938, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna (pdb code 6lae). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna, PDB code: 6lae:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6lae

Go back to Zinc Binding Sites List in 6lae
Zinc binding site 1 out of 2 in the Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:78.9
occ:1.00
SG A:CYS105 2.1 60.5 1.0
SG A:CYS129 2.1 51.9 1.0
SG A:CYS126 2.3 66.8 1.0
SG A:CYS108 2.6 54.8 1.0
CB A:CYS105 2.8 63.4 1.0
CB A:CYS129 3.0 71.0 1.0
CB A:CYS126 3.3 59.1 1.0
CB A:CYS108 3.5 81.0 1.0
N A:CYS126 3.6 64.6 1.0
N A:CYS108 3.7 79.8 1.0
O A:CYS126 3.8 62.3 1.0
CA A:CYS126 3.9 68.0 1.0
N A:CYS129 4.0 64.7 1.0
CA A:CYS129 4.1 77.3 1.0
CA A:CYS108 4.2 79.1 1.0
C A:CYS126 4.2 61.8 1.0
CA A:CYS105 4.3 57.8 1.0
CB A:GLU107 4.4 83.8 1.0
C A:THR125 4.6 73.0 1.0
C A:GLU107 4.7 92.1 1.0
N A:GLU107 4.8 73.8 1.0
CA A:GLU107 4.9 91.8 1.0
N A:GLY109 4.9 76.3 1.0
C A:CYS105 4.9 68.6 1.0
C A:CYS108 5.0 80.2 1.0
CA A:THR125 5.0 73.0 1.0

Zinc binding site 2 out of 2 in 6lae

Go back to Zinc Binding Sites List in 6lae
Zinc binding site 2 out of 2 in the Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Dna-Binding Domain of Human Xpa in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:72.9
occ:1.00
SG B:CYS126 2.1 56.0 1.0
SG B:CYS105 2.3 60.6 1.0
SG B:CYS108 2.4 54.1 1.0
SG B:CYS129 2.4 77.2 1.0
CB B:CYS105 2.8 66.8 1.0
CB B:CYS129 2.9 82.5 1.0
CB B:CYS126 3.3 49.2 1.0
CB B:CYS108 3.5 66.8 1.0
N B:CYS126 3.6 67.2 1.0
N B:CYS108 3.7 78.5 1.0
CA B:CYS126 3.9 53.3 1.0
O B:CYS126 3.9 48.4 1.0
N B:CYS129 4.0 68.0 1.0
CA B:CYS129 4.1 76.0 1.0
CA B:CYS108 4.2 66.2 1.0
C B:CYS126 4.2 49.5 1.0
CA B:CYS105 4.3 75.5 1.0
CB B:GLU107 4.3 96.0 1.0
C B:THR125 4.6 78.4 1.0
C B:GLU107 4.7 0.1 1.0
N B:GLU107 4.8 88.3 1.0
CA B:GLU107 4.8 95.7 1.0
N B:GLY109 4.9 81.4 1.0
C B:CYS105 4.9 84.4 1.0
C B:CYS108 5.0 80.3 1.0

Reference:

F.M.Lian, X.Yang, Y.L.Jiang, F.Yang, C.Li, W.Yang, C.Qian. New Structural Insights Into the Recognition of Undamaged Splayed-Arm Dna with A Single Pair of Non-Complementary Nucleotides By Human Nucleotide Excision Repair Protein Xpa. Int.J.Biol.Macromol. V. 148 466 2020.
ISSN: ISSN 0141-8130
PubMed: 31962067
DOI: 10.1016/J.IJBIOMAC.2020.01.169
Page generated: Wed Dec 16 12:14:04 2020

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