Zinc in PDB 6u9q: Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex

Protein crystallography data

The structure of Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex, PDB code: 6u9q was solved by H.-S.Seo, S.Dhe-Paganon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.56 / 1.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.000, 60.160, 75.790, 90.00, 129.73, 90.00
R / Rfree (%) 17.5 / 19.5

Other elements in 6u9q:

The structure of Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex (pdb code 6u9q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex, PDB code: 6u9q:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6u9q

Go back to Zinc Binding Sites List in 6u9q
Zinc binding site 1 out of 3 in the Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:40.6
occ:1.00
NE2 A:HIS764 2.0 44.2 1.0
NE2 A:HIS760 2.1 40.7 1.0
SG A:CYS744 2.3 41.5 1.0
SG A:CYS747 2.3 47.3 1.0
CD2 A:HIS764 3.0 39.4 1.0
CD2 A:HIS760 3.0 39.8 1.0
CE1 A:HIS764 3.1 55.0 1.0
CE1 A:HIS760 3.1 46.5 1.0
CB A:CYS744 3.2 43.0 1.0
CB A:CYS747 3.3 48.1 1.0
N A:CYS747 3.7 44.9 1.0
CA A:CYS747 4.0 47.9 1.0
CG A:HIS764 4.1 42.6 1.0
ND1 A:HIS764 4.1 41.5 1.0
CG A:HIS760 4.2 40.9 1.0
ND1 A:HIS760 4.2 39.5 1.0
CB A:TYR746 4.4 41.5 1.0
C A:TYR746 4.5 49.3 1.0
O A:HOH1162 4.6 68.8 1.0
CA A:CYS744 4.6 43.7 1.0
C A:CYS747 4.7 54.5 1.0
CB A:LYS749 4.8 48.7 1.0
N A:TYR746 4.8 43.1 1.0
CA A:TYR746 4.8 47.5 1.0
N A:GLY748 4.9 50.0 1.0
N A:LYS749 5.0 48.5 1.0

Zinc binding site 2 out of 3 in 6u9q

Go back to Zinc Binding Sites List in 6u9q
Zinc binding site 2 out of 3 in the Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:36.1
occ:1.00
NE2 A:HIS792 2.0 33.2 1.0
NE2 A:HIS788 2.1 34.8 1.0
SG A:CYS775 2.3 33.4 1.0
SG A:CYS772 2.3 34.3 1.0
CD2 A:HIS792 2.9 34.3 1.0
CD2 A:HIS788 3.0 37.8 1.0
CE1 A:HIS788 3.1 34.9 1.0
CE1 A:HIS792 3.1 37.1 1.0
CB A:CYS772 3.2 33.3 1.0
CB A:CYS775 3.3 35.2 1.0
N A:CYS775 3.6 35.9 1.0
CA A:CYS775 4.0 37.1 1.0
C A:LEU774 4.0 39.5 1.0
CG A:HIS792 4.1 36.1 1.0
CB A:TYR777 4.2 32.4 1.0
ND1 A:HIS792 4.2 35.8 1.0
ND1 A:HIS788 4.2 35.3 1.0
CG A:HIS788 4.2 34.0 1.0
CB A:LEU774 4.3 36.0 1.0
O A:LEU774 4.4 36.1 1.0
C A:CYS775 4.4 35.2 1.0
CA A:LEU774 4.5 35.7 1.0
N A:LEU774 4.6 33.7 1.0
O A:CYS775 4.6 36.7 1.0
CA A:CYS772 4.6 35.2 1.0
O A:HOH1163 4.7 48.2 1.0
N A:TYR777 4.9 33.6 1.0

Zinc binding site 3 out of 3 in 6u9q

Go back to Zinc Binding Sites List in 6u9q
Zinc binding site 3 out of 3 in the Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Dna-BCL11A Znf Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:43.6
occ:1.00
NE2 A:HIS818 2.0 44.2 1.0
NE2 A:HIS823 2.1 51.2 1.0
SG A:CYS802 2.3 49.8 1.0
SG A:CYS805 2.3 39.7 1.0
CD2 A:HIS823 2.9 52.5 1.0
CE1 A:HIS818 3.0 44.7 1.0
CD2 A:HIS818 3.1 45.8 1.0
CB A:CYS802 3.2 53.0 1.0
CE1 A:HIS823 3.2 48.9 1.0
CB A:CYS805 3.3 40.2 1.0
N A:CYS805 3.7 43.9 1.0
CA A:CYS805 4.0 44.8 1.0
CG A:HIS823 4.1 52.4 1.0
ND1 A:HIS818 4.1 41.8 1.0
CG A:HIS818 4.2 44.3 1.0
ND1 A:HIS823 4.2 52.3 1.0
CB A:ILE804 4.6 50.5 1.0
CA A:CYS802 4.6 51.4 1.0
C A:CYS805 4.7 39.5 1.0
C A:ILE804 4.8 47.8 1.0
CB A:MET807 4.8 37.9 1.0
SD A:MET819 4.8 70.8 1.0
N A:LYS806 4.9 43.1 1.0

Reference:

H.-S.Seo, S.Dhe-Paganon. Crystal Structure Analysis of TAF1 Bromodomain To Be Published.
Page generated: Wed Dec 16 12:58:00 2020

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