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Zinc in PDB 8cuc: Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna

Protein crystallography data

The structure of Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna, PDB code: 8cuc 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) 59.68 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.25, 70.51, 112.06, 90, 90, 90
R / Rfree (%) 20.2 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna (pdb code 8cuc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna, PDB code: 8cuc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8cuc

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Zinc binding site 1 out of 6 in the Crystal Structure Analysis of SALL4 Zinc Finger Domain 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 Analysis of SALL4 Zinc Finger Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:45.0
occ:1.00
 NE2 E:HIS920 2.1 32.9 1.0
NE2 E:HIS916 2.1 35.9 1.0
SG E:CYS903 2.3 37.7 1.0
SG E:CYS900 2.3 32.8 1.0
CD2 E:HIS920 2.9 37.0 1.0
CE1 E:HIS916 3.0 30.5 1.0
CD2 E:HIS916 3.1 30.5 1.0
CE1 E:HIS920 3.1 32.6 1.0
CB E:CYS900 3.2 33.3 1.0
CB E:CYS903 3.4 37.2 1.0
N E:CYS903 3.7 36.4 1.0
CG E:HIS920 4.1 36.1 1.0
ND1 E:HIS916 4.1 39.0 1.0
CA E:CYS903 4.1 40.5 1.0
ND1 E:HIS920 4.2 43.9 1.0
CG E:HIS916 4.2 34.6 1.0
CB E:ILE902 4.4 36.6 1.0
CA E:CYS900 4.6 33.3 1.0
CG2 E:ILE902 4.7 34.5 1.0
C E:ILE902 4.7 36.4 1.0
C E:CYS903 4.8 38.5 1.0
N E:GLY904 4.9 37.9 1.0
CA E:ILE902 4.9 35.0 1.0
N E:ILE902 4.9 34.5 1.0
C E:CYS900 5.0 34.2 1.0

Zinc binding site 2 out of 6 in 8cuc

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Zinc binding site 2 out of 6 in the Crystal Structure Analysis of SALL4 Zinc Finger Domain 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 Analysis of SALL4 Zinc Finger Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:53.0
occ:1.00
 NE2 F:HIS888 2.0 46.3 1.0
NE2 F:HIS892 2.0 42.2 1.0
SG F:CYS875 2.2 49.9 1.0
CB F:CYS875 2.4 61.9 1.0
SG F:CYS872 2.4 45.0 1.0
CD2 F:HIS892 2.9 40.5 1.0
CE1 F:HIS888 2.9 39.5 1.0
CD2 F:HIS888 2.9 39.6 1.0
CE1 F:HIS892 3.1 42.8 1.0
CB F:CYS872 3.3 45.9 1.0
CA F:CYS875 3.6 54.0 1.0
N F:CYS875 3.9 68.2 1.0
ND1 F:HIS888 4.0 40.0 1.0
CG F:HIS888 4.1 37.7 1.0
CG F:HIS892 4.1 44.0 1.0
ND1 F:HIS892 4.2 39.9 1.0
C F:CYS875 4.3 59.6 1.0
N F:GLY876 4.7 58.9 1.0
CA F:CYS872 4.8 51.8 1.0
O F:HOH1119 4.8 42.5 1.0
C F:ARG874 4.9 60.4 1.0
N F:LYS877 4.9 55.6 1.0
O F:CYS875 5.0 48.4 1.0
OG1 F:THR891 5.0 41.8 1.0
CB F:LYS877 5.0 47.0 1.0

Zinc binding site 3 out of 6 in 8cuc

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Zinc binding site 3 out of 6 in the Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna


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 SALL4 Zinc Finger Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:39.2
occ:1.00
 NE2 F:HIS916 2.0 30.4 1.0
NE2 F:HIS920 2.1 34.6 1.0
SG F:CYS903 2.3 29.2 1.0
SG F:CYS900 2.4 29.7 1.0
CD2 F:HIS920 3.0 30.7 1.0
CE1 F:HIS916 3.0 29.3 1.0
CD2 F:HIS916 3.0 31.2 1.0
CE1 F:HIS920 3.1 35.2 1.0
CB F:CYS900 3.3 30.5 1.0
CB F:CYS903 3.4 30.4 1.0
N F:CYS903 3.7 34.1 1.0
CA F:CYS903 4.1 35.5 1.0
ND1 F:HIS916 4.1 29.5 1.0
CG F:HIS920 4.2 37.6 1.0
CG F:HIS916 4.2 27.5 1.0
ND1 F:HIS920 4.2 36.8 1.0
O B:HOH132 4.4 41.1 1.0
CB F:ILE902 4.4 32.6 1.0
C F:ILE902 4.7 35.8 1.0
CA F:CYS900 4.7 29.4 1.0
C F:CYS903 4.7 41.3 1.0
N F:GLY904 4.8 30.2 1.0
CB F:ARG905 4.9 28.1 1.0
CG2 F:ILE902 4.9 33.5 1.0
N F:ARG905 4.9 28.6 1.0
CA F:ILE902 4.9 33.7 1.0
N F:ILE902 4.9 40.2 1.0

Zinc binding site 4 out of 6 in 8cuc

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Zinc binding site 4 out of 6 in the Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1001

b:43.2
occ:1.00
 NE2 G:HIS920 2.0 30.9 1.0
NE2 G:HIS916 2.0 31.0 1.0
SG G:CYS903 2.3 31.7 1.0
SG G:CYS900 2.3 31.5 1.0
CD2 G:HIS916 3.0 27.1 1.0
CE1 G:HIS920 3.0 35.2 1.0
CD2 G:HIS920 3.0 32.5 1.0
CE1 G:HIS916 3.0 29.1 1.0
CB G:CYS900 3.2 34.9 1.0
CB G:CYS903 3.3 33.0 1.0
N G:CYS903 3.6 33.2 1.0
CA G:CYS903 4.0 36.6 1.0
ND1 G:HIS920 4.1 34.1 1.0
ND1 G:HIS916 4.1 27.8 1.0
CG G:HIS916 4.2 27.1 1.0
CG G:HIS920 4.2 41.4 1.0
CB G:ILE902 4.4 35.5 1.0
C G:ILE902 4.6 33.5 1.0
CA G:CYS900 4.6 35.8 1.0
C G:CYS903 4.7 35.3 1.0
N G:GLY904 4.8 35.1 1.0
CA G:ILE902 4.9 39.0 1.0
N G:ILE902 4.9 37.0 1.0
CB G:ARG905 4.9 32.4 1.0
CG2 G:ILE902 5.0 31.8 1.0

Zinc binding site 5 out of 6 in 8cuc

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Zinc binding site 5 out of 6 in the Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1002

b:45.7
occ:1.00
 NE2 G:HIS892 2.0 39.0 1.0
NE2 G:HIS888 2.0 42.4 1.0
SG G:CYS875 2.2 41.1 1.0
SG G:CYS872 2.3 42.9 1.0
CD2 G:HIS892 2.9 34.3 1.0
CE1 G:HIS888 2.9 35.8 1.0
CE1 G:HIS892 3.1 34.7 1.0
CD2 G:HIS888 3.1 32.9 1.0
CB G:CYS872 3.3 44.4 1.0
CB G:CYS875 3.4 46.6 1.0
N G:CYS875 3.7 44.5 1.0
ND1 G:HIS888 4.0 40.0 1.0
CG G:HIS892 4.1 34.6 1.0
ND1 G:HIS892 4.1 40.4 1.0
CA G:CYS875 4.1 44.1 1.0
CG G:HIS888 4.2 36.2 1.0
CB G:ARG874 4.4 43.2 1.0
C G:ARG874 4.5 44.7 1.0
CA G:CYS872 4.7 46.8 1.0
O G:HOH1120 4.8 47.1 1.0
CA G:ARG874 4.9 45.4 1.0
OE2 G:GLU889 4.9 69.6 1.0
N G:ARG874 4.9 50.5 1.0
C G:CYS875 4.9 45.8 1.0
N G:GLY876 4.9 47.0 1.0
CD G:LYS877 4.9 49.8 1.0

Zinc binding site 6 out of 6 in 8cuc

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Zinc binding site 6 out of 6 in the Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1001

b:53.2
occ:1.00
 NE2 H:HIS920 2.1 45.9 1.0
NE2 H:HIS916 2.1 42.8 1.0
SG H:CYS903 2.3 43.2 1.0
SG H:CYS900 2.3 40.2 1.0
CE1 H:HIS916 3.0 47.3 1.0
CD2 H:HIS920 3.1 46.8 1.0
CE1 H:HIS920 3.1 51.8 1.0
CD2 H:HIS916 3.1 40.8 1.0
CB H:CYS903 3.3 46.5 1.0
CB H:CYS900 3.3 37.6 1.0
N H:CYS903 3.6 44.3 1.0
CA H:CYS903 4.0 43.5 1.0
ND1 H:HIS916 4.1 52.1 1.0
ND1 H:HIS920 4.2 60.4 1.0
CG H:HIS920 4.2 57.1 1.0
CG H:HIS916 4.2 47.2 1.0
CB H:ILE902 4.5 47.6 1.0
C H:ILE902 4.6 48.1 1.0
C H:CYS903 4.7 42.2 1.0
CA H:CYS900 4.7 36.6 1.0
N H:GLY904 4.8 42.4 1.0
CG2 H:ILE902 4.8 47.5 1.0
CA H:ILE902 5.0 42.4 1.0

Reference:

H.S.Seo, S.Dhe-Paganon. Crystal Structure Analysis of SALL4 Zinc Finger Domain in Complex with Dna To Be Published.
Page generated: Wed Oct 30 18:57:15 2024

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