Zinc in PDB 8a4i: Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna

Protein crystallography data

The structure of Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna, PDB code: 8a4i was solved by J.A.Watson, R.Pantier, U.Jayachandran, K.Chhatbar, B.Alexander-Howden, V.Kruusvee, M.Prendecki, A.Bird, A.G.Cook, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.37 / 2.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.026, 66.111, 77.938, 73.04, 76.43, 76.14
R / Rfree (%) 24.7 / 25.4

Other elements in 8a4i:

The structure of Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna (pdb code 8a4i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna, PDB code: 8a4i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8a4i

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Zinc binding site 1 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich 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 SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1001

b:0.0
occ:1.00
NE2 I:HIS902 2.1 62.9 1.0
NE2 I:HIS898 2.1 59.0 1.0
SG I:CYS882 2.3 60.8 1.0
SG I:CYS885 2.3 79.9 1.0
CD2 I:HIS902 2.8 62.9 1.0
CE1 I:HIS902 2.9 62.9 1.0
CD2 I:HIS898 2.9 59.0 1.0
CE1 I:HIS898 3.1 59.0 1.0
CB I:CYS882 3.5 60.8 1.0
CB I:CYS885 3.6 79.9 1.0
CG I:HIS902 3.7 62.9 1.0
ND1 I:HIS902 3.7 62.9 1.0
N I:CYS885 3.8 71.5 1.0
CG I:HIS898 4.0 59.0 1.0
ND1 I:HIS898 4.0 59.0 1.0
CA I:CYS885 4.1 71.5 1.0
O I:CYS885 4.2 71.5 1.0
C I:CYS885 4.4 71.5 1.0
CB I:LYS887 4.7 66.0 1.0
O I:HIS898 4.8 55.8 1.0
C I:ARG884 4.8 71.8 1.0
CB I:ARG884 4.8 62.9 1.0
CA I:CYS882 4.9 67.0 1.0
N I:ARG884 5.0 71.8 1.0

Zinc binding site 2 out of 8 in 8a4i

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Zinc binding site 2 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich 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 SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1002

b:18.2
occ:1.00
NE2 I:HIS926 2.1 47.7 1.0
CE1 I:HIS930 2.1 56.1 1.0
NE2 I:HIS930 2.2 56.1 1.0
SG I:CYS910 2.3 44.4 1.0
SG I:CYS913 2.3 42.3 1.0
CD2 I:HIS926 2.6 47.7 1.0
CE1 I:HIS926 3.2 47.7 1.0
ND1 I:HIS930 3.4 56.1 1.0
CB I:CYS913 3.5 42.3 1.0
CB I:CYS910 3.6 44.4 1.0
CD2 I:HIS930 3.6 56.1 1.0
N I:CYS913 3.7 43.4 1.0
CG I:HIS926 3.8 47.7 1.0
ND1 I:HIS926 4.0 47.7 1.0
CA I:CYS913 4.1 43.4 1.0
CG I:HIS930 4.2 56.1 1.0
CB I:ILE912 4.5 44.5 1.0
C I:CYS913 4.6 43.4 1.0
O I:CYS913 4.7 43.4 1.0
O I:HIS926 4.8 48.5 1.0
C I:ILE912 4.8 43.5 1.0
OG1 I:THR929 4.9 46.8 1.0
CB I:ARG915 4.9 50.2 1.0
CD1 I:ILE912 4.9 44.5 1.0
CA I:CYS910 5.0 42.4 1.0

Zinc binding site 3 out of 8 in 8a4i

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Zinc binding site 3 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich 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 of SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1001

b:96.4
occ:1.00
NE2 J:HIS898 2.1 84.4 1.0
NE2 J:HIS902 2.1 91.8 1.0
SG J:CYS885 2.3 90.7 1.0
SG J:CYS882 2.3 94.0 1.0
CD2 J:HIS902 2.7 91.8 1.0
CD2 J:HIS898 2.9 84.4 1.0
CE1 J:HIS898 3.0 84.4 1.0
CB J:CYS882 3.1 94.0 1.0
CE1 J:HIS902 3.3 91.8 1.0
CB J:CYS885 3.8 90.7 1.0
CG J:HIS902 4.0 91.8 1.0
CG J:HIS898 4.0 84.4 1.0
ND1 J:HIS898 4.0 84.4 1.0
N J:CYS885 4.1 96.0 1.0
ND1 J:HIS902 4.2 91.8 1.0
CA J:CYS885 4.3 96.0 1.0
O J:CYS885 4.4 96.0 1.0
C J:CYS885 4.5 96.0 1.0
CA J:CYS882 4.6 96.1 1.0
CB J:LYS887 4.6 87.9 1.0
O J:HIS898 4.9 85.1 1.0
N J:LYS887 4.9 91.5 1.0

Zinc binding site 4 out of 8 in 8a4i

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Zinc binding site 4 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich 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 of SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1002

b:51.6
occ:1.00
NE2 J:HIS926 2.0 71.7 1.0
NE2 J:HIS930 2.1 67.6 1.0
SG J:CYS910 2.3 78.8 1.0
SG J:CYS913 2.3 72.5 1.0
CD2 J:HIS926 2.9 71.7 1.0
CE1 J:HIS930 2.9 67.6 1.0
CE1 J:HIS926 3.0 71.7 1.0
CB J:CYS913 3.1 72.5 1.0
N J:CYS913 3.2 77.8 1.0
CD2 J:HIS930 3.2 67.6 1.0
CB J:CYS910 3.4 78.8 1.0
CA J:CYS913 3.7 77.8 1.0
CB J:ILE912 3.8 64.7 1.0
CG J:HIS926 4.0 71.7 1.0
ND1 J:HIS926 4.0 71.7 1.0
ND1 J:HIS930 4.1 67.6 1.0
C J:ILE912 4.2 77.0 1.0
CG J:HIS930 4.3 67.6 1.0
CA J:ILE912 4.4 77.0 1.0
N J:ILE912 4.5 77.0 1.0
N J:GLY914 4.6 76.7 1.0
C J:CYS913 4.6 77.8 1.0
CA J:CYS910 4.7 76.5 1.0
C J:CYS910 5.0 76.5 1.0

Zinc binding site 5 out of 8 in 8a4i

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Zinc binding site 5 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich 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 of SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1001

b:21.1
occ:1.00
NE2 K:HIS926 2.1 91.4 1.0
NE2 K:HIS930 2.1 80.7 1.0
SG K:CYS913 2.3 82.4 1.0
SG K:CYS910 2.3 66.8 1.0
CD2 K:HIS930 2.8 82.5 1.0
CE1 K:HIS926 2.9 80.2 1.0
CD2 K:HIS926 3.2 75.5 1.0
CB K:CYS913 3.2 66.0 1.0
CE1 K:HIS930 3.3 81.3 1.0
CB K:CYS910 3.3 65.2 1.0
N K:CYS913 3.4 77.2 1.0
CA K:CYS913 3.9 79.2 1.0
CB K:ILE912 3.9 69.7 1.0
ND1 K:HIS926 4.0 74.3 1.0
CG K:HIS930 4.1 85.3 1.0
ND1 K:HIS930 4.2 86.0 1.0
CG K:HIS926 4.2 69.4 1.0
C K:ILE912 4.5 66.7 1.0
CA K:ILE912 4.6 68.2 1.0
N K:GLY914 4.6 67.9 1.0
C K:CYS913 4.7 61.7 1.0
N K:ILE912 4.7 63.1 1.0
CA K:CYS910 4.7 56.2 1.0

Zinc binding site 6 out of 8 in 8a4i

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Zinc binding site 6 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich 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 of SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1002

b:92.0
occ:1.00
NE2 K:HIS898 2.0 104.3 1.0
NE2 K:HIS902 2.1 102.2 1.0
SG K:CYS885 2.3 122.7 1.0
SG K:CYS882 2.3 131.2 1.0
CD2 K:HIS902 3.0 102.2 1.0
CE1 K:HIS898 3.0 104.3 1.0
CD2 K:HIS898 3.0 104.3 1.0
CE1 K:HIS902 3.1 102.2 1.0
CB K:CYS882 3.5 131.2 1.0
CB K:CYS885 3.5 122.7 1.0
N K:CYS885 3.7 128.4 1.0
CA K:CYS885 4.1 128.4 1.0
ND1 K:HIS898 4.1 104.3 1.0
CG K:HIS902 4.1 102.2 1.0
CG K:HIS898 4.1 104.3 1.0
ND1 K:HIS902 4.1 102.2 1.0
CB K:ARG884 4.5 115.4 1.0
C K:CYS885 4.5 128.4 1.0
O K:CYS885 4.5 128.4 1.0
C K:ARG884 4.6 121.5 1.0
CB K:LYS887 4.7 123.0 1.0
N K:ARG884 4.8 121.5 1.0
CA K:ARG884 4.9 121.5 1.0
CA K:CYS882 4.9 126.1 1.0

Zinc binding site 7 out of 8 in 8a4i

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Zinc binding site 7 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:50.6
occ:1.00
NE2 L:HIS898 2.0 78.6 1.0
NE2 L:HIS902 2.1 79.2 1.0
SG L:CYS882 2.3 81.9 1.0
SG L:CYS885 2.3 95.7 1.0
CD2 L:HIS902 2.9 73.9 1.0
CE1 L:HIS898 2.9 66.2 1.0
CD2 L:HIS898 3.0 66.2 1.0
CB L:CYS882 3.2 79.5 1.0
CE1 L:HIS902 3.2 72.5 1.0
CB L:CYS885 3.4 88.7 1.0
N L:CYS885 3.4 92.2 1.0
CA L:CYS885 3.9 86.3 1.0
ND1 L:HIS898 4.0 62.0 1.0
CG L:HIS898 4.0 62.0 1.0
CG L:HIS902 4.1 69.8 1.0
ND1 L:HIS902 4.2 71.6 1.0
C L:CYS885 4.3 87.9 1.0
O L:CYS885 4.3 92.7 1.0
CB L:ARG884 4.4 81.9 1.0
C L:ARG884 4.4 86.1 1.0
CA L:CYS882 4.6 71.0 1.0
N L:ARG884 4.6 85.2 1.0
CA L:ARG884 4.7 91.0 1.0
CB L:LYS887 5.0 77.4 1.0

Zinc binding site 8 out of 8 in 8a4i

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Zinc binding site 8 out of 8 in the Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of SALL4 Zinc Finger Cluster 4 with at-Rich Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1002

b:16.3
occ:1.00
NE2 L:HIS930 2.1 58.1 1.0
NE2 L:HIS926 2.1 79.0 1.0
SG L:CYS910 2.3 48.3 1.0
SG L:CYS913 2.3 60.7 1.0
CE1 L:HIS930 3.0 58.8 1.0
CD2 L:HIS926 3.0 63.2 1.0
CE1 L:HIS926 3.1 67.8 1.0
CD2 L:HIS930 3.2 60.0 1.0
CB L:CYS910 3.2 46.8 1.0
CB L:CYS913 3.5 44.3 1.0
N L:CYS913 3.9 62.0 1.0
ND1 L:HIS930 4.1 63.5 1.0
CG L:HIS926 4.2 57.0 1.0
ND1 L:HIS926 4.2 61.9 1.0
CG L:HIS930 4.3 62.8 1.0
CA L:CYS913 4.3 64.0 1.0
CB L:ILE912 4.5 49.2 1.0
CB L:ARG915 4.6 56.1 1.0
CA L:CYS910 4.7 44.0 1.0
C L:ILE912 5.0 53.7 1.0
CG2 L:ILE912 5.0 49.2 1.0

Reference:

J.A.Watson, R.Pantier, U.Jayachandran, K.Chhatbar, B.Alexander-Howden, V.Kruusvee, M.Prendecki, A.Bird, A.G.Cook. Structural Analysis of SALL4 Zinc-Finger Domain Reveals A Link Between at-Rich Dna Binding and Okihiro Syndrome To Be Published.
Page generated: Sat Apr 8 07:28:56 2023

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