Zinc in PDB 7y3i: Structure of Dna Bound SALL4

Protein crystallography data

The structure of Structure of Dna Bound SALL4, PDB code: 7y3i was solved by W.Ru, C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.13 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.975, 69.197, 110.295, 90, 90, 90
R / Rfree (%) 19.4 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Dna Bound SALL4 (pdb code 7y3i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Dna Bound SALL4, PDB code: 7y3i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7y3i

Go back to Zinc Binding Sites List in 7y3i
Zinc binding site 1 out of 6 in the Structure of Dna Bound SALL4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Dna Bound SALL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:30.4
occ:1.00
NE2 A:HIS892 1.9 45.5 1.0
NE2 A:HIS888 2.0 39.0 1.0
SG A:CYS875 2.2 37.6 1.0
SG A:CYS872 2.3 40.2 1.0
CD2 A:HIS892 2.8 43.6 1.0
CE1 A:HIS888 3.0 35.1 1.0
CE1 A:HIS892 3.0 43.4 1.0
CD2 A:HIS888 3.0 34.8 1.0
CB A:CYS872 3.2 37.8 1.0
CB A:CYS875 3.2 33.2 1.0
N A:CYS875 3.7 32.4 1.0
CG A:HIS892 4.0 42.7 1.0
CA A:CYS875 4.0 31.7 1.0
ND1 A:HIS892 4.1 41.8 1.0
ND1 A:HIS888 4.1 34.9 1.0
CG A:HIS888 4.2 32.8 1.0
CB A:ARG874 4.4 42.3 1.0
C A:ARG874 4.5 37.3 1.0
CA A:CYS872 4.6 37.2 1.0
C A:CYS875 4.7 32.5 1.0
CA A:ARG874 4.8 39.4 1.0
N A:ARG874 4.8 37.8 1.0
N A:GLY876 4.9 33.0 1.0
OG1 A:THR891 4.9 37.9 1.0

Zinc binding site 2 out of 6 in 7y3i

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Zinc binding site 2 out of 6 in the Structure of Dna Bound SALL4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Dna Bound SALL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:32.7
occ:1.00
NE2 A:HIS916 2.1 40.5 1.0
NE2 A:HIS920 2.1 40.1 1.0
SG A:CYS900 2.3 33.0 1.0
SG A:CYS903 2.3 40.0 1.0
CD2 A:HIS916 2.9 38.8 1.0
CE1 A:HIS920 3.0 36.1 1.0
CD2 A:HIS920 3.1 38.3 1.0
CB A:CYS900 3.1 32.6 1.0
CE1 A:HIS916 3.1 38.7 1.0
CB A:CYS903 3.1 37.2 1.0
N A:CYS903 3.6 33.0 1.0
CA A:CYS903 3.9 34.8 1.0
CG A:HIS916 4.1 37.4 1.0
ND1 A:HIS920 4.1 38.8 1.0
ND1 A:HIS916 4.1 37.4 1.0
CG A:HIS920 4.2 39.9 1.0
CB A:ILE902 4.5 40.3 1.0
C A:CYS903 4.5 34.7 1.0
CA A:CYS900 4.6 31.6 1.0
C A:ILE902 4.6 31.9 1.0
N A:GLY904 4.7 32.2 1.0
CB A:ARG905 4.8 45.1 1.0
CG2 A:ILE902 4.9 26.6 1.0
N A:ARG905 4.9 35.6 1.0
CA A:ILE902 4.9 34.1 1.0
N A:ILE902 5.0 31.5 1.0

Zinc binding site 3 out of 6 in 7y3i

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Zinc binding site 3 out of 6 in the Structure of Dna Bound SALL4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Dna Bound SALL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:36.1
occ:1.00
NE2 B:HIS892 2.0 46.0 1.0
NE2 B:HIS888 2.0 45.5 1.0
SG B:CYS875 2.3 37.4 1.0
SG B:CYS872 2.4 44.5 1.0
CE1 B:HIS892 3.0 42.0 1.0
CD2 B:HIS892 3.0 42.6 1.0
CE1 B:HIS888 3.0 40.8 1.0
CD2 B:HIS888 3.0 41.6 1.0
CB B:CYS872 3.1 42.6 1.0
N B:CYS875 3.5 46.4 1.0
CB B:CYS875 3.6 40.2 1.0
CA B:CYS875 4.0 47.0 1.0
ND1 B:HIS892 4.1 41.6 1.0
ND1 B:HIS888 4.1 39.7 1.0
CG B:HIS892 4.1 41.7 1.0
CG B:HIS888 4.2 39.6 1.0
O B:CYS875 4.2 59.6 1.0
C B:CYS875 4.4 55.0 1.0
C B:ARG874 4.5 47.6 1.0
CB B:ARG874 4.5 45.2 1.0
CA B:CYS872 4.6 49.4 1.0
CA B:ARG874 4.9 49.4 1.0
N B:ARG874 4.9 53.6 1.0
OG1 B:THR891 4.9 34.2 1.0
O B:HOH1103 5.0 36.3 1.0

Zinc binding site 4 out of 6 in 7y3i

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Zinc binding site 4 out of 6 in the Structure of Dna Bound SALL4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Dna Bound SALL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:26.7
occ:1.00
NE2 B:HIS916 2.0 31.7 1.0
NE2 B:HIS920 2.1 36.5 1.0
SG B:CYS900 2.3 24.0 1.0
SG B:CYS903 2.3 26.7 1.0
CE1 B:HIS916 2.9 28.3 1.0
CD2 B:HIS920 3.0 36.4 1.0
CD2 B:HIS916 3.1 28.0 1.0
CE1 B:HIS920 3.1 34.5 1.0
CB B:CYS900 3.2 24.8 1.0
CB B:CYS903 3.4 21.8 1.0
N B:CYS903 3.7 27.6 1.0
ND1 B:HIS916 4.0 29.5 1.0
CA B:CYS903 4.1 23.1 1.0
CG B:HIS916 4.1 28.5 1.0
ND1 B:HIS920 4.1 36.1 1.0
CG B:HIS920 4.2 37.5 1.0
CB B:ILE902 4.4 29.5 1.0
C B:ILE902 4.6 27.0 1.0
CA B:CYS900 4.6 25.8 1.0
C B:CYS903 4.7 26.0 1.0
CG2 B:ILE902 4.7 26.4 1.0
N B:GLY904 4.7 22.5 1.0
CB B:ARG905 4.7 23.7 1.0
N B:ARG905 4.9 23.2 1.0
CA B:ILE902 4.9 27.1 1.0
N B:ILE902 4.9 23.9 1.0

Zinc binding site 5 out of 6 in 7y3i

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Zinc binding site 5 out of 6 in the Structure of Dna Bound SALL4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Dna Bound SALL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:29.1
occ:0.99
NE2 C:HIS916 2.1 36.2 1.0
SG C:CYS903 2.2 38.2 1.0
NE2 C:HIS920 2.2 34.6 1.0
SG C:CYS900 2.3 30.9 1.0
CD2 C:HIS920 2.7 31.2 1.0
CE1 C:HIS916 3.1 33.3 1.0
CB C:CYS900 3.1 29.6 1.0
CD2 C:HIS916 3.1 35.1 1.0
CB C:CYS903 3.3 33.7 1.0
CE1 C:HIS920 3.4 33.8 1.0
N C:CYS903 3.6 32.7 1.0
CG C:HIS920 4.0 32.6 1.0
CA C:CYS903 4.0 33.8 1.0
ND1 C:HIS916 4.2 34.4 1.0
CG C:HIS916 4.2 35.1 1.0
ND1 C:HIS920 4.3 33.8 1.0
CB C:ILE902 4.3 35.0 1.0
CA C:CYS900 4.5 28.2 1.0
C C:ILE902 4.5 34.0 1.0
C C:CYS903 4.7 35.1 1.0
CB C:ARG905 4.7 35.3 1.0
O C:CYS900 4.8 28.5 1.0
CA C:ILE902 4.8 33.6 1.0
N C:ILE902 4.8 31.6 1.0
C C:CYS900 4.8 29.2 1.0
N C:GLY904 4.9 33.4 1.0
CG2 C:ILE902 4.9 28.5 1.0
CG C:ARG905 4.9 36.4 1.0
N C:ARG905 5.0 29.6 1.0

Zinc binding site 6 out of 6 in 7y3i

Go back to Zinc Binding Sites List in 7y3i
Zinc binding site 6 out of 6 in the Structure of Dna Bound SALL4


Mono view


Stereo pair view

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

b:41.8
occ:1.00
NE2 D:HIS916 2.1 55.1 1.0
NE2 D:HIS920 2.1 70.5 1.0
SG D:CYS900 2.3 34.2 1.0
SG D:CYS903 2.4 39.5 1.0
CD2 D:HIS920 2.9 71.0 1.0
CE1 D:HIS916 3.0 52.4 1.0
CD2 D:HIS916 3.1 52.0 1.0
CB D:CYS903 3.2 41.4 1.0
CB D:CYS900 3.2 30.3 1.0
CE1 D:HIS920 3.2 70.7 1.0
N D:CYS903 3.5 43.0 1.0
CA D:CYS903 3.8 42.4 1.0
ND1 D:HIS916 4.1 52.9 1.0
CG D:HIS920 4.1 71.3 1.0
CG D:HIS916 4.2 51.8 1.0
ND1 D:HIS920 4.3 71.5 1.0
CB D:ILE902 4.5 43.6 1.0
C D:CYS903 4.5 42.2 1.0
C D:ILE902 4.6 42.7 1.0
CA D:CYS900 4.6 32.3 1.0
N D:GLY904 4.7 37.1 1.0
CG2 D:ILE902 4.8 41.5 1.0
CA D:ILE902 4.9 42.1 1.0
N D:ILE902 5.0 39.5 1.0
C D:CYS900 5.0 37.7 1.0

Reference:

W.Ru, T.Koga, X.Wang, Q.Guo, M.D.Gearhart, S.Zhao, M.Murphy, H.Kawakami, D.Corcoran, J.Zhang, Z.Zhu, X.Yao, Y.Kawakami, C.Xu. Structural Studies of Sall Family Protein Zinc Finger Cluster Domains in Complex with Dna Reveal Preferential Binding to An Aata Tetranucleotide Motif. J.Biol.Chem. V. 298 02607 2022.
ISSN: ESSN 1083-351X
PubMed: 36257403
DOI: 10.1016/J.JBC.2022.102607
Page generated: Sat Apr 8 06:05:34 2023

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