Zinc in PDB 7y3m: Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna

Protein crystallography data

The structure of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna, PDB code: 7y3m 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) 33.79 / 2.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.587, 65.706, 102.98, 90, 106.78, 90
R / Rfree (%) 22.3 / 26.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna (pdb code 7y3m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna, PDB code: 7y3m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7y3m

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Zinc binding site 1 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1000

b:128.4
occ:1.00
 SG B:CYS384 2.1 202.3 1.0
NE2 B:HIS404 2.2 130.2 1.0
NE2 B:HIS400 2.3 104.4 1.0
SG B:CYS387 2.3 139.2 1.0
CB B:CYS387 2.7 141.0 1.0
CE1 B:HIS400 3.0 101.1 1.0
N B:CYS387 3.0 145.6 1.0
CB B:CYS384 3.0 175.7 1.0
CD2 B:HIS404 3.0 125.0 1.0
CE1 B:HIS404 3.2 125.4 1.0
CA B:CYS387 3.4 141.5 1.0
CD2 B:HIS400 3.4 104.0 1.0
CB B:TYR386 3.9 126.5 1.0
C B:TYR386 3.9 140.5 1.0
CG B:HIS404 4.2 123.4 1.0
ND1 B:HIS400 4.2 100.0 1.0
C B:CYS387 4.2 138.8 1.0
ND1 B:HIS404 4.3 125.1 1.0
CA B:TYR386 4.3 140.6 1.0
N B:TYR386 4.4 148.8 1.0
CA B:CYS384 4.4 169.5 1.0
CG B:HIS400 4.5 100.8 1.0
N B:SER388 4.7 127.8 1.0
C B:CYS384 4.8 157.7 1.0
O B:TYR386 4.8 137.1 1.0
CD1 B:TYR386 4.8 119.1 1.0
CG B:TYR386 4.9 119.2 1.0
O B:CYS387 4.9 138.4 1.0

Zinc binding site 2 out of 12 in 7y3m

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Zinc binding site 2 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:74.5
occ:1.00
 NE2 B:HIS432 2.0 117.9 1.0
NE2 B:HIS428 2.2 79.2 1.0
CE1 B:HIS432 2.3 113.2 1.0
CB B:CYS415 2.4 96.5 1.0
SG B:CYS412 2.6 91.2 1.0
SG B:CYS415 2.7 87.7 1.0
CE1 B:HIS428 3.1 77.5 1.0
CD2 B:HIS428 3.2 84.7 1.0
CD2 B:HIS432 3.3 112.2 1.0
CB B:CYS412 3.6 95.3 1.0
ND1 B:HIS432 3.6 112.8 1.0
CA B:CYS415 3.8 100.1 1.0
CG B:HIS432 4.1 111.1 1.0
CG2 B:VAL414 4.1 101.0 1.0
N B:CYS415 4.2 104.1 1.0
ND1 B:HIS428 4.2 81.0 1.0
CG B:HIS428 4.3 85.0 1.0
C B:CYS415 4.7 100.7 1.0
CB B:HIS417 4.9 109.8 1.0
C B:VAL414 5.0 107.2 1.0
O B:HIS428 5.0 88.3 1.0

Zinc binding site 3 out of 12 in 7y3m

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Zinc binding site 3 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:90.7
occ:1.00
 NE2 C:HIS400 2.0 116.8 1.0
CB C:CYS387 2.1 132.5 1.0
SG C:CYS384 2.3 97.9 1.0
NE2 C:HIS404 2.4 95.5 1.0
CD2 C:HIS400 2.9 111.4 1.0
CD2 C:HIS404 3.1 97.9 1.0
CE1 C:HIS400 3.1 110.6 1.0
SG C:CYS387 3.2 120.5 1.0
CA C:CYS387 3.3 124.7 1.0
N C:CYS387 3.4 117.6 1.0
CB C:CYS384 3.4 104.8 1.0
CE1 C:HIS404 3.5 97.5 1.0
CG C:HIS400 4.1 103.9 1.0
ND1 C:HIS400 4.2 108.4 1.0
C C:CYS387 4.2 116.2 1.0
CG C:HIS404 4.3 98.3 1.0
ND1 C:HIS404 4.5 99.5 1.0
CB C:LYS389 4.6 104.5 1.0
C C:TYR386 4.6 108.7 1.0
N C:SER388 4.6 110.4 1.0
N C:LYS389 4.8 109.2 1.0
CA C:CYS384 4.8 115.8 1.0
O C:CYS387 4.9 109.7 1.0
CD2 C:LEU401 5.0 75.7 1.0

Zinc binding site 4 out of 12 in 7y3m

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Zinc binding site 4 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:120.9
occ:1.00
 NE2 C:HIS432 2.2 131.6 1.0
SG C:CYS415 2.2 121.8 1.0
SG C:CYS412 2.3 124.6 1.0
NE2 C:HIS428 2.3 104.8 1.0
CB C:CYS415 3.0 125.1 1.0
CE1 C:HIS428 3.0 103.2 1.0
CD2 C:HIS432 3.1 127.8 1.0
CB C:CYS412 3.2 124.8 1.0
CE1 C:HIS432 3.2 131.0 1.0
CD2 C:HIS428 3.4 102.1 1.0
N C:CYS415 3.6 125.7 1.0
CG2 C:VAL414 3.8 109.9 1.0
CA C:CYS415 3.8 126.8 1.0
ND1 C:HIS428 4.2 100.5 1.0
CG C:HIS432 4.3 127.1 1.0
ND1 C:HIS432 4.3 129.7 1.0
CG C:HIS428 4.5 99.3 1.0
C C:CYS415 4.6 130.6 1.0
CA C:CYS412 4.6 122.2 1.0
C C:VAL414 4.7 129.2 1.0
N C:VAL414 4.8 120.7 1.0
N C:GLY416 4.8 131.0 1.0
CB C:VAL414 5.0 115.0 1.0

Zinc binding site 5 out of 12 in 7y3m

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Zinc binding site 5 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:77.1
occ:1.00
 NE2 A:HIS400 2.1 87.9 1.0
NE2 A:HIS404 2.1 80.5 1.0
SG A:CYS387 2.3 75.7 1.0
SG A:CYS384 2.4 73.0 1.0
CD2 A:HIS404 3.0 75.5 1.0
CD2 A:HIS400 3.0 85.2 1.0
CE1 A:HIS400 3.0 85.5 1.0
CB A:CYS387 3.2 79.0 1.0
CE1 A:HIS404 3.2 75.5 1.0
CB A:CYS384 3.4 75.4 1.0
N A:CYS387 3.5 92.7 1.0
CA A:CYS387 3.9 89.1 1.0
ND1 A:HIS400 4.1 83.6 1.0
CG A:HIS400 4.1 79.0 1.0
CG A:HIS404 4.2 72.5 1.0
ND1 A:HIS404 4.2 73.5 1.0
CB A:TYR386 4.3 70.4 1.0
C A:TYR386 4.5 88.1 1.0
C A:CYS387 4.7 96.4 1.0
CA A:TYR386 4.8 78.4 1.0
CA A:CYS384 4.8 82.5 1.0
N A:TYR386 4.9 82.3 1.0
N A:SER388 4.9 102.5 1.0

Zinc binding site 6 out of 12 in 7y3m

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Zinc binding site 6 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:91.7
occ:1.00
 NE2 A:HIS432 1.8 136.8 1.0
NE2 A:HIS428 2.1 108.2 1.0
SG A:CYS415 2.3 73.9 1.0
SG A:CYS412 2.3 102.5 1.0
CE1 A:HIS428 2.6 103.8 1.0
CE1 A:HIS432 2.6 136.6 1.0
CD2 A:HIS432 3.0 136.1 1.0
CB A:CYS415 3.2 78.3 1.0
CB A:CYS412 3.3 96.6 1.0
CD2 A:HIS428 3.4 101.8 1.0
CG2 A:VAL414 3.6 124.4 1.0
ND1 A:HIS432 3.7 138.2 1.0
ND1 A:HIS428 3.8 100.4 1.0
CG A:HIS432 3.9 137.8 1.0
N A:CYS415 4.0 104.6 1.0
CA A:CYS415 4.1 92.0 1.0
CG A:HIS428 4.2 94.8 1.0
C A:CYS415 4.8 90.2 1.0
CA A:CYS412 4.8 94.8 1.0
CB A:HIS417 4.9 95.5 1.0
C A:VAL414 4.9 114.5 1.0
CB A:VAL414 5.0 123.5 1.0

Zinc binding site 7 out of 12 in 7y3m

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Zinc binding site 7 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:75.5
occ:1.00
 NE2 F:HIS400 1.9 94.5 1.0
CB F:CYS387 2.1 128.1 1.0
SG F:CYS384 2.3 78.1 1.0
NE2 F:HIS404 2.4 76.1 1.0
CE1 F:HIS400 2.6 85.3 1.0
SG F:CYS387 3.0 122.6 1.0
CD2 F:HIS404 3.1 77.6 1.0
CD2 F:HIS400 3.1 85.6 1.0
CB F:CYS384 3.2 82.6 1.0
CA F:CYS387 3.2 128.2 1.0
N F:CYS387 3.3 115.7 1.0
CE1 F:HIS404 3.5 74.7 1.0
ND1 F:HIS400 3.9 82.4 1.0
C F:CYS387 4.1 134.2 1.0
CG F:HIS400 4.1 82.7 1.0
CG F:HIS404 4.4 76.9 1.0
C F:TYR386 4.5 108.0 1.0
ND1 F:HIS404 4.5 74.1 1.0
N F:SER388 4.5 142.2 1.0
CA F:CYS384 4.6 87.3 1.0
CB F:TYR386 4.7 80.2 1.0
O F:CYS387 4.7 134.8 1.0

Zinc binding site 8 out of 12 in 7y3m

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Zinc binding site 8 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:91.3
occ:1.00
 NE2 F:HIS432 2.0 129.3 1.0
CB F:CYS415 2.2 123.4 1.0
NE2 F:HIS428 2.2 105.7 1.0
SG F:CYS412 2.4 99.4 1.0
CD2 F:HIS432 2.6 125.1 1.0
CE1 F:HIS428 3.0 102.5 1.0
SG F:CYS415 3.0 125.2 1.0
CA F:CYS415 3.2 121.4 1.0
N F:CYS415 3.2 121.2 1.0
CE1 F:HIS432 3.2 128.1 1.0
CD2 F:HIS428 3.3 103.4 1.0
CB F:CYS412 3.3 100.3 1.0
CG F:HIS432 3.8 122.8 1.0
C F:VAL414 4.1 120.1 1.0
ND1 F:HIS432 4.1 126.8 1.0
ND1 F:HIS428 4.1 102.1 1.0
CG F:HIS428 4.3 102.2 1.0
CB F:VAL414 4.4 109.3 1.0
C F:CYS415 4.5 121.2 1.0
CA F:VAL414 4.6 121.0 1.0
CA F:CYS412 4.8 100.4 1.0
O F:VAL414 4.8 117.0 1.0
N F:VAL414 4.8 127.7 1.0
O F:HIS428 5.0 106.0 1.0

Zinc binding site 9 out of 12 in 7y3m

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Zinc binding site 9 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1000

b:110.8
occ:1.00
 NE2 J:HIS400 2.1 158.1 1.0
SG J:CYS387 2.4 132.1 1.0
NE2 J:HIS404 2.5 128.9 1.0
SG J:CYS384 2.7 137.8 1.0
CB J:CYS387 2.8 134.1 1.0
CD2 J:HIS404 3.0 128.7 1.0
CD2 J:HIS400 3.0 151.8 1.0
CE1 J:HIS400 3.0 154.8 1.0
N J:CYS387 3.4 144.3 1.0
CA J:CYS387 3.7 140.1 1.0
CE1 J:HIS404 3.8 130.9 1.0
ND1 J:HIS400 4.1 152.8 1.0
CG J:HIS400 4.1 146.6 1.0
CB J:CYS384 4.1 137.6 1.0
CG J:HIS404 4.3 127.5 1.0
C J:CYS387 4.4 137.9 1.0
CB J:TYR386 4.5 147.8 1.0
C J:TYR386 4.6 143.6 1.0
N J:SER388 4.6 132.1 1.0
ND1 J:HIS404 4.6 130.2 1.0
CD1 J:LEU401 4.9 121.9 1.0
CA J:TYR386 5.0 142.3 1.0
N J:TYR386 5.0 138.4 1.0

Zinc binding site 10 out of 12 in 7y3m

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Zinc binding site 10 out of 12 in the Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of SALL4 ZFC1 Bound with 16 Bp at-Rich Dsdna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1001

b:122.9
occ:1.00
 NE2 J:HIS432 2.2 179.0 1.0
NE2 J:HIS428 2.3 117.8 1.0
CE1 J:HIS432 2.4 177.1 1.0
CB J:CYS415 2.5 148.4 1.0
SG J:CYS412 2.6 123.4 1.0
SG J:CYS415 2.9 143.2 1.0
CE1 J:HIS428 3.0 118.0 1.0
N J:CYS415 3.3 159.7 1.0
CG2 J:VAL414 3.3 162.7 1.0
CD2 J:HIS428 3.4 116.5 1.0
CA J:CYS415 3.5 154.8 1.0
CD2 J:HIS432 3.5 175.3 1.0
CB J:CYS412 3.7 128.8 1.0
ND1 J:HIS432 3.7 177.4 1.0
ND1 J:HIS428 4.2 116.8 1.0
CG J:HIS432 4.2 175.4 1.0
C J:VAL414 4.2 164.4 1.0
CG J:HIS428 4.3 117.3 1.0
C J:CYS415 4.6 156.6 1.0
CB J:VAL414 4.6 165.5 1.0
CA J:VAL414 4.8 166.9 1.0
N J:VAL414 4.8 168.4 1.0
O J:HIS428 4.9 134.9 1.0
N J:GLY416 5.0 158.7 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 06:07:25 2023

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