Zinc in PDB 7cux: Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding

Protein crystallography data

The structure of Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding, PDB code: 7cux was solved by J.Y.Yang, M.Luo, J.Y.Ou, Z.W.Wang, S.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.08 / 3.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 211.86, 156.442, 131.459, 90, 110.38, 90
R / Rfree (%) 20.1 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding (pdb code 7cux). 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 of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding, PDB code: 7cux:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7cux

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Zinc binding site 1 out of 6 in the Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding


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 Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:172.9
occ:1.00
 ND1 A:HIS266 2.1 201.3 1.0
SG A:CYS302 2.4 187.6 1.0
SG A:CYS303 2.7 152.2 1.0
CE1 A:HIS266 3.0 158.7 1.0
CG A:HIS266 3.2 175.3 1.0
SG A:CYS268 3.3 246.8 1.0
CB A:HIS266 3.6 183.0 1.0
CB A:CYS303 3.6 176.4 1.0
CB A:CYS268 3.6 219.6 1.0
CB A:CYS302 3.7 193.9 1.0
N A:CYS268 3.7 200.5 1.0
O A:GLN270 3.8 235.9 1.0
CA A:HIS266 4.0 165.5 1.0
N A:PHE267 4.0 207.9 1.0
NE2 A:HIS266 4.2 157.8 1.0
N A:CYS303 4.2 202.1 1.0
CA A:CYS268 4.3 206.8 1.0
CD2 A:HIS266 4.3 167.0 1.0
CD A:PRO272 4.3 177.4 1.0
CA A:ARG271 4.5 195.2 1.0
CA A:CYS303 4.5 177.6 1.0
C A:HIS266 4.5 187.7 1.0
C A:CYS302 4.6 201.4 1.0
CA A:CYS302 4.8 190.4 1.0
C A:PHE267 4.8 184.9 1.0
C A:GLN270 4.9 224.0 1.0
CA A:PHE267 5.0 190.3 1.0
C A:CYS268 5.0 209.3 1.0
CE2 A:PHE301 5.0 160.9 1.0
CB A:ARG271 5.0 195.8 1.0

Zinc binding site 2 out of 6 in 7cux

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Zinc binding site 2 out of 6 in the Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding


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 Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:123.0
occ:1.00
 ND1 B:HIS266 2.1 146.6 1.0
SG B:CYS302 2.3 147.8 1.0
SG B:CYS303 2.4 144.5 1.0
SG B:CYS268 2.5 190.8 1.0
CE1 B:HIS266 3.0 134.5 1.0
CG B:HIS266 3.2 143.8 1.0
CB B:CYS303 3.2 104.5 1.0
CB B:HIS266 3.6 128.3 1.0
CB B:CYS302 3.8 154.2 1.0
CB B:CYS268 3.8 174.4 1.0
N B:CYS303 3.9 129.8 1.0
CA B:HIS266 3.9 121.9 1.0
N B:CYS268 3.9 139.1 1.0
CD B:PRO272 4.0 156.3 1.0
N B:PHE267 4.0 136.7 1.0
NE2 B:HIS266 4.1 126.2 1.0
CA B:CYS303 4.1 106.3 1.0
CD2 B:HIS266 4.2 150.6 1.0
C B:CYS302 4.4 168.3 1.0
CA B:CYS268 4.5 157.8 1.0
C B:HIS266 4.5 130.8 1.0
CA B:CYS302 4.7 157.1 1.0
CA B:ARG271 4.7 180.7 1.0
CE2 B:PHE301 4.9 136.3 1.0
CG B:PRO272 4.9 155.9 1.0
C B:PHE267 5.0 132.4 1.0

Zinc binding site 3 out of 6 in 7cux

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Zinc binding site 3 out of 6 in the Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding


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 Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:177.6
occ:1.00
 ND1 C:HIS266 2.1 207.8 1.0
SG C:CYS302 2.3 203.2 1.0
SG C:CYS303 2.8 164.5 1.0
CE1 C:HIS266 3.0 167.2 1.0
SG C:CYS268 3.1 228.4 1.0
CG C:HIS266 3.3 200.6 1.0
CB C:CYS268 3.5 223.5 1.0
CB C:HIS266 3.7 206.3 1.0
CB C:CYS302 3.7 207.8 1.0
CB C:CYS303 3.8 163.6 1.0
N C:CYS268 3.8 218.7 1.0
O C:GLN270 4.0 228.5 1.0
N C:PHE267 4.1 204.9 1.0
CA C:HIS266 4.1 203.2 1.0
NE2 C:HIS266 4.2 178.3 1.0
CD C:PRO272 4.2 200.6 1.0
CA C:CYS268 4.3 225.0 1.0
N C:CYS303 4.3 205.5 1.0
CD2 C:HIS266 4.3 191.7 1.0
CA C:ARG271 4.5 223.5 1.0
C C:HIS266 4.6 210.7 1.0
CA C:CYS303 4.6 163.3 1.0
C C:CYS302 4.7 201.7 1.0
CA C:CYS302 4.8 207.1 1.0
C C:PHE267 4.8 196.7 1.0

Zinc binding site 4 out of 6 in 7cux

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Zinc binding site 4 out of 6 in the Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding


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 Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:164.4
occ:1.00
 ND1 D:HIS266 2.2 190.2 1.0
SG D:CYS268 2.5 232.4 1.0
SG D:CYS303 2.6 168.4 1.0
CE1 D:HIS266 2.8 149.4 1.0
CB D:CYS302 3.0 234.4 1.0
CB D:CYS303 3.3 166.9 1.0
SG D:CYS302 3.4 276.2 1.0
CG D:HIS266 3.4 182.1 1.0
N D:CYS303 3.5 198.8 1.0
CD D:PRO272 3.8 190.4 1.0
CB D:CYS268 3.8 221.6 1.0
C D:CYS302 3.9 192.0 1.0
CA D:CYS303 4.0 165.2 1.0
CA D:CYS302 4.0 188.5 1.0
NE2 D:HIS266 4.0 161.3 1.0
CB D:HIS266 4.0 206.2 1.0
N D:CYS268 4.3 224.3 1.0
CD2 D:HIS266 4.4 176.9 1.0
CA D:HIS266 4.4 201.1 1.0
CA D:ARG271 4.5 231.6 1.0
CE2 D:PHE301 4.5 167.7 1.0
N D:PHE267 4.5 216.5 1.0
CZ D:PHE301 4.6 192.9 1.0
O D:CYS302 4.7 190.6 1.0
CG D:PRO272 4.7 185.5 1.0
CA D:CYS268 4.7 219.7 1.0
N D:PRO272 4.7 200.3 1.0
N D:CYS302 4.7 162.4 1.0

Zinc binding site 5 out of 6 in 7cux

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Zinc binding site 5 out of 6 in the Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding


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 Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:156.4
occ:1.00
 CD2 E:HIS266 2.4 150.6 1.0
SG E:CYS268 2.6 219.6 1.0
SG E:CYS303 2.9 138.3 1.0
CB E:CYS302 3.0 217.6 1.0
NE2 E:HIS266 3.2 154.1 1.0
CG E:HIS266 3.4 167.2 1.0
SG E:CYS302 3.4 269.1 1.0
CB E:CYS303 3.6 136.2 1.0
N E:CYS303 3.8 183.5 1.0
CB E:HIS266 3.9 188.0 1.0
CD E:PRO272 4.0 179.4 1.0
C E:CYS302 4.1 171.8 1.0
CB E:CYS268 4.1 210.6 1.0
CA E:CYS302 4.1 181.4 1.0
O E:GLN270 4.3 245.8 1.0
CA E:CYS303 4.3 145.0 1.0
CE1 E:HIS266 4.4 165.8 1.0
CA E:HIS266 4.4 173.6 1.0
ND1 E:HIS266 4.4 171.8 1.0
CE2 E:PHE301 4.5 180.0 1.0
N E:CYS268 4.6 197.9 1.0
CZ E:PHE301 4.6 182.8 1.0
N E:PHE267 4.7 178.6 1.0
CA E:ARG271 4.7 221.8 1.0
CG E:PRO272 4.8 169.2 1.0
N E:CYS302 4.8 169.8 1.0
O E:CYS302 4.9 175.9 1.0
CA E:CYS268 4.9 211.4 1.0
N E:PRO272 5.0 207.1 1.0

Zinc binding site 6 out of 6 in 7cux

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Zinc binding site 6 out of 6 in the Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding


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 Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:171.9
occ:1.00
 ND1 F:HIS266 2.2 178.7 1.0
SG F:CYS302 2.4 178.4 1.0
SG F:CYS303 3.0 143.6 1.0
CE1 F:HIS266 3.1 157.0 1.0
CG F:HIS266 3.2 176.6 1.0
SG F:CYS268 3.2 230.2 1.0
CB F:CYS268 3.4 211.9 1.0
CB F:HIS266 3.6 185.4 1.0
CD F:PRO272 3.6 171.5 1.0
N F:CYS268 3.7 188.1 1.0
CB F:CYS302 3.8 196.9 1.0
CB F:CYS303 3.9 136.4 1.0
CA F:HIS266 4.1 166.4 1.0
N F:PHE267 4.1 182.2 1.0
CA F:CYS268 4.1 197.9 1.0
CA F:ARG271 4.1 204.3 1.0
NE2 F:HIS266 4.2 165.6 1.0
CD2 F:HIS266 4.3 176.7 1.0
N F:CYS303 4.4 193.7 1.0
O F:GLN270 4.5 205.6 1.0
C F:HIS266 4.6 170.9 1.0
N F:PRO272 4.6 188.4 1.0
CG F:PRO272 4.7 163.9 1.0
CB F:ARG271 4.8 208.4 1.0
C F:CYS268 4.8 214.6 1.0
C F:PHE267 4.8 173.1 1.0
CA F:CYS303 4.8 153.7 1.0
C F:CYS302 4.8 187.5 1.0
C F:ARG271 4.8 198.0 1.0
CG F:ARG271 4.9 214.2 1.0
N F:ARG271 4.9 204.3 1.0
CA F:CYS302 4.9 190.6 1.0
O F:CYS268 4.9 216.8 1.0

Reference:

J.Y.Yang, M.Luo, J.Y.Ou, Z.W.Wang, S.Gao. Crystal Structure of Human Schlafen 5 N'-Terminal Domain (SLFN5-N) Involved in Ssrna Cleaving and Dna Binding To Be Published.
Page generated: Fri Sep 24 17:04:34 2021

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