Zinc in PDB 7dde: Cryo-Em Structure of the APE4 and NBR1 Complex

All present enzymatic activity of Cryo-Em Structure of the APE4 and NBR1 Complex:
3.4.11.21;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the APE4 and NBR1 Complex (pdb code 7dde). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 48 binding sites of Zinc where determined in the Cryo-Em Structure of the APE4 and NBR1 Complex, PDB code: 7dde:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:132.2 occ:1.00 OD2 A:ASP262 2.3 102.3 1.0 OE1 A:GLU299 2.3 99.7 1.0 NE2 A:HIS437 2.3 97.2 1.0 ZN A:ZN1502 2.3 122.8 1.0 CE1 A:HIS437 3.0 97.2 1.0 CD A:GLU299 3.1 99.7 1.0 CG A:ASP262 3.2 102.3 1.0 OE2 A:GLU299 3.3 99.7 1.0 CD2 A:HIS437 3.5 97.2 1.0 OE1 A:GLU298 3.5 101.5 1.0 OD1 A:ASP262 3.6 102.3 1.0 O A:HOH1631 3.6 102.8 1.0 OE2 A:GLU298 4.0 101.5 1.0 CD A:GLU298 4.2 101.5 1.0 ND1 A:HIS437 4.2 97.2 1.0 NE2 A:HIS93 4.4 97.0 1.0 CG A:GLU299 4.5 99.7 1.0 CB A:ASP262 4.5 102.3 1.0 CG A:HIS437 4.5 97.2 1.0 CE1 A:HIS93 4.6 97.0 1.0 NE2 C:HIS168 4.7 97.8 1.0 OD2 A:ASP343 4.7 97.7 1.0 CE1 C:HIS168 4.8 97.8 1.0 CB A:GLU299 4.9 99.7 1.0 CA A:GLU299 4.9 99.7 1.0 SD A:MET436 4.9 98.4 1.0

Zinc binding site 2 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:122.8 occ:1.00 OD1 A:ASP262 2.3 102.3 1.0 NE2 A:HIS93 2.3 97.0 1.0 ZN A:ZN1501 2.3 132.2 1.0 CG A:ASP262 2.7 102.3 1.0 OD2 A:ASP262 2.7 102.3 1.0 CE1 A:HIS93 2.9 97.0 1.0 O A:HOH1631 3.0 102.8 1.0 OD1 A:ASP343 3.1 97.7 1.0 OD2 A:ASP343 3.2 97.7 1.0 OE1 A:GLU298 3.2 101.5 1.0 CD2 A:HIS93 3.4 97.0 1.0 OE2 A:GLU299 3.5 99.7 1.0 CG A:ASP343 3.5 97.7 1.0 OE2 A:GLU298 3.6 101.5 1.0 CD A:GLU298 3.7 101.5 1.0 OE1 A:GLU299 3.8 99.7 1.0 OD1 A:ASN263 3.8 100.6 1.0 CB A:ASP262 3.9 102.3 1.0 CD A:GLU299 3.9 99.7 1.0 ND1 A:HIS93 4.1 97.0 1.0 O A:ASP262 4.1 102.3 1.0 CG A:ASN263 4.1 100.6 1.0 NE2 A:HIS437 4.3 97.2 1.0 C A:ASP262 4.3 102.3 1.0 CG A:HIS93 4.4 97.0 1.0 ND2 A:ASN263 4.5 100.6 1.0 CA A:ASP262 4.6 102.3 1.0 CB A:ASN263 4.7 100.6 1.0 N A:ASN263 5.0 100.6 1.0

Zinc binding site 3 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:185.3 occ:1.00 SG A:CYS1076 2.3 164.8 1.0 SG A:CYS1098 2.3 176.3 1.0 NE2 A:HIS1096 2.3 170.8 1.0 N A:CYS1079 2.3 175.4 1.0 CB A:CYS1079 2.5 175.4 1.0 CA A:CYS1079 2.8 175.4 1.0 CB A:CYS1098 3.1 176.3 1.0 C A:LYS1078 3.1 170.8 1.0 CD2 A:HIS1096 3.2 170.8 1.0 CE1 A:HIS1096 3.3 170.8 1.0 CB A:LYS1078 3.5 170.8 1.0 CA A:LYS1078 3.7 170.8 1.0 CB A:CYS1076 3.8 164.8 1.0 O A:LYS1078 3.9 170.8 1.0 N A:LYS1078 4.1 170.8 1.0 SG A:CYS1079 4.1 175.4 1.0 C A:CYS1079 4.2 175.4 1.0 CG A:HIS1096 4.4 170.8 1.0 CB A:PRO1101 4.4 167.0 1.0 ND1 A:HIS1096 4.4 170.8 1.0 CA A:CYS1098 4.5 176.3 1.0 O A:CYS1079 4.8 175.4 1.0 CG A:LYS1078 4.9 170.8 1.0 CA A:PRO1101 4.9 167.0 1.0 N A:CYS1098 4.9 176.3 1.0 CA A:CYS1076 5.0 164.8 1.0

Zinc binding site 4 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1504 b:192.4 occ:1.00 SG A:CYS1065 2.3 167.2 1.0 SG A:CYS1085 2.3 165.2 1.0 SG A:CYS1088 2.3 165.9 1.0 SG A:CYS1062 2.3 166.8 1.0 OG1 A:THR1064 2.7 169.3 1.0 CB A:CYS1088 3.1 165.9 1.0 CB A:CYS1062 3.3 166.8 1.0 CB A:CYS1085 3.5 165.2 1.0 N A:CYS1065 3.7 167.2 1.0 CB A:CYS1065 3.8 167.2 1.0 N A:CYS1085 4.1 165.2 1.0 CB A:THR1064 4.2 169.3 1.0 N A:CYS1088 4.2 165.9 1.0 CA A:CYS1088 4.2 165.9 1.0 CA A:CYS1065 4.3 167.2 1.0 CA A:CYS1085 4.4 165.2 1.0 O A:CYS1065 4.4 167.2 1.0 C A:THR1064 4.7 169.3 1.0 CA A:CYS1062 4.8 166.8 1.0 CA A:THR1064 4.8 169.3 1.0 CG2 A:THR1064 4.8 169.3 1.0 CE A:LYS1067 4.8 161.2 1.0 C A:CYS1065 4.9 167.2 1.0 N A:THR1064 4.9 169.3 1.0

Zinc binding site 5 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1501 b:133.9 occ:1.00 OD2 C:ASP262 2.3 103.3 1.0 OE1 C:GLU299 2.3 100.4 1.0 NE2 C:HIS437 2.3 97.8 1.0 ZN C:ZN1502 2.3 130.2 1.0 O A:HOH1691 2.4 107.4 1.0 CE1 C:HIS437 3.0 97.8 1.0 CD C:GLU299 3.1 100.4 1.0 CG C:ASP262 3.1 103.3 1.0 OE2 C:GLU299 3.3 100.4 1.0 OD1 C:ASP262 3.4 103.3 1.0 CD2 C:HIS437 3.5 97.8 1.0 OE1 C:GLU298 3.5 100.6 1.0 OE2 C:GLU298 4.0 100.6 1.0 CD C:GLU298 4.2 100.6 1.0 ND1 C:HIS437 4.2 97.8 1.0 NE2 C:HIS93 4.4 97.3 1.0 CG C:GLU299 4.5 100.4 1.0 CG C:HIS437 4.5 97.8 1.0 CB C:ASP262 4.5 103.3 1.0 CE1 C:HIS93 4.6 97.3 1.0 NE2 A:HIS168 4.6 100.8 1.0 OD2 C:ASP343 4.7 100.1 1.0 CE1 A:HIS168 4.8 100.8 1.0 CB C:GLU299 4.9 100.4 1.0 CA C:GLU299 4.9 100.4 1.0 SD C:MET436 4.9 99.5 1.0

Zinc binding site 6 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1502 b:130.2 occ:1.00 OD1 C:ASP262 2.3 103.3 1.0 NE2 C:HIS93 2.3 97.3 1.0 ZN C:ZN1501 2.3 133.9 1.0 CG C:ASP262 2.7 103.3 1.0 OD2 C:ASP262 2.8 103.3 1.0 CE1 C:HIS93 2.9 97.3 1.0 OD1 C:ASP343 3.1 100.1 1.0 OD2 C:ASP343 3.2 100.1 1.0 OE1 C:GLU298 3.3 100.6 1.0 CD2 C:HIS93 3.4 97.3 1.0 OE2 C:GLU299 3.5 100.4 1.0 CG C:ASP343 3.5 100.1 1.0 OE2 C:GLU298 3.6 100.6 1.0 CD C:GLU298 3.7 100.6 1.0 OE1 C:GLU299 3.8 100.4 1.0 CD C:GLU299 3.9 100.4 1.0 O A:HOH1691 4.0 107.4 1.0 CB C:ASP262 4.0 103.3 1.0 ND1 C:HIS93 4.1 97.3 1.0 NE2 C:HIS437 4.3 97.8 1.0 O C:ASP262 4.3 103.3 1.0 C C:ASP262 4.4 103.3 1.0 CG C:HIS93 4.4 97.3 1.0 CA C:ASP262 4.6 103.3 1.0 CB C:ASN263 4.7 101.2 1.0 N C:ASN263 4.9 101.2 1.0 CG C:ASN263 4.9 101.2 1.0

Zinc binding site 7 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1503 b:191.2 occ:1.00 SG C:CYS1076 2.3 166.3 1.0 SG C:CYS1098 2.3 177.4 1.0 NE2 C:HIS1096 2.3 174.2 1.0 N C:CYS1079 2.3 177.4 1.0 CB C:CYS1079 2.5 177.4 1.0 CA C:CYS1079 2.8 177.4 1.0 CB C:CYS1098 3.1 177.4 1.0 C C:LYS1078 3.1 172.1 1.0 CD2 C:HIS1096 3.2 174.2 1.0 CE1 C:HIS1096 3.3 174.2 1.0 CB C:LYS1078 3.5 172.1 1.0 CA C:LYS1078 3.7 172.1 1.0 CB C:CYS1076 3.8 166.3 1.0 O C:LYS1078 3.9 172.1 1.0 N C:LYS1078 4.1 172.1 1.0 SG C:CYS1079 4.1 177.4 1.0 C C:CYS1079 4.2 177.4 1.0 CG C:HIS1096 4.4 174.2 1.0 CB C:PRO1101 4.4 167.5 1.0 ND1 C:HIS1096 4.4 174.2 1.0 CA C:CYS1098 4.5 177.4 1.0 O C:CYS1079 4.8 177.4 1.0 CG C:LYS1078 4.9 172.1 1.0 CA C:PRO1101 4.9 167.5 1.0 N C:CYS1098 4.9 177.4 1.0

Zinc binding site 8 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1504 b:197.7 occ:1.00 SG C:CYS1065 2.3 172.3 1.0 SG C:CYS1085 2.3 166.4 1.0 SG C:CYS1088 2.3 166.9 1.0 SG C:CYS1062 2.3 170.6 1.0 OG1 C:THR1064 2.7 172.8 1.0 CB C:CYS1088 3.1 166.9 1.0 CB C:CYS1062 3.3 170.6 1.0 CB C:CYS1085 3.5 166.4 1.0 N C:CYS1065 3.7 172.3 1.0 CB C:CYS1065 3.8 172.3 1.0 N C:CYS1085 4.1 166.4 1.0 CB C:THR1064 4.2 172.8 1.0 N C:CYS1088 4.2 166.9 1.0 CA C:CYS1088 4.2 166.9 1.0 CA C:CYS1065 4.3 172.3 1.0 CA C:CYS1085 4.4 166.4 1.0 O C:CYS1065 4.4 172.3 1.0 C C:THR1064 4.7 172.8 1.0 CA C:CYS1062 4.8 170.6 1.0 CA C:THR1064 4.8 172.8 1.0 CG2 C:THR1064 4.8 172.8 1.0 CE C:LYS1067 4.8 164.7 1.0 C C:CYS1065 4.9 172.3 1.0 N C:THR1064 4.9 172.8 1.0

Zinc binding site 9 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1501 b:131.5 occ:1.00 OE1 E:GLU299 2.3 95.2 1.0 O X:HOH1677 2.3 102.4 1.0 NE2 E:HIS437 2.3 92.8 1.0 ZN E:ZN1502 2.3 125.5 1.0 OD2 E:ASP262 2.5 97.9 1.0 CE1 E:HIS437 3.0 92.8 1.0 CD E:GLU299 3.1 95.2 1.0 OE2 E:GLU299 3.3 95.2 1.0 CG E:ASP262 3.3 97.9 1.0 OD1 E:ASP262 3.5 97.9 1.0 CD2 E:HIS437 3.5 92.8 1.0 OE1 E:GLU298 3.5 97.6 1.0 O E:HOH1667 3.9 98.6 1.0 OE2 E:GLU298 3.9 97.6 1.0 CD E:GLU298 4.1 97.6 1.0 ND1 E:HIS437 4.2 92.8 1.0 NE2 E:HIS93 4.4 92.4 1.0 NE2 X:HIS168 4.4 92.8 1.0 CG E:GLU299 4.5 95.2 1.0 CG E:HIS437 4.5 92.8 1.0 CE1 E:HIS93 4.6 92.4 1.0 CE1 X:HIS168 4.6 92.8 1.0 O E:HOH1657 4.7 95.0 1.0 CB E:ASP262 4.7 97.9 1.0 OD2 E:ASP343 4.7 96.5 1.0 CB E:GLU299 4.9 95.2 1.0 CA E:GLU299 4.9 95.2 1.0 SD E:MET436 4.9 93.2 1.0

Zinc binding site 10 out of 48 in the Cryo-Em Structure of the APE4 and NBR1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of the APE4 and NBR1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1502 b:125.5 occ:1.00 OD1 E:ASP262 2.3 97.9 1.0 NE2 E:HIS93 2.3 92.4 1.0 ZN E:ZN1501 2.3 131.5 1.0 OD2 E:ASP262 2.5 97.9 1.0 CG E:ASP262 2.6 97.9 1.0 CE1 E:HIS93 2.9 92.4 1.0 OD1 E:ASP343 3.1 96.5 1.0 OD2 E:ASP343 3.2 96.5 1.0 O E:HOH1667 3.2 98.6 1.0 OE1 E:GLU298 3.3 97.6 1.0 CD2 E:HIS93 3.4 92.4 1.0 OE2 E:GLU299 3.5 95.2 1.0 CG E:ASP343 3.5 96.5 1.0 OE2 E:GLU298 3.6 97.6 1.0 CD E:GLU298 3.7 97.6 1.0 OE1 E:GLU299 3.8 95.2 1.0 CD E:GLU299 3.9 95.2 1.0 O X:HOH1677 4.0 102.4 1.0 CB E:ASP262 4.1 97.9 1.0 ND1 E:HIS93 4.1 92.4 1.0 NE2 E:HIS437 4.3 92.8 1.0 CG E:HIS93 4.4 92.4 1.0 C E:ASP262 4.5 97.9 1.0 O E:ASP262 4.6 97.9 1.0 CB E:ASN263 4.6 96.5 1.0 CA E:ASP262 4.7 97.9 1.0 N E:ASN263 4.9 96.5 1.0

Y.Y.Wang, J.Zhang, X.M.Liu, Y.Li, J.Sui, M.Q.Dong, K.Ye, L.L.Du. Molecular and Structural Mechanisms of Zz Domain-Mediated Cargo Selection By NBR1. Embo J. 07497 2021.
ISSN: ESSN 1460-2075
PubMed: 34169534
DOI: 10.15252/EMBJ.2020107497