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Zinc in PDB 8jas: Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) (pdb code 8jas). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer), PDB code: 8jas:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8jas

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Zinc binding site 1 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:70.3
occ:1.00
 NE2 A:HIS89 2.0 47.5 1.0
NE2 B:HIS89 2.0 20.0 1.0
CE1 A:HIS89 2.3 47.5 1.0
SG B:CYS54 2.3 22.7 1.0
SG A:CYS54 2.3 48.5 1.0
CD2 B:HIS89 2.8 20.0 1.0
CE1 B:HIS89 3.2 20.0 1.0
CD2 A:HIS89 3.4 47.5 1.0
CB B:CYS54 3.5 22.7 1.0
ND1 A:HIS89 3.6 47.5 1.0
CB A:CYS54 3.7 48.5 1.0
CA B:CYS54 3.7 22.7 1.0
CG B:HIS89 4.0 20.0 1.0
CA A:CYS54 4.0 48.5 1.0
N B:CYS54 4.1 22.7 1.0
CG A:HIS89 4.1 47.5 1.0
ND1 B:HIS89 4.1 20.0 1.0
N A:CYS54 4.4 48.5 1.0
C B:LEU53 4.6 20.3 1.0
O B:LEU53 4.7 20.3 1.0
CG2 A:VAL91 4.8 49.3 1.0
C A:LEU53 4.9 42.6 1.0
CB B:VAL91 5.0 17.9 1.0
CG1 B:VAL91 5.0 17.9 1.0

Zinc binding site 2 out of 8 in 8jas

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Zinc binding site 2 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn200

b:123.7
occ:1.00
 ND1 R:HIS82 2.1 95.2 1.0
SG R:CYS56 2.3 99.7 1.0
SG R:CYS68 2.3 104.1 1.0
SG R:CYS53 2.3 95.1 1.0
CE1 R:HIS82 2.8 95.2 1.0
CG R:HIS82 2.9 95.2 1.0
CB R:CYS56 3.0 99.7 1.0
CB R:HIS82 3.4 95.2 1.0
CB R:CYS68 3.6 104.1 1.0
CB R:CYS53 3.7 95.1 1.0
NE2 R:HIS82 3.8 95.2 1.0
CD2 R:HIS82 3.8 95.2 1.0
N R:CYS56 4.0 99.7 1.0
CA R:CYS56 4.1 99.7 1.0
N R:CYS53 4.2 95.1 1.0
CA R:CYS68 4.2 104.1 1.0
CA R:CYS53 4.5 95.1 1.0
CA R:HIS82 4.7 95.2 1.0
N R:HIS82 4.8 95.2 1.0
O R:CYS53 4.9 95.1 1.0
CB R:GLU55 4.9 99.2 1.0
C R:GLU55 4.9 99.2 1.0
C R:CYS53 5.0 95.1 1.0

Zinc binding site 3 out of 8 in 8jas

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Zinc binding site 3 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:106.5
occ:1.00
 ND1 R:HIS80 2.1 80.0 1.0
SG R:CYS45 2.3 76.1 1.0
SG R:CYS83 2.3 90.4 1.0
SG R:CYS42 2.3 72.4 1.0
CB R:CYS45 2.9 76.1 1.0
CG R:HIS80 2.9 80.0 1.0
CB R:CYS42 3.0 72.4 1.0
CB R:HIS80 3.1 80.0 1.0
CE1 R:HIS80 3.2 80.0 1.0
CB R:CYS83 3.2 90.4 1.0
N R:CYS45 3.6 76.1 1.0
CB R:CYS53 3.8 95.1 1.0
CA R:CYS45 3.9 76.1 1.0
CD2 R:HIS80 4.1 80.0 1.0
NE2 R:HIS80 4.2 80.0 1.0
N R:HIS80 4.2 80.0 1.0
CA R:HIS80 4.3 80.0 1.0
CA R:CYS53 4.3 95.1 1.0
CA R:CYS42 4.4 72.4 1.0
CA R:CYS83 4.6 90.4 1.0
C R:CYS45 4.7 76.1 1.0
C R:ILE44 4.9 73.0 1.0
N R:ARG46 4.9 72.4 1.0
N R:CYS83 5.0 90.4 1.0

Zinc binding site 4 out of 8 in 8jas

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Zinc binding site 4 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:104.9
occ:1.00
 OD1 R:ASP97 2.0 97.3 1.0
SG R:CYS75 2.3 94.7 1.0
SG R:CYS94 2.3 95.5 1.0
ND1 R:HIS77 2.3 85.5 1.0
CB R:CYS75 2.8 94.7 1.0
CE1 R:HIS77 2.9 85.5 1.0
CG R:ASP97 3.1 97.3 1.0
CB R:CYS94 3.4 95.5 1.0
CG R:HIS77 3.5 85.5 1.0
OD2 R:ASP97 3.6 97.3 1.0
N R:ASP97 3.9 97.3 1.0
CB R:LEU96 4.0 89.7 1.0
CB R:HIS77 4.0 85.5 1.0
NE2 R:HIS77 4.2 85.5 1.0
O R:ASP97 4.2 97.3 1.0
CA R:CYS75 4.2 94.7 1.0
CB R:ASP97 4.4 97.3 1.0
CD2 R:HIS77 4.4 85.5 1.0
O R:CYS75 4.5 94.7 1.0
CA R:ASP97 4.6 97.3 1.0
N R:LEU96 4.6 89.7 1.0
C R:CYS75 4.6 94.7 1.0
CA R:LEU96 4.7 89.7 1.0
CA R:CYS94 4.7 95.5 1.0
C R:LEU96 4.7 89.7 1.0
C R:ASP97 4.8 97.3 1.0
CD1 R:LEU96 4.9 89.7 1.0
NH2 R:ARG99 5.0 96.6 1.0
CG R:LEU96 5.0 89.7 1.0
C R:CYS94 5.0 95.5 1.0

Zinc binding site 5 out of 8 in 8jas

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Zinc binding site 5 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn601

b:34.8
occ:1.00
 NE2 K:HIS89 2.0 65.3 1.0
NE2 J:HIS89 2.0 32.8 1.0
SG J:CYS54 2.3 31.8 1.0
SG K:CYS54 2.3 82.0 1.0
CE1 K:HIS89 2.7 65.3 1.0
CE1 J:HIS89 2.8 32.8 1.0
CD2 J:HIS89 3.0 32.8 1.0
CD2 K:HIS89 3.2 65.3 1.0
CB K:CYS54 3.4 82.0 1.0
CB J:CYS54 3.6 31.8 1.0
CA K:CYS54 3.7 82.0 1.0
CG2 J:VAL91 3.7 38.2 1.0
CA J:CYS54 3.8 31.8 1.0
ND1 J:HIS89 3.9 32.8 1.0
ND1 K:HIS89 3.9 65.3 1.0
CG J:HIS89 4.0 32.8 1.0
CG K:HIS89 4.2 65.3 1.0
N K:CYS54 4.3 82.0 1.0
N J:CYS54 4.3 31.8 1.0
C J:LEU53 4.9 29.7 1.0
O K:HIS89 4.9 65.3 1.0
O J:LEU53 5.0 29.7 1.0
C K:LEU53 5.0 74.3 1.0
C K:CYS54 5.0 82.0 1.0

Zinc binding site 6 out of 8 in 8jas

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Zinc binding site 6 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn200

b:111.2
occ:1.00
 ND1 V:HIS82 2.1 84.9 1.0
SG V:CYS53 2.3 86.5 1.0
SG V:CYS56 2.3 93.3 1.0
SG V:CYS68 2.3 91.4 1.0
CG V:HIS82 3.0 84.9 1.0
CB V:CYS68 3.0 91.4 1.0
CE1 V:HIS82 3.1 84.9 1.0
CB V:CYS56 3.1 93.3 1.0
CB V:CYS53 3.3 86.5 1.0
CB V:HIS82 3.3 84.9 1.0
CA V:CYS68 3.9 91.4 1.0
N V:CYS53 3.9 86.5 1.0
N V:CYS56 3.9 93.3 1.0
CA V:CYS56 4.1 93.3 1.0
CA V:CYS53 4.1 86.5 1.0
CD2 V:HIS82 4.2 84.9 1.0
NE2 V:HIS82 4.2 84.9 1.0
CA V:HIS82 4.6 84.9 1.0
N V:HIS82 4.7 84.9 1.0
C V:CYS53 4.7 86.5 1.0
O V:CYS53 4.8 86.5 1.0
N V:CYS68 4.9 91.4 1.0
C V:CYS68 4.9 91.4 1.0
CD1 V:LEU52 5.0 86.2 1.0

Zinc binding site 7 out of 8 in 8jas

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Zinc binding site 7 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn201

b:88.0
occ:1.00
 ND1 V:HIS80 2.1 75.7 1.0
SG V:CYS45 2.3 75.0 1.0
SG V:CYS83 2.3 78.5 1.0
SG V:CYS42 2.3 74.6 1.0
CG V:HIS80 2.9 75.7 1.0
CB V:HIS80 3.1 75.7 1.0
CB V:CYS45 3.1 75.0 1.0
CE1 V:HIS80 3.2 75.7 1.0
CB V:CYS42 3.2 74.6 1.0
CB V:CYS83 3.2 78.5 1.0
N V:CYS45 3.6 75.0 1.0
CA V:CYS45 3.9 75.0 1.0
N V:HIS80 4.0 75.7 1.0
CB V:CYS53 4.1 86.5 1.0
CD2 V:HIS80 4.1 75.7 1.0
CA V:HIS80 4.1 75.7 1.0
NE2 V:HIS80 4.2 75.7 1.0
CA V:CYS53 4.5 86.5 1.0
CA V:CYS42 4.6 74.6 1.0
CA V:CYS83 4.6 78.5 1.0
C V:ILE44 4.7 71.4 1.0
CB V:ILE44 4.8 71.4 1.0
O V:CYS42 4.8 74.6 1.0
C V:CYS42 4.8 74.6 1.0
C V:CYS45 4.8 75.0 1.0
O V:HIS80 4.9 75.7 1.0
N V:ILE44 5.0 71.4 1.0
N V:CYS83 5.0 78.5 1.0
C V:HIS80 5.0 75.7 1.0

Zinc binding site 8 out of 8 in 8jas

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Zinc binding site 8 out of 8 in the Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of CRL2APPBP2 Bound with Rxxgpaa Degron (Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn202

b:98.4
occ:1.00
 OD1 V:ASP97 2.1 83.8 1.0
SG V:CYS94 2.3 78.5 1.0
SG V:CYS75 2.3 89.0 1.0
ND1 V:HIS77 2.3 81.2 1.0
CG V:HIS77 3.1 81.2 1.0
CG V:ASP97 3.2 83.8 1.0
CB V:CYS75 3.2 89.0 1.0
CE1 V:HIS77 3.2 81.2 1.0
CB V:CYS94 3.3 78.5 1.0
CB V:HIS77 3.4 81.2 1.0
OD2 V:ASP97 3.7 83.8 1.0
N V:ASP97 4.1 83.8 1.0
O V:ASP97 4.2 83.8 1.0
CD2 V:HIS77 4.2 81.2 1.0
NE2 V:HIS77 4.3 81.2 1.0
CB V:ASP97 4.3 83.8 1.0
CB V:LEU96 4.4 77.6 1.0
O V:CYS75 4.4 89.0 1.0
CA V:CYS75 4.5 89.0 1.0
CA V:ASP97 4.6 83.8 1.0
CA V:CYS94 4.7 78.5 1.0
C V:CYS75 4.7 89.0 1.0
CA V:HIS77 4.7 81.2 1.0
N V:HIS77 4.8 81.2 1.0
C V:ASP97 4.9 83.8 1.0
N V:LEU96 4.9 77.6 1.0
C V:LEU96 4.9 77.6 1.0
CA V:LEU96 5.0 77.6 1.0
C V:CYS94 5.0 78.5 1.0

Reference:

S.Zhao, K.Zhang, C.Xu. Molecular Basis For CRL2APPBP2-Mediated C-Degron Recognition To Be Published.
Page generated: Thu Dec 28 13:21:34 2023

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