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Zinc in PDB 7qe7: High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1

Zinc Binding Sites:

The binding sites of Zinc atom in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1 (pdb code 7qe7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1, PDB code: 7qe7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7qe7

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Zinc binding site 1 out of 6 in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn901

b:105.0
occ:1.00
SG N:CYS224 2.2 105.4 1.0
SG N:CYS221 2.3 87.8 1.0
SG N:CYS233 2.3 95.7 1.0
SG N:CYS231 2.3 106.0 1.0
CB N:CYS224 2.9 88.5 1.0
CB N:CYS231 3.3 93.7 1.0
CB N:CYS221 3.4 89.5 1.0
N N:CYS224 3.4 79.1 1.0
CA N:CYS224 3.7 83.8 1.0
CB N:CYS233 3.7 83.6 1.0
CA N:CYS231 3.9 89.5 1.0
N N:CYS233 4.1 80.8 1.0
N N:TRP232 4.3 82.8 1.0
C N:CYS231 4.4 85.3 1.0
CA N:CYS233 4.5 82.1 1.0
C N:GLY223 4.5 77.9 1.0
C N:CYS224 4.6 82.1 1.0
CA N:CYS221 4.7 87.2 1.0
N N:GLY223 4.7 77.8 1.0
C N:CYS221 4.9 84.2 1.0
CA N:GLY223 4.9 76.8 1.0
N N:SER225 5.0 80.2 1.0

Zinc binding site 2 out of 6 in 7qe7

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Zinc binding site 2 out of 6 in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn501

b:186.3
occ:1.00
SG S:CYS381 2.4 175.0 1.0
SG S:CYS396 2.4 177.5 1.0
SG S:CYS401 2.4 164.0 1.0
SG S:CYS378 2.5 171.2 1.0
CB S:CYS381 2.7 170.7 1.0
O S:CYS401 3.4 148.8 1.0
CB S:CYS396 3.4 169.1 1.0
CB S:CYS378 3.4 170.9 1.0
N S:CYS381 3.5 167.7 1.0
CB S:CYS401 3.5 152.6 1.0
CA S:CYS381 3.7 169.2 1.0
C S:CYS401 4.0 150.4 1.0
CB S:ARG380 4.3 160.1 1.0
CA S:CYS401 4.5 146.3 1.0
C S:ARG380 4.5 165.0 1.0
C S:CYS381 4.8 169.7 1.0
CB S:ARG398 4.8 146.9 1.0
CA S:ARG380 4.8 162.4 1.0
N S:GLY402 4.8 153.9 1.0
CA S:CYS396 4.9 166.4 1.0
CA S:CYS378 4.9 170.6 1.0
N S:PHE403 4.9 161.8 1.0
N S:ARG380 4.9 164.7 1.0
CA S:GLY402 5.0 154.7 1.0

Zinc binding site 3 out of 6 in 7qe7

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Zinc binding site 3 out of 6 in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn502

b:208.6
occ:1.00
SG S:CYS409 2.2 175.5 1.0
NE2 S:HIS414 2.2 206.2 1.0
SG S:CYS419 2.3 200.1 1.0
SG S:CYS406 2.4 187.7 1.0
CE1 S:HIS414 2.4 203.2 1.0
CB S:LYS408 3.1 169.8 1.0
CB S:CYS409 3.6 165.2 1.0
CB S:CYS419 3.6 204.6 1.0
CD2 S:HIS414 3.6 204.3 1.0
N S:CYS409 3.7 166.5 1.0
ND1 S:HIS414 3.7 203.6 1.0
CG S:LYS408 4.0 170.7 1.0
CB S:CYS406 4.0 183.6 1.0
C S:LYS408 4.1 164.4 1.0
CA S:LYS408 4.2 165.8 1.0
CA S:CYS409 4.3 165.7 1.0
NZ S:LYS417 4.3 192.2 1.0
CG S:HIS414 4.3 204.0 1.0
CA S:CYS419 4.5 207.9 1.0
N S:LYS408 4.7 166.4 1.0
O S:LYS408 4.9 159.5 1.0
O S:CYS406 4.9 171.4 1.0

Zinc binding site 4 out of 6 in 7qe7

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Zinc binding site 4 out of 6 in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:191.4
occ:1.00
ND1 C:HIS56 2.0 189.7 1.0
SG C:CYS59 2.2 189.2 1.0
SG C:CYS23 2.3 186.8 1.0
SG C:CYS26 2.3 185.5 1.0
CE1 C:HIS56 2.8 187.6 1.0
CG C:HIS56 3.2 190.2 1.0
CB C:CYS59 3.3 190.7 1.0
CB C:CYS23 3.3 180.2 1.0
CB C:CYS26 3.5 181.7 1.0
CB C:HIS56 3.7 190.7 1.0
N C:HIS56 3.8 190.7 1.0
N C:CYS26 3.8 180.8 1.0
NE2 C:HIS56 4.0 185.8 1.0
CD2 C:HIS56 4.2 188.6 1.0
CA C:CYS26 4.3 180.4 1.0
CA C:HIS56 4.4 190.9 1.0
CB C:ILE25 4.6 183.1 1.0
N C:ILE25 4.6 182.5 1.0
CA C:CYS59 4.7 191.2 1.0
C C:ILE25 4.7 181.4 1.0
CB C:PHE55 4.7 187.7 1.0
C C:PHE55 4.7 187.4 1.0
CA C:CYS23 4.7 177.3 1.0
CA C:PHE55 4.8 187.3 1.0
CA C:ILE25 4.9 182.4 1.0
N C:GLY24 4.9 179.9 1.0

Zinc binding site 5 out of 6 in 7qe7

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Zinc binding site 5 out of 6 in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:212.3
occ:1.00
ND1 C:HIS58 2.2 196.2 1.0
SG C:CYS44 2.2 199.0 1.0
CB C:CYS44 2.3 193.8 1.0
SG C:CYS34 2.3 192.7 1.0
SG C:CYS37 2.3 195.0 1.0
CE1 C:HIS58 2.5 193.5 1.0
CB C:CYS37 2.7 185.2 1.0
CG C:HIS58 3.5 194.9 1.0
CA C:CYS44 3.5 191.5 1.0
NE2 C:HIS58 3.8 191.4 1.0
CB C:CYS34 3.9 185.7 1.0
CA C:CYS37 4.2 182.8 1.0
CD2 C:HIS58 4.2 192.8 1.0
CB C:HIS58 4.2 193.5 1.0
N C:CYS44 4.3 188.6 1.0
C C:CYS44 4.6 189.8 1.0
N C:CYS37 4.6 186.3 1.0
O C:ASP43 4.7 190.1 1.0
C C:ASP43 4.9 188.4 1.0
O C:CYS44 4.9 187.6 1.0

Zinc binding site 6 out of 6 in 7qe7

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Zinc binding site 6 out of 6 in the High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High-Resolution Structure of the Anaphase-Promoting Complex/Cyclosome (Apc/C) Bound to Co-Activator CDH1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn103

b:205.4
occ:1.00
CB C:CYS51 1.9 194.1 1.0
ND1 C:HIS53 2.1 192.6 1.0
SG C:CYS76 2.4 196.6 1.0
SG C:CYS73 2.4 194.7 1.0
SG C:CYS51 2.4 197.7 1.0
CE1 C:HIS53 2.7 191.3 1.0
CB C:CYS73 3.0 191.2 1.0
CG C:HIS53 3.3 190.5 1.0
CA C:CYS51 3.4 192.9 1.0
O C:CYS51 3.8 190.8 1.0
CB C:CYS76 3.8 192.4 1.0
CB C:HIS53 3.9 190.3 1.0
N C:CYS76 3.9 193.1 1.0
NE2 C:HIS53 3.9 188.5 1.0
C C:CYS51 3.9 191.6 1.0
CB C:MET75 4.0 189.1 1.0
CD2 C:HIS53 4.2 188.8 1.0
N C:CYS51 4.4 191.5 1.0
CA C:CYS76 4.4 192.7 1.0
CA C:CYS73 4.5 190.4 1.0
NE2 C:GLN78 4.5 181.3 1.0
CZ3 C:TRP80 4.6 189.5 1.0
CA C:MET75 4.7 191.4 1.0
N C:MET75 4.7 190.2 1.0
N C:HIS53 4.7 188.1 1.0
C C:MET75 4.7 193.2 1.0
CG C:MET75 4.8 189.2 1.0
C C:CYS73 4.9 191.2 1.0
CA C:HIS53 4.9 188.5 1.0

Reference:

A.Hoefler, J.Yu, L.Chang, Z.Zhang, J.Yang, A.Boland, D.Barford. High-Resolution Structure of the Anaphase-Promoting Complex (Apc/C) Bound to Co-Activator CDH1 To Be Published.
Page generated: Sat Apr 8 01:54:19 2023

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