Zinc in PDB 9gaw: 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 9gaw). 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: 9gaw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9gaw

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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 2.1 30.0 1.0
SG N:CYS221 2.3 64.2 1.0
SG N:CYS231 2.3 60.4 1.0
SG N:CYS233 2.3 70.2 1.0
N N:CYS224 3.1 69.5 1.0
CB N:CYS224 3.1 30.0 1.0
CB N:CYS231 3.4 65.5 1.0
CB N:CYS233 3.4 74.1 1.0
CB N:CYS221 3.4 67.4 1.0
CA N:CYS224 3.7 68.6 1.0
NE2 N:GLN186 4.0 30.0 1.0
N N:CYS233 4.0 76.0 1.0
CA N:CYS231 4.1 68.0 1.0
C N:GLY223 4.2 71.3 1.0
O N:CYS224 4.2 64.2 1.0
CA N:CYS233 4.3 76.1 1.0
CA N:GLY223 4.4 68.9 1.0
N N:GLY223 4.5 69.2 1.0
C N:CYS224 4.5 69.2 1.0
N N:TRP232 4.5 70.7 1.0
C N:CYS231 4.6 69.1 1.0
CA N:CYS221 4.8 68.9 1.0

Zinc binding site 2 out of 6 in 9gaw

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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 2.3 89.4 1.0
SG S:CYS401 2.3 92.7 1.0
SG S:CYS378 2.3 93.1 1.0
SG S:CYS396 2.3 93.6 1.0
CB S:CYS378 3.0 93.6 1.0
CB S:CYS401 3.1 94.2 1.0
CB S:CYS396 3.4 94.4 1.0
CB S:CYS381 4.0 90.7 1.0
N S:CYS381 4.2 92.5 1.0
CB S:SER383 4.5 91.0 1.0
CA S:CYS401 4.5 95.5 1.0
CB S:PHE403 4.5 91.7 1.0
CA S:CYS378 4.5 94.0 1.0
CB S:ARG380 4.5 90.9 1.0
CA S:CYS381 4.6 92.2 1.0
CG S:ARG380 4.7 87.0 1.0
CA S:CYS396 4.8 94.8 1.0
CB S:ARG398 4.8 91.8 1.0
N S:PHE403 4.9 93.6 1.0
OG S:SER383 4.9 82.3 1.0
C S:CYS401 4.9 95.2 1.0
N S:GLY402 5.0 94.2 1.0

Zinc binding site 3 out of 6 in 9gaw

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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
 NE2 S:HIS414 2.3 59.5 1.0
SG S:CYS406 2.3 87.7 1.0
SG S:CYS409 2.4 30.0 1.0
CD2 S:HIS414 3.0 59.4 1.0
CB S:CYS409 3.2 30.0 1.0
N S:CYS409 3.2 90.4 1.0
CB S:CYS406 3.2 90.3 1.0
CE1 S:HIS414 3.4 58.9 1.0
O S:CYS406 3.5 89.8 1.0
CA S:CYS409 3.7 89.3 1.0
SG S:CYS411 3.7 30.0 1.0
CB S:LYS408 3.7 30.0 1.0
C S:LYS408 3.9 89.1 1.0
CA S:LYS408 4.2 89.3 1.0
CG S:HIS414 4.2 65.5 1.0
C S:CYS406 4.2 91.2 1.0
CA S:CYS406 4.3 91.8 1.0
ND1 S:HIS414 4.4 59.1 1.0
N S:LYS408 4.4 90.2 1.0
C S:CYS409 4.4 89.4 1.0
O S:LYS408 4.8 86.4 1.0
N S:LEU410 4.8 90.5 1.0

Zinc binding site 4 out of 6 in 9gaw

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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 2.1 82.1 1.0
SG C:CYS26 2.3 81.4 1.0
SG C:CYS59 2.3 83.1 1.0
SG C:CYS23 2.3 84.1 1.0
CB C:CYS23 2.7 86.0 1.0
CG C:HIS56 2.9 88.0 1.0
CB C:HIS56 3.0 88.4 1.0
CE1 C:HIS56 3.2 82.7 1.0
CB C:CYS26 3.3 84.2 1.0
CB C:CYS59 3.3 87.2 1.0
N C:HIS56 3.9 88.7 1.0
N C:CYS26 4.0 87.1 1.0
CA C:HIS56 4.0 88.9 1.0
CD2 C:HIS56 4.1 81.9 1.0
NE2 C:HIS56 4.2 83.4 1.0
CA C:CYS26 4.2 86.5 1.0
CA C:CYS23 4.2 86.8 1.0
CA C:CYS59 4.8 88.5 1.0
CB C:CYS34 4.8 84.4 1.0
C C:CYS23 4.9 86.6 1.0
C C:HIS56 4.9 89.0 1.0
O C:HIS56 5.0 87.6 1.0
CD C:PRO35 5.0 85.1 1.0
C C:CYS26 5.0 86.3 1.0
CB C:ILE25 5.0 84.8 1.0

Zinc binding site 5 out of 6 in 9gaw

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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
 SG C:CYS44 2.2 82.9 1.0
ND1 C:HIS58 2.3 78.9 1.0
SG C:CYS37 2.3 77.9 1.0
SG C:CYS34 2.4 80.4 1.0
CE1 C:HIS58 2.7 80.4 1.0
CB C:CYS44 3.0 85.1 1.0
CB C:CYS37 3.1 81.5 1.0
CB C:CYS34 3.3 84.4 1.0
CG C:HIS58 3.5 87.4 1.0
CA C:CYS44 3.7 86.3 1.0
NE2 C:HIS58 3.9 81.6 1.0
N C:CYS34 4.0 86.0 1.0
CA C:CYS34 4.2 86.0 1.0
CB C:HIS58 4.2 88.3 1.0
CD2 C:HIS58 4.3 79.7 1.0
CA C:CYS37 4.3 83.3 1.0
N C:CYS37 4.3 84.5 1.0
O C:ASP43 4.5 81.8 1.0
N C:CYS44 4.7 85.8 1.0
O C:CYS34 4.8 84.5 1.0
C C:CYS34 4.8 86.4 1.0
C C:CYS44 4.8 86.6 1.0

Zinc binding site 6 out of 6 in 9gaw

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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
 SG C:CYS73 2.3 82.2 1.0
SG C:CYS76 2.3 78.8 1.0
ND1 C:HIS53 2.3 77.9 1.0
SG C:CYS51 2.4 78.2 1.0
CE1 C:HIS53 2.9 79.0 1.0
CG C:HIS53 3.0 86.1 1.0
CB C:CYS73 3.0 85.6 1.0
CB C:HIS53 3.6 86.4 1.0
N C:CYS76 3.6 86.2 1.0
CB C:CYS51 3.6 83.4 1.0
NE2 C:HIS53 3.7 79.9 1.0
NE2 C:GLN78 3.7 66.0 1.0
CB C:CYS76 3.8 82.8 1.0
CD2 C:HIS53 3.8 78.5 1.0
CB C:MET75 3.9 30.0 1.0
CG C:GLN78 3.9 78.3 1.0
CA C:CYS76 4.2 85.4 1.0
CD C:GLN78 4.4 75.3 1.0
CA C:CYS73 4.5 86.8 1.0
C C:MET75 4.5 85.3 1.0
CA C:MET75 4.6 85.2 1.0
N C:MET75 4.6 85.8 1.0
O C:CYS51 4.6 80.9 1.0
C C:CYS76 4.7 85.3 1.0
C C:CYS73 4.9 87.0 1.0
N C:ARG77 4.9 84.6 1.0
CA C:CYS51 4.9 85.6 1.0
CA C:HIS53 5.0 86.8 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: Thu Oct 31 15:38:43 2024

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