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Zinc in PDB 4r2y: Crystal Structure of APC11 Ring Domain

Protein crystallography data

The structure of Crystal Structure of APC11 Ring Domain, PDB code: 4r2y was solved by N.G.Brown, E.R.Watson, F.Weissmann, M.A.Jarvis, R.Vanderlinden, C.R.R.Grace, J.J.Frye, P.Dube, R.Qiao, G.Petzold, S.E.Cho, O.Alsharif, J.Bao, J.Zheng, A.Nourse, I.Kurinov, J.M.Peters, H.Stark, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.68 / 1.75
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.446, 39.876, 65.038, 90.00, 108.49, 90.00
R / Rfree (%) 19.2 / 22.9

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of APC11 Ring Domain (pdb code 4r2y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of APC11 Ring Domain, PDB code: 4r2y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4r2y

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Zinc binding site 1 out of 12 in the Crystal Structure of APC11 Ring Domain


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 APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:20.1
occ:1.00
 ND1 A:HIS56 2.1 12.0 1.0
SG A:CYS59 2.3 11.0 1.0
SG A:CYS23 2.3 12.6 1.0
SG A:CYS26 2.4 12.5 1.0
CB A:CYS23 3.0 16.0 1.0
CE1 A:HIS56 3.0 12.6 1.0
CG A:HIS56 3.1 11.8 1.0
CB A:CYS26 3.3 12.2 1.0
CB A:CYS59 3.3 10.3 1.0
CB A:HIS56 3.5 11.1 1.0
N A:CYS26 3.9 11.8 1.0
N A:HIS56 4.0 12.0 1.0
CB A:CYS34 4.1 12.0 1.0
NE2 A:HIS56 4.1 12.8 1.0
CA A:CYS26 4.2 12.3 1.0
CD2 A:HIS56 4.2 12.2 1.0
CA A:HIS56 4.3 12.6 1.0
CA A:CYS23 4.5 14.6 1.0
CA A:CYS34 4.6 12.5 1.0
CA A:CYS59 4.7 9.8 1.0
CB A:ILE25 4.9 10.6 1.0
C A:CYS26 4.9 14.8 1.0
O A:HIS56 5.0 10.5 1.0
CD A:PRO35 5.0 12.5 1.0
C A:CYS23 5.0 15.9 1.0
N A:CYS59 5.0 9.8 1.0
N A:ARG27 5.0 13.7 1.0
C A:ILE25 5.0 17.1 1.0

Zinc binding site 2 out of 12 in 4r2y

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Zinc binding site 2 out of 12 in the Crystal Structure of APC11 Ring Domain


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 APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:23.3
occ:1.00
 ND1 A:HIS53 2.0 15.8 1.0
SG A:CYS51 2.3 16.1 1.0
SG B:CYS73 2.4 13.2 1.0
SG B:CYS76 2.4 17.4 1.0
CE1 A:HIS53 2.9 21.1 1.0
CG A:HIS53 3.0 15.6 1.0
CB B:CYS73 3.1 9.8 1.0
CB A:CYS51 3.2 14.3 1.0
CB A:HIS53 3.4 13.9 1.0
CB B:CYS76 3.5 20.6 1.0
N B:CYS76 3.9 22.4 1.0
NE2 A:HIS53 4.0 22.5 1.0
CD2 A:HIS53 4.1 23.6 1.0
CA B:CYS76 4.2 22.6 1.0
O A:CYS51 4.3 20.8 1.0
N A:HIS53 4.3 18.8 1.0
C A:CYS51 4.4 17.6 1.0
CB B:MET75 4.5 19.8 1.0
CA A:CYS51 4.5 15.2 1.0
CA A:HIS53 4.5 17.6 1.0
CA B:CYS73 4.6 8.7 1.0
C B:MET75 4.9 25.6 1.0
C B:CYS76 5.0 20.7 1.0

Zinc binding site 3 out of 12 in 4r2y

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Zinc binding site 3 out of 12 in the Crystal Structure of APC11 Ring Domain


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 APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:22.3
occ:1.00
 ND1 A:HIS58 2.1 13.0 1.0
SG A:CYS34 2.3 11.5 1.0
SG A:CYS44 2.4 11.8 1.0
SG A:CYS37 2.4 15.6 1.0
CE1 A:HIS58 3.0 12.3 1.0
CB A:CYS44 3.2 16.4 1.0
CG A:HIS58 3.2 10.2 1.0
CB A:CYS37 3.3 14.0 1.0
CB A:CYS34 3.4 12.0 1.0
CB A:HIS58 3.6 10.1 1.0
N A:CYS34 3.9 14.0 1.0
O A:HOH202 3.9 10.8 1.0
CA A:CYS44 4.0 14.0 1.0
CA A:CYS34 4.1 12.5 1.0
NE2 A:HIS58 4.1 10.5 1.0
CD2 A:HIS58 4.3 10.4 1.0
N A:CYS37 4.3 14.2 1.0
CA A:CYS37 4.4 17.9 1.0
O A:CYS34 4.5 14.8 1.0
C A:CYS34 4.5 12.8 1.0
CB A:ASP36 4.7 16.2 1.0
O A:ASP43 4.7 16.0 1.0
CB A:CYS33 4.8 23.8 1.0
CA A:HIS58 5.0 9.7 1.0
C A:CYS33 5.0 14.5 1.0
C A:CYS44 5.0 11.7 1.0

Zinc binding site 4 out of 12 in 4r2y

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Zinc binding site 4 out of 12 in the Crystal Structure of APC11 Ring Domain


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 APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:17.6
occ:1.00
 ND1 B:HIS56 2.1 9.3 1.0
SG B:CYS59 2.3 8.5 1.0
SG B:CYS26 2.3 11.5 1.0
SG B:CYS23 2.4 10.3 1.0
CE1 B:HIS56 3.1 9.7 1.0
CB B:CYS23 3.1 11.0 1.0
CG B:HIS56 3.2 9.1 1.0
CB B:CYS26 3.2 11.8 1.0
CB B:CYS59 3.3 8.1 1.0
CB B:HIS56 3.5 8.7 1.0
N B:CYS26 3.8 9.1 1.0
N B:HIS56 3.9 8.6 1.0
CA B:CYS26 4.1 12.2 1.0
NE2 B:HIS56 4.2 10.1 1.0
CD2 B:HIS56 4.3 9.9 1.0
CA B:HIS56 4.3 9.2 1.0
CB B:CYS34 4.3 9.2 1.0
CD B:PRO35 4.6 9.4 1.0
CA B:CYS23 4.6 11.4 1.0
CA B:CYS34 4.7 10.5 1.0
CA B:CYS59 4.7 9.2 1.0
CB B:ILE25 4.7 9.4 1.0
C B:ILE25 4.9 13.3 1.0
C B:CYS26 4.9 16.0 1.0
C B:CYS23 5.0 10.7 1.0
O B:CYS23 5.0 13.0 1.0
O B:HIS56 5.0 8.0 1.0
N B:CYS59 5.0 7.9 1.0

Zinc binding site 5 out of 12 in 4r2y

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Zinc binding site 5 out of 12 in the Crystal Structure of APC11 Ring Domain


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 APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:21.0
occ:1.00
 ND1 B:HIS53 2.1 19.0 1.0
SG A:CYS73 2.3 11.7 1.0
SG A:CYS76 2.3 14.6 1.0
SG B:CYS51 2.4 11.6 1.0
CB A:CYS73 2.9 8.0 1.0
CG B:HIS53 3.1 17.7 1.0
CE1 B:HIS53 3.1 25.7 1.0
CB B:CYS51 3.3 18.6 1.0
CB B:HIS53 3.4 13.6 1.0
CB A:CYS76 3.4 22.7 1.0
N A:CYS76 3.9 16.3 1.0
CA A:CYS76 4.2 19.1 1.0
NE2 B:HIS53 4.2 26.4 1.0
CD2 B:HIS53 4.2 26.7 1.0
CA A:CYS73 4.4 9.2 1.0
N B:HIS53 4.5 8.9 1.0
C A:MET75 4.5 18.7 1.0
CA B:HIS53 4.6 12.3 1.0
CA B:CYS51 4.6 13.7 1.0
O B:CYS51 4.6 17.3 1.0
C B:CYS51 4.7 16.6 1.0
CB A:MET75 4.7 17.3 1.0
N A:MET75 4.8 12.1 1.0
C A:CYS76 4.8 17.5 1.0
CA A:MET75 4.9 11.8 1.0
C A:CYS73 5.0 10.8 1.0

Zinc binding site 6 out of 12 in 4r2y

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Zinc binding site 6 out of 12 in the Crystal Structure of APC11 Ring Domain


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 APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn103

b:20.4
occ:1.00
 ND1 B:HIS58 2.1 8.6 1.0
SG B:CYS37 2.3 12.8 1.0
SG B:CYS44 2.4 12.0 1.0
SG B:CYS34 2.4 11.8 1.0
CE1 B:HIS58 2.9 8.7 1.0
CG B:HIS58 3.2 11.2 1.0
CB B:CYS44 3.3 12.0 1.0
CB B:CYS37 3.3 12.9 1.0
CB B:CYS34 3.5 9.2 1.0
CB B:HIS58 3.6 10.5 1.0
O B:HOH217 3.9 10.3 1.0
N B:CYS34 4.0 11.1 1.0
NE2 B:HIS58 4.1 12.2 1.0
CA B:CYS44 4.1 12.9 1.0
N B:CYS37 4.2 18.3 1.0
CD2 B:HIS58 4.2 10.6 1.0
CA B:CYS34 4.3 10.5 1.0
CA B:CYS37 4.4 12.6 1.0
C B:CYS34 4.7 9.8 1.0
O B:CYS34 4.8 12.4 1.0
C B:ASP36 4.9 19.1 1.0
O B:ASP43 4.9 18.0 1.0
CA B:HIS58 5.0 7.9 1.0
N B:ASP36 5.0 14.3 1.0

Zinc binding site 7 out of 12 in 4r2y

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Zinc binding site 7 out of 12 in the Crystal Structure of APC11 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:16.8
occ:0.76
 ND1 C:HIS56 2.2 13.3 1.0
SG C:CYS59 2.3 13.0 1.0
SG C:CYS23 2.3 15.0 1.0
SG C:CYS26 2.4 14.2 1.0
CB C:CYS23 3.0 16.4 1.0
CE1 C:HIS56 3.2 14.0 1.0
CB C:CYS26 3.2 14.3 1.0
CG C:HIS56 3.2 13.6 1.0
CB C:CYS59 3.3 11.8 1.0
CB C:HIS56 3.5 14.9 1.0
N C:CYS26 3.7 13.3 1.0
CA C:CYS26 4.1 13.6 1.0
N C:HIS56 4.1 12.4 1.0
NE2 C:HIS56 4.3 15.0 1.0
CB C:CYS34 4.3 15.8 1.0
CD2 C:HIS56 4.3 14.1 1.0
CA C:HIS56 4.4 15.4 1.0
CA C:CYS23 4.5 17.2 1.0
CA C:CYS59 4.7 11.4 1.0
CB C:ILE25 4.8 12.3 1.0
CA C:CYS34 4.8 13.7 1.0
C C:CYS26 4.8 14.6 1.0
C C:ILE25 4.9 15.8 1.0
N C:ARG27 4.9 17.6 1.0
C C:CYS23 5.0 17.4 1.0
O C:HIS56 5.0 13.6 1.0

Zinc binding site 8 out of 12 in 4r2y

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Zinc binding site 8 out of 12 in the Crystal Structure of APC11 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:15.6
occ:0.63
 ND1 C:HIS58 2.1 12.2 1.0
SG C:CYS34 2.3 13.5 1.0
SG C:CYS44 2.3 15.6 1.0
SG C:CYS37 2.4 17.7 1.0
CE1 C:HIS58 3.0 14.0 1.0
CG C:HIS58 3.2 11.8 1.0
CB C:CYS44 3.3 17.8 1.0
CB C:CYS34 3.3 15.8 1.0
CB C:CYS37 3.4 17.4 1.0
CB C:HIS58 3.6 11.7 1.0
N C:CYS34 3.8 16.6 1.0
O C:HOH203 4.0 14.0 1.0
CA C:CYS34 4.1 13.7 1.0
CA C:CYS44 4.1 14.8 1.0
NE2 C:HIS58 4.1 13.8 1.0
N C:CYS37 4.2 19.8 1.0
CD2 C:HIS58 4.3 13.1 1.0
CA C:CYS37 4.4 18.0 1.0
O C:CYS34 4.4 19.0 1.0
O C:HOH238 4.5 33.3 1.0
C C:CYS34 4.5 13.9 1.0
CB C:ASP36 4.7 20.7 1.0
O C:ASP43 4.8 14.9 1.0
O C:HOH218 4.9 30.4 1.0
C C:CYS33 5.0 21.1 1.0

Zinc binding site 9 out of 12 in 4r2y

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Zinc binding site 9 out of 12 in the Crystal Structure of APC11 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn103

b:18.1
occ:0.67
 ND1 C:HIS53 2.1 17.8 1.0
SG C:CYS51 2.3 16.6 1.0
SG D:CYS73 2.4 14.9 1.0
SG D:CYS76 2.4 20.7 1.0
CE1 C:HIS53 3.1 25.5 1.0
CB D:CYS73 3.1 12.9 1.0
CG C:HIS53 3.2 19.4 1.0
CB C:CYS51 3.3 15.4 1.0
CB D:CYS76 3.4 18.1 1.0
CB C:HIS53 3.5 18.4 1.0
N D:CYS76 3.8 18.4 1.0
CA D:CYS76 4.2 18.5 1.0
NE2 C:HIS53 4.2 27.3 1.0
CD2 C:HIS53 4.3 25.9 1.0
O C:CYS51 4.4 22.0 1.0
N C:HIS53 4.4 20.3 1.0
CB D:MET75 4.4 19.0 1.0
C C:CYS51 4.5 19.9 1.0
CA C:CYS51 4.5 17.6 1.0
CA D:CYS73 4.5 11.9 1.0
CA C:HIS53 4.6 19.9 1.0
C D:MET75 4.8 22.2 1.0
C D:CYS76 4.9 21.4 1.0
N D:ARG77 5.0 22.1 1.0
N D:MET75 5.0 13.7 1.0
CA D:MET75 5.0 15.4 1.0

Zinc binding site 10 out of 12 in 4r2y

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Zinc binding site 10 out of 12 in the Crystal Structure of APC11 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of APC11 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:15.9
occ:0.71
 ND1 D:HIS58 2.1 10.6 1.0
SG D:CYS44 2.3 13.5 1.0
SG D:CYS34 2.3 12.2 1.0
SG D:CYS37 2.3 17.1 1.0
CE1 D:HIS58 3.0 13.4 1.0
CG D:HIS58 3.2 10.1 1.0
CB D:CYS37 3.3 22.0 1.0
CB D:CYS44 3.3 13.0 1.0
CB D:CYS34 3.4 12.9 1.0
CB D:HIS58 3.6 9.6 1.0
O D:HOH212 3.8 11.9 1.0
N D:CYS34 4.0 8.9 1.0
CA D:CYS44 4.2 15.8 1.0
NE2 D:HIS58 4.2 12.4 1.0
CA D:CYS34 4.2 11.0 1.0
N D:CYS37 4.2 16.6 1.0
CD2 D:HIS58 4.3 10.6 1.0
CA D:CYS37 4.4 19.1 1.0
C D:CYS34 4.7 10.5 1.0
O D:CYS34 4.8 14.1 1.0
C D:ASP36 4.9 19.5 1.0
O D:ASP43 5.0 18.0 1.0

Reference:

N.G.Brown, E.R.Watson, F.Weissmann, M.A.Jarvis, R.Vanderlinden, C.R.Grace, J.J.Frye, R.Qiao, P.Dube, G.Petzold, S.E.Cho, O.Alsharif, J.Bao, I.F.Davidson, J.J.Zheng, A.Nourse, I.Kurinov, J.M.Peters, H.Stark, B.A.Schulman. Mechanism of Polyubiquitination By Human Anaphase-Promoting Complex: Ring Repurposing For Ubiquitin Chain Assembly. Mol.Cell 2014.
ISSN: ISSN 1097-2765
PubMed: 25306923
DOI: 10.1016/J.MOLCEL.2014.09.009
Page generated: Sun Oct 27 06:50:20 2024

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