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Zinc in PDB 5tqr: CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine

Protein crystallography data

The structure of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine, PDB code: 5tqr was solved by M.A.Bratkowski, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.32 / 2.57
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 117.454, 138.008, 223.063, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine (pdb code 5tqr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine, PDB code: 5tqr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5tqr

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Zinc binding site 1 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8001

b:36.6
occ:1.00
SG B:CYS748 2.3 40.0 1.0
SG B:CYS755 2.4 40.0 1.0
SG B:CYS760 2.4 36.0 1.0
SG B:CYS727 2.4 34.4 1.0
CB B:CYS727 3.0 34.9 1.0
CB B:CYS755 3.1 38.3 1.0
CB B:CYS748 3.2 38.5 1.0
CB B:CYS760 3.4 33.2 1.0
N B:CYS727 3.5 35.2 1.0
CA B:CYS755 3.6 37.6 1.0
ZN B:ZN8002 3.8 33.9 1.0
ZN B:ZN8003 3.9 40.5 1.0
CA B:CYS727 3.9 35.8 1.0
SG B:CYS746 4.3 45.8 1.0
N B:CYS755 4.5 30.3 1.0
C B:GLY726 4.6 36.1 1.0
N B:ASP756 4.6 35.9 1.0
SG B:CYS763 4.6 36.4 1.0
CA B:CYS760 4.6 42.4 1.0
CA B:CYS748 4.6 46.0 1.0
O B:HOH8197 4.6 39.7 1.0
C B:CYS755 4.6 31.4 1.0
C B:CYS727 4.8 36.7 1.0
N B:CYS748 4.8 41.8 1.0
CA B:GLY726 4.9 46.0 1.0
SG B:CYS736 4.9 33.7 1.0
O B:CYS727 5.0 43.5 1.0

Zinc binding site 2 out of 8 in 5tqr

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Zinc binding site 2 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8002

b:33.9
occ:1.00
SG B:CYS784 2.2 34.7 1.0
SG B:CYS763 2.3 36.4 1.0
SG B:CYS755 2.4 40.0 1.0
SG B:CYS736 2.4 33.7 1.0
CB B:CYS784 2.7 37.3 1.0
CB B:CYS763 3.2 39.9 1.0
CB B:CYS755 3.3 38.3 1.0
CB B:CYS736 3.3 32.3 1.0
ZN B:ZN8001 3.8 36.6 1.0
ZN B:ZN8003 3.8 40.5 1.0
SG B:CYS727 3.9 34.4 1.0
CA B:CYS784 3.9 31.9 1.0
CB B:ALA765 4.6 33.3 1.0
CA B:CYS763 4.6 35.0 1.0
CB B:CYS760 4.7 33.2 1.0
CB B:ASN786 4.7 29.6 1.0
CA B:CYS755 4.7 37.6 1.0
CA B:CYS736 4.8 33.0 1.0
C B:CYS784 4.8 35.6 1.0
N B:CYS784 5.0 32.5 1.0

Zinc binding site 3 out of 8 in 5tqr

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Zinc binding site 3 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8003

b:40.5
occ:1.00
SG B:CYS746 2.2 45.8 1.0
SG B:CYS729 2.3 38.9 1.0
SG B:CYS727 2.3 34.4 1.0
SG B:CYS736 2.5 33.7 1.0
CB B:CYS729 3.1 37.5 1.0
CB B:CYS727 3.1 34.9 1.0
CB B:CYS746 3.2 40.7 1.0
CB B:CYS736 3.4 32.3 1.0
CA B:CYS736 3.8 33.0 1.0
ZN B:ZN8002 3.8 33.9 1.0
ZN B:ZN8001 3.9 36.6 1.0
CA B:CYS746 4.0 36.6 1.0
SG B:CYS755 4.1 40.0 1.0
N B:CYS729 4.2 38.5 1.0
CA B:CYS729 4.3 37.6 1.0
N B:CYS736 4.3 33.8 1.0
CA B:CYS727 4.5 35.8 1.0
CB B:CYS748 4.8 38.5 1.0
C B:CYS727 4.8 36.7 1.0
C B:CYS746 4.8 36.2 1.0
CB B:CYS763 4.9 39.9 1.0
SG B:CYS763 4.9 36.4 1.0
N B:ALA728 4.9 46.5 1.0

Zinc binding site 4 out of 8 in 5tqr

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Zinc binding site 4 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8004

b:52.7
occ:1.00
NE2 B:HIS687 2.1 53.4 1.0
SG B:CYS685 2.1 59.6 1.0
SG B:CYS691 2.2 53.7 1.0
SG B:CYS697 2.4 55.1 1.0
CE1 B:HIS687 2.9 54.0 1.0
CB B:CYS697 3.1 57.3 1.0
CB B:CYS691 3.1 48.9 1.0
CD2 B:HIS687 3.2 50.2 1.0
CB B:CYS685 3.3 51.5 1.0
CA B:CYS691 3.6 50.8 1.0
ZN B:ZN8006 3.8 49.9 1.0
ZN B:ZN8005 4.0 48.4 1.0
CA B:CYS697 4.0 53.5 1.0
ND1 B:HIS687 4.1 55.7 1.0
CG B:HIS687 4.2 50.6 1.0
SG B:CYS709 4.2 44.6 1.0
CA B:CYS685 4.4 45.1 1.0
N B:CYS691 4.5 56.6 1.0
C B:CYS691 4.7 48.2 1.0
SG B:CYS699 4.8 52.3 1.0
C B:CYS697 4.8 50.8 1.0
SG B:CYS715 4.9 51.6 1.0

Zinc binding site 5 out of 8 in 5tqr

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Zinc binding site 5 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8005

b:48.4
occ:1.00
SG B:CYS720 2.2 48.1 1.0
SG B:CYS715 2.3 51.6 1.0
SG B:CYS709 2.4 44.6 1.0
SG B:CYS691 2.6 53.7 1.0
CB B:CYS720 3.1 46.0 1.0
CB B:CYS715 3.2 41.4 1.0
CB B:CYS709 3.3 46.4 1.0
CB B:CYS691 3.4 48.9 1.0
ZN B:ZN8006 3.9 49.9 1.0
ZN B:ZN8004 4.0 52.7 1.0
SG B:CYS685 4.2 59.6 1.0
CA B:CYS720 4.5 55.1 1.0
CA B:CYS715 4.7 42.8 1.0
CA B:CYS709 4.7 41.7 1.0
CB B:LEU722 4.7 55.5 1.0
CA B:CYS691 4.8 50.8 1.0

Zinc binding site 6 out of 8 in 5tqr

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Zinc binding site 6 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8006

b:49.9
occ:1.00
SG B:CYS685 2.2 59.6 1.0
SG B:CYS699 2.3 52.3 1.0
SG B:CYS713 2.4 46.2 1.0
SG B:CYS709 2.4 44.6 1.0
CB B:CYS709 3.1 46.4 1.0
CB B:CYS713 3.2 35.1 1.0
CB B:CYS685 3.3 51.5 1.0
CB B:CYS699 3.4 40.9 1.0
CA B:CYS709 3.6 41.7 1.0
ZN B:ZN8004 3.8 52.7 1.0
N B:CYS685 3.9 49.1 1.0
ZN B:ZN8005 3.9 48.4 1.0
SG B:CYS715 4.2 51.6 1.0
CA B:CYS685 4.2 45.1 1.0
SG B:CYS697 4.2 55.1 1.0
SG B:CYS691 4.6 53.7 1.0
CA B:CYS713 4.6 43.9 1.0
N B:CYS709 4.6 38.5 1.0
C B:CYS709 4.6 47.7 1.0
N B:GLU710 4.7 44.5 1.0
CA B:CYS699 4.7 44.7 1.0
N B:CYS699 4.9 44.3 1.0

Zinc binding site 7 out of 8 in 5tqr

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Zinc binding site 7 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8007

b:32.9
occ:1.00
ND1 B:HIS518 2.1 32.9 1.0
SG B:CYS516 2.3 29.1 1.0
SG B:CYS511 2.3 31.6 1.0
SG B:CYS508 2.4 35.9 1.0
CE1 B:HIS518 2.8 34.5 1.0
CB B:CYS508 3.0 32.0 1.0
CB B:CYS516 3.2 29.9 1.0
CG B:HIS518 3.2 38.0 1.0
CB B:CYS511 3.4 24.4 1.0
CB B:HIS518 3.7 36.0 1.0
N B:CYS511 3.9 28.5 1.0
NE2 B:HIS518 4.0 36.8 1.0
N B:HIS518 4.1 42.6 1.0
CA B:CYS511 4.2 29.1 1.0
CD2 B:HIS518 4.2 28.9 1.0
N B:GLU517 4.4 31.9 1.0
CA B:CYS508 4.5 30.7 1.0
CA B:HIS518 4.5 35.0 1.0
CA B:CYS516 4.5 34.8 1.0
C B:CYS511 4.7 32.5 1.0
C B:CYS516 4.8 28.9 1.0
N B:PHE512 4.8 35.1 1.0
O B:SER513 4.8 41.8 1.0
CB B:ILE510 4.8 30.1 1.0
N B:SER513 4.9 39.5 1.0

Zinc binding site 8 out of 8 in 5tqr

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Zinc binding site 8 out of 8 in the CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of CTPRC2 in An Autoinhibited Conformation Bound to S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8008

b:73.2
occ:1.00
SG B:CYS570 2.2 72.2 1.0
SG B:CYS574 2.5 88.3 1.0
SG B:CYS625 2.5 84.3 1.0
SG B:CYS615 2.7 86.6 1.0
CB B:CYS574 3.1 78.8 1.0
CB B:CYS615 3.2 79.5 1.0
CB B:CYS625 3.2 75.6 1.0
CB B:CYS570 3.3 67.1 1.0
CA B:CYS574 3.3 70.0 1.0
CA B:CYS615 3.7 75.7 1.0
N B:CYS570 3.9 80.7 1.0
N B:TYR575 4.0 79.4 1.0
CA B:CYS570 4.1 75.4 1.0
CD1 B:TYR575 4.2 96.2 1.0
C B:CYS574 4.2 75.7 1.0
N B:CYS615 4.2 76.8 1.0
N B:CYS574 4.4 67.6 1.0
O B:CYS570 4.5 85.5 1.0
CE1 B:TYR575 4.7 95.0 1.0
C B:CYS570 4.7 79.1 1.0
CA B:CYS625 4.7 73.3 1.0
C B:GLU614 5.0 74.0 1.0

Reference:

M.Bratkowski, X.Yang, X.Liu. Polycomb Repressive Complex 2 in An Autoinhibited State. J. Biol. Chem. V. 292 13323 2017.
ISSN: ESSN 1083-351X
PubMed: 28607149
DOI: 10.1074/JBC.M117.787572
Page generated: Wed Dec 16 10:56:34 2020

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