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Zinc in PDB 6gys: Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore (pdb code 6gys). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore, PDB code: 6gys:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6gys

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:0.8
occ:1.00
 SG B:CYS17 2.0 0.3 1.0
SG B:CYS14 2.0 0.1 1.0
CB B:CYS17 2.6 0.3 1.0
SG B:CYS24 3.1 0.5 1.0
SG B:CYS30 3.2 0.3 1.0
ZN B:ZN702 3.4 0.7 1.0
CB B:CYS24 3.4 0.5 1.0
CA B:CYS24 3.6 0.5 1.0
CB B:CYS14 3.6 0.1 1.0
N B:CYS17 3.6 0.3 1.0
CA B:CYS17 3.7 0.3 1.0
SG B:CYS33 3.8 0.2 1.0
O B:LYS23 4.0 0.0 1.0
CB B:CYS30 4.2 0.3 1.0
N B:CYS14 4.4 0.1 1.0
O B:CYS14 4.4 0.1 1.0
CA B:CYS14 4.4 0.1 1.0
CB B:ASN32 4.6 0.9 1.0
C B:CYS24 4.6 0.5 1.0
N B:CYS24 4.6 0.5 1.0
C B:CYS14 4.6 0.1 1.0
C B:LYS23 4.7 0.0 1.0
C B:VAL16 4.8 0.4 1.0
N B:ASP25 4.9 0.7 1.0
C B:CYS17 4.9 0.3 1.0
ND2 B:ASN32 4.9 0.9 1.0

Zinc binding site 2 out of 8 in 6gys

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:0.7
occ:1.00
 SG B:CYS33 1.9 0.2 1.0
SG B:CYS42 2.1 0.5 1.0
SG B:CYS14 2.6 0.1 1.0
CB B:CYS42 2.8 0.5 1.0
CB B:CYS33 3.1 0.2 1.0
ZN B:ZN701 3.4 0.8 1.0
CB B:CYS14 3.4 0.1 1.0
CB B:VAL16 3.5 0.4 1.0
SG B:CYS30 3.5 0.3 1.0
CB B:CYS30 3.9 0.3 1.0
CG2 B:VAL16 4.0 0.4 1.0
CA B:CYS42 4.1 0.5 1.0
O B:PRO29 4.2 0.5 1.0
SG B:CYS17 4.2 0.3 1.0
CG1 B:VAL16 4.3 0.4 1.0
N B:VAL16 4.3 0.4 1.0
N B:CYS17 4.4 0.3 1.0
CA B:VAL16 4.4 0.4 1.0
CA B:CYS33 4.5 0.2 1.0
C B:PRO29 4.6 0.5 1.0
N B:CYS33 4.8 0.2 1.0
CA B:CYS14 4.8 0.1 1.0
C B:VAL16 4.8 0.4 1.0
N B:CYS30 4.9 0.3 1.0
CA B:CYS30 5.0 0.3 1.0
C B:CYS14 5.0 0.1 1.0

Zinc binding site 3 out of 8 in 6gys

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:0.8
occ:1.00
 SG C:CYS17 2.1 0.8 1.0
CB C:ASN32 2.8 0.5 1.0
SG C:CYS30 2.8 0.5 1.0
ND2 C:ASN32 2.8 0.5 1.0
CG C:ASN32 3.3 0.5 1.0
SG C:CYS14 3.4 0.6 1.0
ZN C:ZN702 3.4 0.7 1.0
SG C:CYS24 3.5 0.7 1.0
CB C:CYS30 3.5 0.5 1.0
CB C:CYS17 3.8 0.8 1.0
CB C:CYS24 4.1 0.7 1.0
CA C:CYS24 4.2 0.7 1.0
CA C:ASN32 4.2 0.5 1.0
N C:CYS17 4.3 0.8 1.0
N C:ASN32 4.4 0.5 1.0
CA C:CYS17 4.5 0.8 1.0
OD1 C:ASN32 4.5 0.5 1.0
O C:ASP25 4.5 0.3 1.0
SG C:CYS33 4.5 0.9 1.0
N C:CYS14 4.6 0.6 1.0
CB C:CYS14 4.7 0.6 1.0
O C:LYS23 4.8 0.9 1.0
N C:CYS33 4.9 0.9 1.0
C C:CYS24 4.9 0.7 1.0
C C:ASN32 4.9 0.5 1.0
CA C:CYS30 5.0 0.5 1.0
N C:ASP25 5.0 0.3 1.0

Zinc binding site 4 out of 8 in 6gys

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:0.7
occ:1.00
 SG C:CYS33 1.6 0.9 1.0
SG C:CYS14 2.6 0.6 1.0
SG C:CYS30 3.0 0.5 1.0
CB C:CYS33 3.2 0.9 1.0
CB C:VAL16 3.3 0.3 1.0
ZN C:ZN701 3.4 0.8 1.0
CB C:CYS30 3.5 0.5 1.0
SG C:CYS42 3.5 0.3 1.0
CG2 C:VAL16 3.7 0.3 1.0
CG1 C:VAL16 3.9 0.3 1.0
N C:CYS33 3.9 0.9 1.0
CB C:CYS42 4.0 0.3 1.0
CA C:CYS33 4.1 0.9 1.0
CB C:ASN32 4.2 0.5 1.0
ND2 C:ASN32 4.2 0.5 1.0
CB C:CYS14 4.2 0.6 1.0
O C:PRO29 4.2 0.4 1.0
CG C:ASN32 4.4 0.5 1.0
CA C:VAL16 4.5 0.3 1.0
C C:PRO29 4.6 0.4 1.0
N C:CYS30 4.6 0.5 1.0
N C:VAL16 4.6 0.3 1.0
CA C:CYS30 4.6 0.5 1.0
CA C:CYS42 4.6 0.3 1.0
C C:ASN32 4.7 0.5 1.0
SG C:CYS17 4.8 0.8 1.0
N C:CYS17 4.9 0.8 1.0

Zinc binding site 5 out of 8 in 6gys

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn701

b:0.8
occ:1.00
 SG I:CYS17 1.8 0.9 1.0
NH2 I:ARG20 1.9 0.7 1.0
NH1 I:ARG20 2.0 0.7 1.0
CZ I:ARG20 2.1 0.7 1.0
SG I:CYS30 2.4 0.1 1.0
CB I:CYS17 2.9 0.9 1.0
NE I:ARG20 3.2 0.7 1.0
ZN I:ZN702 3.4 0.7 1.0
SG I:CYS33 3.4 0.5 1.0
CA I:CYS17 3.6 0.9 1.0
CB I:CYS30 3.9 0.1 1.0
CD I:ARG20 4.2 0.7 1.0
N I:CYS17 4.3 0.9 1.0
SG I:CYS42 4.3 0.6 1.0
N I:ASP25 4.4 0.6 1.0
SG I:CYS24 4.7 0.9 1.0
CA I:CYS24 4.7 0.9 1.0
O I:ASP25 4.8 0.6 1.0
C I:CYS17 4.9 0.9 1.0
C I:CYS24 4.9 0.9 1.0
CB I:CYS33 5.0 0.5 1.0
O I:LYS23 5.0 0.2 1.0

Zinc binding site 6 out of 8 in 6gys

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn702

b:0.7
occ:1.00
 SG I:CYS42 1.9 0.6 1.0
CB I:CYS42 2.1 0.6 1.0
SG I:CYS33 2.2 0.5 1.0
CB I:CYS33 3.0 0.5 1.0
SG I:CYS17 3.1 0.9 1.0
SG I:CYS30 3.3 0.1 1.0
CA I:CYS42 3.4 0.6 1.0
ZN I:ZN701 3.4 0.8 1.0
SG I:CYS14 3.5 0.0 1.0
NH1 I:ARG20 3.8 0.7 1.0
CB I:CYS30 3.9 0.1 1.0
CB I:VAL16 4.2 0.2 1.0
CG1 I:VAL16 4.2 0.2 1.0
N I:CYS42 4.2 0.6 1.0
N I:CYS17 4.3 0.9 1.0
C I:CYS42 4.5 0.6 1.0
O I:PRO29 4.5 0.8 1.0
CA I:CYS33 4.5 0.5 1.0
CB I:CYS17 4.6 0.9 1.0
O I:CYS42 4.7 0.6 1.0
C I:PRO29 4.7 0.8 1.0
CZ I:ARG20 4.7 0.7 1.0
C I:VAL16 4.8 0.2 1.0
CA I:CYS17 4.8 0.9 1.0
CB I:PRO29 4.9 0.8 1.0
N I:CYS33 4.9 0.5 1.0
N I:CYS30 5.0 0.1 1.0

Zinc binding site 7 out of 8 in 6gys

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn701

b:0.8
occ:1.00
 SG J:CYS30 1.8 0.9 1.0
SG J:CYS17 1.8 0.3 1.0
SG J:CYS14 3.2 0.9 1.0
O J:ASP25 3.4 0.1 1.0
ZN J:ZN702 3.4 0.7 1.0
CB J:CYS17 3.4 0.3 1.0
CB J:CYS30 3.4 0.9 1.0
CG2 J:VAL22 3.6 0.3 1.0
CB J:ASP25 3.6 0.1 1.0
N J:CYS17 3.8 0.3 1.0
CA J:CYS17 3.9 0.3 1.0
O J:LYS23 4.0 1.0 1.0
C J:ASP25 4.2 0.1 1.0
SG J:CYS42 4.2 0.6 1.0
CA J:ASP25 4.3 0.1 1.0
OD1 J:ASP25 4.3 0.1 1.0
N J:ASP25 4.4 0.1 1.0
SG J:CYS33 4.5 0.5 1.0
CG J:ASP25 4.5 0.1 1.0
CA J:CYS30 4.6 0.9 1.0
O J:PRO29 4.6 0.2 1.0
C J:VAL16 4.7 0.1 1.0
CB J:CYS14 4.8 0.9 1.0
N J:CYS14 4.9 0.9 1.0

Zinc binding site 8 out of 8 in 6gys

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of the CBF3-CEN3 Complex of the Budding Yeast Kinetochore within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn702

b:0.7
occ:1.00
 SG J:CYS42 0.9 0.6 1.0
CB J:CYS42 2.7 0.6 1.0
SG J:CYS30 2.8 0.9 1.0
SG J:CYS14 3.0 0.9 1.0
CB J:CYS30 3.3 0.9 1.0
ZN J:ZN701 3.4 0.8 1.0
O J:PRO29 3.5 0.2 1.0
O J:CYS42 3.5 0.6 1.0
CA J:CYS42 3.7 0.6 1.0
C J:PRO29 3.8 0.2 1.0
CB J:CYS33 3.9 0.5 1.0
CB J:VAL16 3.9 0.1 1.0
N J:CYS30 4.0 0.9 1.0
C J:CYS42 4.0 0.6 1.0
SG J:CYS33 4.2 0.5 1.0
CA J:CYS30 4.2 0.9 1.0
CG2 J:VAL16 4.3 0.1 1.0
CB J:PRO29 4.4 0.2 1.0
N J:VAL16 4.5 0.1 1.0
CB J:CYS14 4.6 0.9 1.0
CA J:PRO29 4.6 0.2 1.0
N J:CYS17 4.7 0.3 1.0
CA J:VAL16 4.7 0.1 1.0
SG J:CYS17 4.8 0.3 1.0
CG1 J:VAL16 4.9 0.1 1.0
N J:CYS42 5.0 0.6 1.0

Reference:

K.Yan, Z.Zhang, J.Yang, S.H.Mclaughlin, D.Barford. Architecture of the CBF3-Centromere Complex of the Budding Yeast Kinetochore. Nat. Struct. Mol. Biol. V. 25 1103 2018.
ISSN: ESSN 1545-9985
PubMed: 30478265
DOI: 10.1038/S41594-018-0154-1
Page generated: Mon Oct 28 22:05:45 2024

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