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
Go back to
Zinc Binding Sites List in 6gys
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 Sites List in 6gys
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 Sites List in 6gys
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 Sites List in 6gys
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 Sites List in 6gys
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 Sites List in 6gys
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 Sites List in 6gys
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
Go back to
Zinc Binding Sites List in 6gys
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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