Zinc in PDB 8ssu: Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
Protein crystallography data
The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna, PDB code: 8ssu
was solved by
J.R.Horton,
J.Yang,
X.Cheng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.34 /
2.89
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.464,
80.464,
187.598,
90,
90,
120
|
R / Rfree (%)
|
20 /
24
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
(pdb code 8ssu). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna, PDB code: 8ssu:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 8ssu
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Zinc Binding Sites List in 8ssu
Zinc binding site 1 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn702
b:97.7
occ:1.00
|
NE2
|
A:HIS340
|
2.0
|
91.7
|
1.0
|
NE2
|
A:HIS345
|
2.0
|
113.2
|
1.0
|
SG
|
A:CYS327
|
2.2
|
95.7
|
1.0
|
SG
|
A:CYS324
|
2.3
|
109.5
|
1.0
|
CE1
|
A:HIS345
|
2.8
|
112.1
|
1.0
|
CD2
|
A:HIS340
|
2.8
|
85.7
|
1.0
|
CD2
|
A:HIS345
|
2.9
|
112.4
|
1.0
|
CE1
|
A:HIS340
|
3.1
|
87.8
|
1.0
|
CB
|
A:CYS324
|
3.4
|
113.8
|
1.0
|
CB
|
A:CYS327
|
3.7
|
111.1
|
1.0
|
ND1
|
A:HIS345
|
3.7
|
108.1
|
1.0
|
CG
|
A:HIS345
|
3.8
|
109.2
|
1.0
|
CG
|
A:HIS340
|
4.0
|
82.7
|
1.0
|
ND1
|
A:HIS340
|
4.1
|
78.8
|
1.0
|
N
|
A:CYS327
|
4.3
|
119.9
|
1.0
|
CG
|
A:MET329
|
4.5
|
106.1
|
1.0
|
CA
|
A:CYS327
|
4.6
|
106.5
|
1.0
|
CB
|
A:MET329
|
4.6
|
99.2
|
1.0
|
CA
|
A:CYS324
|
4.8
|
98.2
|
1.0
|
C
|
A:ASP326
|
4.8
|
122.0
|
1.0
|
CB
|
A:ASP326
|
5.0
|
117.3
|
1.0
|
CG
|
A:ARG341
|
5.0
|
95.9
|
1.0
|
|
Zinc binding site 2 out
of 8 in 8ssu
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Zinc Binding Sites List in 8ssu
Zinc binding site 2 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn703
b:70.4
occ:1.00
|
NE2
|
A:HIS373
|
2.0
|
80.4
|
1.0
|
NE2
|
A:HIS369
|
2.0
|
59.3
|
1.0
|
SG
|
A:CYS356
|
2.2
|
61.8
|
1.0
|
SG
|
A:CYS353
|
2.3
|
96.3
|
1.0
|
CD2
|
A:HIS373
|
2.5
|
69.1
|
1.0
|
CD2
|
A:HIS369
|
2.9
|
80.0
|
1.0
|
CE1
|
A:HIS369
|
3.1
|
76.2
|
1.0
|
CE1
|
A:HIS373
|
3.3
|
85.2
|
1.0
|
CB
|
A:CYS353
|
3.3
|
83.5
|
1.0
|
CB
|
A:CYS356
|
3.3
|
63.1
|
1.0
|
N
|
A:CYS356
|
3.6
|
88.0
|
1.0
|
CG
|
A:HIS373
|
3.8
|
72.1
|
1.0
|
CA
|
A:CYS356
|
4.0
|
66.3
|
1.0
|
CG
|
A:HIS369
|
4.1
|
68.0
|
1.0
|
ND1
|
A:HIS373
|
4.1
|
75.1
|
1.0
|
ND1
|
A:HIS369
|
4.1
|
67.6
|
1.0
|
CB
|
A:MET355
|
4.3
|
77.2
|
1.0
|
C
|
A:MET355
|
4.3
|
76.0
|
1.0
|
CB
|
A:TYR358
|
4.5
|
62.1
|
1.0
|
N
|
A:MET355
|
4.6
|
78.7
|
1.0
|
CA
|
A:MET355
|
4.6
|
82.0
|
1.0
|
C
|
A:CYS356
|
4.6
|
90.0
|
1.0
|
CA
|
A:CYS353
|
4.7
|
79.3
|
1.0
|
O
|
A:CYS356
|
5.0
|
94.6
|
1.0
|
|
Zinc binding site 3 out
of 8 in 8ssu
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Zinc Binding Sites List in 8ssu
Zinc binding site 3 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn704
b:81.5
occ:1.00
|
NE2
|
A:HIS401
|
2.0
|
94.9
|
1.0
|
NE2
|
A:HIS397
|
2.0
|
69.9
|
1.0
|
SG
|
A:CYS384
|
2.2
|
73.4
|
1.0
|
SG
|
A:CYS381
|
2.3
|
104.6
|
1.0
|
CD2
|
A:HIS401
|
2.9
|
86.5
|
1.0
|
CD2
|
A:HIS397
|
2.9
|
81.4
|
1.0
|
CE1
|
A:HIS401
|
3.0
|
96.4
|
1.0
|
CE1
|
A:HIS397
|
3.1
|
76.1
|
1.0
|
CB
|
A:CYS381
|
3.3
|
87.8
|
1.0
|
CB
|
A:CYS384
|
3.4
|
79.5
|
1.0
|
N
|
A:CYS384
|
3.6
|
107.8
|
1.0
|
CG
|
A:HIS401
|
4.0
|
90.1
|
1.0
|
ND1
|
A:HIS401
|
4.0
|
92.6
|
1.0
|
CA
|
A:CYS384
|
4.0
|
86.3
|
1.0
|
CB
|
A:LEU383
|
4.1
|
98.4
|
1.0
|
CG
|
A:HIS397
|
4.1
|
74.8
|
1.0
|
ND1
|
A:HIS397
|
4.1
|
77.5
|
1.0
|
CB
|
A:TYR386
|
4.4
|
72.0
|
1.0
|
C
|
A:LEU383
|
4.5
|
109.4
|
1.0
|
C
|
A:CYS384
|
4.6
|
102.4
|
1.0
|
CA
|
A:LEU383
|
4.6
|
106.2
|
1.0
|
N
|
A:LEU383
|
4.7
|
95.4
|
1.0
|
CA
|
A:CYS381
|
4.8
|
92.1
|
1.0
|
O
|
A:CYS384
|
4.9
|
107.4
|
1.0
|
CD2
|
A:LEU383
|
4.9
|
106.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 8ssu
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Zinc Binding Sites List in 8ssu
Zinc binding site 4 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn705
b:114.0
occ:1.00
|
NE2
|
A:HIS430
|
2.0
|
101.9
|
1.0
|
NE2
|
A:HIS425
|
2.0
|
108.5
|
1.0
|
SG
|
A:CYS412
|
2.3
|
109.7
|
1.0
|
SG
|
A:CYS409
|
2.4
|
134.4
|
1.0
|
CD2
|
A:HIS425
|
2.8
|
105.5
|
1.0
|
CD2
|
A:HIS430
|
3.0
|
104.9
|
1.0
|
CE1
|
A:HIS430
|
3.0
|
111.0
|
1.0
|
CE1
|
A:HIS425
|
3.2
|
113.0
|
1.0
|
CB
|
A:CYS412
|
3.4
|
111.5
|
1.0
|
CB
|
A:CYS409
|
3.5
|
120.6
|
1.0
|
N
|
A:CYS412
|
3.7
|
124.6
|
1.0
|
CG
|
A:HIS425
|
4.0
|
88.8
|
1.0
|
ND1
|
A:HIS430
|
4.1
|
108.7
|
1.0
|
CG
|
A:HIS430
|
4.1
|
108.2
|
1.0
|
CA
|
A:CYS412
|
4.1
|
121.5
|
1.0
|
ND1
|
A:HIS425
|
4.2
|
108.1
|
1.0
|
CB
|
A:ILE411
|
4.3
|
122.3
|
1.0
|
C
|
A:ILE411
|
4.7
|
125.3
|
1.0
|
CG2
|
A:ILE426
|
4.7
|
98.6
|
1.0
|
CA
|
A:CYS409
|
4.9
|
117.3
|
1.0
|
C
|
A:CYS412
|
4.9
|
128.3
|
1.0
|
N
|
A:ILE411
|
4.9
|
113.7
|
1.0
|
CA
|
A:ILE411
|
4.9
|
122.5
|
1.0
|
CG2
|
A:ILE411
|
5.0
|
113.3
|
1.0
|
|
Zinc binding site 5 out
of 8 in 8ssu
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Zinc Binding Sites List in 8ssu
Zinc binding site 5 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn706
b:76.3
occ:1.00
|
NE2
|
A:HIS455
|
2.0
|
69.8
|
1.0
|
NE2
|
A:HIS460
|
2.0
|
72.2
|
1.0
|
SG
|
A:CYS442
|
2.3
|
103.8
|
1.0
|
SG
|
A:CYS439
|
2.3
|
88.0
|
1.0
|
CD2
|
A:HIS455
|
2.8
|
80.9
|
1.0
|
CE1
|
A:HIS460
|
2.9
|
85.9
|
1.0
|
CD2
|
A:HIS460
|
3.0
|
81.8
|
1.0
|
CE1
|
A:HIS455
|
3.2
|
83.5
|
1.0
|
CB
|
A:CYS439
|
3.2
|
90.4
|
1.0
|
CB
|
A:CYS442
|
3.4
|
95.5
|
1.0
|
N
|
A:CYS442
|
3.8
|
94.3
|
1.0
|
ND1
|
A:HIS460
|
4.0
|
81.3
|
1.0
|
CG
|
A:HIS455
|
4.0
|
77.8
|
1.0
|
CG
|
A:HIS460
|
4.1
|
81.5
|
1.0
|
CA
|
A:CYS442
|
4.1
|
87.2
|
1.0
|
ND1
|
A:HIS455
|
4.1
|
90.8
|
1.0
|
CG2
|
A:THR444
|
4.3
|
97.5
|
1.0
|
CB
|
A:HIS441
|
4.7
|
103.2
|
1.0
|
O
|
A:CYS442
|
4.7
|
96.4
|
1.0
|
C
|
A:CYS442
|
4.7
|
83.5
|
1.0
|
CA
|
A:CYS439
|
4.7
|
93.7
|
1.0
|
C
|
A:HIS441
|
4.7
|
88.9
|
1.0
|
CD2
|
A:LEU456
|
4.8
|
79.8
|
1.0
|
N
|
A:HIS441
|
5.0
|
97.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 8ssu
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Zinc Binding Sites List in 8ssu
Zinc binding site 6 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn707
b:135.5
occ:1.00
|
NE2
|
A:HIS485
|
2.0
|
114.6
|
1.0
|
NE2
|
A:HIS489
|
2.0
|
146.1
|
1.0
|
SG
|
A:CYS472
|
2.1
|
124.4
|
1.0
|
SG
|
A:CYS469
|
2.4
|
103.2
|
1.0
|
CD2
|
A:HIS485
|
2.5
|
113.3
|
1.0
|
CD2
|
A:HIS489
|
2.9
|
144.3
|
1.0
|
CE1
|
A:HIS489
|
3.1
|
142.5
|
1.0
|
CE1
|
A:HIS485
|
3.2
|
116.0
|
1.0
|
CB
|
A:CYS472
|
3.5
|
106.3
|
1.0
|
CB
|
A:CYS469
|
3.5
|
121.9
|
1.0
|
CG
|
A:HIS485
|
3.7
|
107.7
|
1.0
|
N
|
A:CYS472
|
3.9
|
115.5
|
1.0
|
ND1
|
A:HIS485
|
4.0
|
110.9
|
1.0
|
CG
|
A:HIS489
|
4.1
|
139.7
|
1.0
|
ND1
|
A:HIS489
|
4.2
|
138.7
|
1.0
|
CA
|
A:CYS472
|
4.3
|
112.5
|
1.0
|
O
|
A:HIS485
|
4.5
|
114.9
|
1.0
|
CB
|
A:TYR471
|
4.5
|
104.7
|
1.0
|
C
|
A:TYR471
|
4.6
|
116.4
|
1.0
|
C
|
A:HIS485
|
4.8
|
101.6
|
1.0
|
N
|
A:TYR471
|
4.9
|
115.1
|
1.0
|
CA
|
A:GLN486
|
4.9
|
91.5
|
1.0
|
CA
|
A:TYR471
|
4.9
|
112.0
|
1.0
|
CA
|
A:CYS469
|
4.9
|
117.1
|
1.0
|
CB
|
A:HIS485
|
5.0
|
102.7
|
1.0
|
N
|
A:GLN486
|
5.0
|
90.4
|
1.0
|
|
Zinc binding site 7 out
of 8 in 8ssu
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Zinc Binding Sites List in 8ssu
Zinc binding site 7 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_07.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn708
b:117.6
occ:1.00
|
NE2
|
A:HIS513
|
2.0
|
87.5
|
1.0
|
NE2
|
A:HIS517
|
2.0
|
134.1
|
1.0
|
SG
|
A:CYS500
|
2.3
|
92.5
|
1.0
|
SG
|
A:CYS497
|
2.3
|
190.5
|
1.0
|
CD2
|
A:HIS517
|
2.8
|
126.0
|
1.0
|
CD2
|
A:HIS513
|
2.8
|
88.6
|
1.0
|
CE1
|
A:HIS517
|
3.0
|
123.7
|
1.0
|
CE1
|
A:HIS513
|
3.1
|
89.0
|
1.0
|
CB
|
A:CYS500
|
3.4
|
103.2
|
1.0
|
N
|
A:CYS500
|
3.5
|
122.3
|
1.0
|
CB
|
A:GLN499
|
3.9
|
122.2
|
1.0
|
CG
|
A:HIS517
|
3.9
|
119.3
|
1.0
|
CB
|
A:CYS497
|
3.9
|
115.3
|
1.0
|
CA
|
A:CYS500
|
4.0
|
110.6
|
1.0
|
ND1
|
A:HIS517
|
4.0
|
123.4
|
1.0
|
O
|
A:CYS497
|
4.0
|
137.1
|
1.0
|
C
|
A:GLN499
|
4.0
|
120.0
|
1.0
|
CG
|
A:HIS513
|
4.1
|
88.4
|
1.0
|
ND1
|
A:HIS513
|
4.2
|
86.8
|
1.0
|
CA
|
A:GLN499
|
4.3
|
117.1
|
1.0
|
N
|
A:GLN499
|
4.5
|
125.0
|
1.0
|
CB
|
A:TYR502
|
4.5
|
97.5
|
1.0
|
C
|
A:CYS497
|
4.6
|
130.4
|
1.0
|
C
|
A:CYS500
|
4.6
|
115.2
|
1.0
|
O
|
A:GLN499
|
4.8
|
114.8
|
1.0
|
CA
|
A:CYS497
|
4.8
|
136.8
|
1.0
|
CG
|
A:GLN499
|
4.9
|
112.9
|
1.0
|
O
|
A:HIS513
|
4.9
|
105.2
|
1.0
|
O
|
A:CYS500
|
5.0
|
129.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 8ssu
Go back to
Zinc Binding Sites List in 8ssu
Zinc binding site 8 out
of 8 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_08.jpg) Mono view
![](/pictures/ZN/pdb/ss/8ssu-ZN-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 19MER Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn709
b:73.5
occ:1.00
|
NE2
|
A:HIS546
|
2.0
|
90.6
|
1.0
|
NE2
|
A:HIS541
|
2.0
|
70.6
|
1.0
|
SG
|
A:CYS528
|
2.2
|
73.0
|
1.0
|
SG
|
A:CYS525
|
2.3
|
97.6
|
1.0
|
CD2
|
A:HIS546
|
2.7
|
78.0
|
1.0
|
CD2
|
A:HIS541
|
2.9
|
69.5
|
1.0
|
CE1
|
A:HIS541
|
3.1
|
70.5
|
1.0
|
CB
|
A:CYS525
|
3.2
|
93.2
|
1.0
|
CE1
|
A:HIS546
|
3.2
|
97.5
|
1.0
|
CB
|
A:CYS528
|
3.3
|
76.1
|
1.0
|
N
|
A:CYS528
|
3.6
|
91.5
|
1.0
|
CG
|
A:HIS546
|
3.9
|
81.7
|
1.0
|
CA
|
A:CYS528
|
3.9
|
91.5
|
1.0
|
CG
|
A:HIS541
|
4.1
|
70.1
|
1.0
|
ND1
|
A:HIS541
|
4.2
|
70.7
|
1.0
|
ND1
|
A:HIS546
|
4.2
|
93.1
|
1.0
|
C
|
A:HIS527
|
4.4
|
94.7
|
1.0
|
C
|
A:CYS528
|
4.5
|
90.9
|
1.0
|
O
|
A:CYS528
|
4.5
|
91.5
|
1.0
|
CA
|
A:CYS525
|
4.6
|
93.7
|
1.0
|
CB
|
A:HIS527
|
4.7
|
94.2
|
1.0
|
N
|
A:HIS527
|
4.8
|
98.8
|
1.0
|
CA
|
A:HIS527
|
4.9
|
99.6
|
1.0
|
|
Reference:
J.Yang,
J.R.Horton,
B.Liu,
V.G.Corces,
R.M.Blumenthal,
X.Zhang,
X.Cheng.
Structures of Ctcf-Dna Complexes Including All 11 Zinc Fingers. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37439339
DOI: 10.1093/NAR/GKAD594
Page generated: Thu Dec 28 13:40:42 2023
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