Zinc in PDB 6j6q: Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
Enzymatic activity of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
All present enzymatic activity of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom:
2.3.2.27;
Other elements in 6j6q:
The structure of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
(pdb code 6j6q). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the
Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom, PDB code: 6j6q:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
Zinc binding site 1 out
of 7 in 6j6q
Go back to
Zinc Binding Sites List in 6j6q
Zinc binding site 1 out
of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
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 Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Zn400
b:74.8
occ:1.00
|
SG
|
Q:CYS74
|
2.3
|
40.9
|
1.0
|
SG
|
Q:CYS71
|
2.3
|
38.0
|
1.0
|
SG
|
Q:CYS13
|
2.3
|
46.9
|
1.0
|
SG
|
Q:CYS16
|
2.3
|
43.4
|
1.0
|
CB
|
Q:CYS13
|
2.9
|
46.9
|
1.0
|
CB
|
Q:CYS71
|
3.2
|
38.0
|
1.0
|
CB
|
Q:CYS74
|
3.3
|
40.9
|
1.0
|
N
|
Q:CYS74
|
3.4
|
40.9
|
1.0
|
CA
|
Q:CYS74
|
3.8
|
40.9
|
1.0
|
N
|
Q:CYS13
|
3.8
|
46.9
|
1.0
|
CA
|
Q:CYS13
|
3.9
|
46.9
|
1.0
|
CB
|
Q:CYS16
|
4.0
|
43.4
|
1.0
|
C
|
Q:CYS74
|
4.3
|
40.9
|
1.0
|
N
|
Q:MET75
|
4.3
|
39.5
|
1.0
|
C
|
Q:CYS73
|
4.6
|
37.8
|
1.0
|
CA
|
Q:CYS71
|
4.6
|
38.0
|
1.0
|
N
|
Q:LEU76
|
4.7
|
39.4
|
1.0
|
CB
|
Q:CYS73
|
4.7
|
37.8
|
1.0
|
N
|
Q:CYS16
|
4.8
|
43.4
|
1.0
|
N
|
Q:CYS73
|
4.8
|
37.8
|
1.0
|
CA
|
Q:CYS16
|
4.9
|
43.4
|
1.0
|
CA
|
Q:CYS73
|
4.9
|
37.8
|
1.0
|
C
|
Q:ILE12
|
5.0
|
40.0
|
1.0
|
|
Zinc binding site 2 out
of 7 in 6j6q
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Zinc Binding Sites List in 6j6q
Zinc binding site 2 out
of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
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 Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Zn401
b:62.7
occ:1.00
|
SG
|
Q:CYS37
|
2.3
|
28.1
|
1.0
|
SG
|
Q:CYS61
|
2.3
|
33.7
|
1.0
|
SG
|
Q:CYS64
|
2.3
|
34.1
|
1.0
|
SG
|
Q:CYS34
|
2.3
|
29.3
|
1.0
|
CB
|
Q:CYS34
|
3.0
|
29.3
|
1.0
|
CB
|
Q:CYS64
|
3.1
|
34.1
|
1.0
|
CB
|
Q:CYS37
|
3.1
|
28.1
|
1.0
|
N
|
Q:CYS37
|
3.6
|
28.1
|
1.0
|
CB
|
Q:CYS61
|
3.6
|
33.7
|
1.0
|
N
|
Q:CYS61
|
3.9
|
33.7
|
1.0
|
CA
|
Q:CYS37
|
3.9
|
28.1
|
1.0
|
N
|
Q:CYS64
|
4.2
|
34.1
|
1.0
|
CA
|
Q:CYS64
|
4.2
|
34.1
|
1.0
|
CA
|
Q:CYS61
|
4.3
|
33.7
|
1.0
|
CB
|
Q:ILE36
|
4.5
|
29.0
|
1.0
|
CA
|
Q:CYS34
|
4.5
|
29.3
|
1.0
|
C
|
Q:ILE36
|
4.7
|
29.0
|
1.0
|
C
|
Q:CYS37
|
4.8
|
28.1
|
1.0
|
N
|
Q:ILE36
|
4.9
|
29.0
|
1.0
|
C
|
Q:CYS61
|
4.9
|
33.7
|
1.0
|
O
|
Q:CYS61
|
4.9
|
33.7
|
1.0
|
CB
|
Q:SER114
|
4.9
|
30.1
|
1.0
|
CA
|
Q:ILE36
|
4.9
|
29.0
|
1.0
|
O
|
Q:LEU39
|
5.0
|
28.3
|
1.0
|
|
Zinc binding site 3 out
of 7 in 6j6q
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Zinc Binding Sites List in 6j6q
Zinc binding site 3 out
of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
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 Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Zn400
b:31.7
occ:1.00
|
SG
|
R:CYS81
|
2.3
|
31.1
|
1.0
|
NE2
|
R:HIS91
|
2.3
|
32.1
|
1.0
|
SG
|
R:CYS73
|
2.3
|
29.8
|
1.0
|
SG
|
R:CYS87
|
2.3
|
37.0
|
1.0
|
CE1
|
R:HIS91
|
2.7
|
32.1
|
1.0
|
CB
|
R:CYS73
|
3.2
|
29.8
|
1.0
|
CB
|
R:CYS87
|
3.2
|
37.0
|
1.0
|
CB
|
R:CYS81
|
3.3
|
31.1
|
1.0
|
CD2
|
R:HIS91
|
3.5
|
32.1
|
1.0
|
ND1
|
R:HIS91
|
3.9
|
32.1
|
1.0
|
CG
|
R:HIS91
|
4.3
|
32.1
|
1.0
|
N6
|
E:A35
|
4.5
|
20.4
|
1.0
|
CA
|
R:CYS73
|
4.6
|
29.8
|
1.0
|
CA
|
R:CYS81
|
4.6
|
31.1
|
1.0
|
CA
|
R:CYS87
|
4.7
|
37.0
|
1.0
|
N
|
R:PHE76
|
4.7
|
30.3
|
1.0
|
O
|
R:TYR89
|
4.7
|
34.3
|
1.0
|
CB
|
R:PHE76
|
4.9
|
30.3
|
1.0
|
O
|
R:GLY84
|
4.9
|
37.4
|
1.0
|
|
Zinc binding site 4 out
of 7 in 6j6q
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Zinc Binding Sites List in 6j6q
Zinc binding site 4 out
of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
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 Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Zn1000
b:42.6
occ:1.00
|
SG
|
T:CYS148
|
2.3
|
26.3
|
1.0
|
SG
|
T:CYS104
|
2.3
|
35.5
|
1.0
|
SG
|
T:CYS108
|
2.3
|
35.3
|
1.0
|
SG
|
T:CYS105
|
2.3
|
35.9
|
1.0
|
CB
|
T:CYS104
|
3.1
|
35.5
|
1.0
|
CB
|
T:CYS108
|
3.2
|
35.3
|
1.0
|
N
|
T:CYS105
|
3.7
|
35.9
|
1.0
|
ZN
|
T:ZN1002
|
3.8
|
45.6
|
1.0
|
CB
|
T:CYS148
|
3.8
|
26.3
|
1.0
|
CB
|
T:CYS105
|
3.8
|
35.9
|
1.0
|
ZN
|
T:ZN1001
|
3.9
|
44.3
|
1.0
|
C
|
T:CYS104
|
4.2
|
35.5
|
1.0
|
CA
|
T:CYS104
|
4.2
|
35.5
|
1.0
|
N
|
T:CYS108
|
4.3
|
35.3
|
1.0
|
SG
|
T:CYS145
|
4.3
|
31.2
|
1.0
|
CA
|
T:CYS108
|
4.3
|
35.3
|
1.0
|
CA
|
T:CYS105
|
4.4
|
35.9
|
1.0
|
SG
|
T:CYS122
|
4.5
|
30.1
|
1.0
|
CB
|
T:HIS147
|
4.5
|
29.9
|
1.0
|
CB
|
T:CYS150
|
4.7
|
30.1
|
1.0
|
N
|
T:CYS148
|
4.8
|
26.3
|
1.0
|
CA
|
T:CYS148
|
4.9
|
26.3
|
1.0
|
|
Zinc binding site 5 out
of 7 in 6j6q
Go back to
Zinc Binding Sites List in 6j6q
Zinc binding site 5 out
of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
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 Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Zn1001
b:44.3
occ:1.00
|
SG
|
T:CYS153
|
2.3
|
33.6
|
1.0
|
SG
|
T:CYS150
|
2.3
|
30.1
|
1.0
|
SG
|
T:CYS122
|
2.3
|
30.1
|
1.0
|
SG
|
T:CYS104
|
2.3
|
35.5
|
1.0
|
CB
|
T:CYS150
|
2.3
|
30.1
|
1.0
|
CB
|
T:CYS104
|
2.7
|
35.5
|
1.0
|
CB
|
T:CYS122
|
3.2
|
30.1
|
1.0
|
CA
|
T:CYS104
|
3.8
|
35.5
|
1.0
|
ZN
|
T:ZN1002
|
3.8
|
45.6
|
1.0
|
CA
|
T:CYS150
|
3.9
|
30.1
|
1.0
|
ZN
|
T:ZN1000
|
3.9
|
42.6
|
1.0
|
CB
|
T:CYS153
|
3.9
|
33.6
|
1.0
|
N
|
T:CYS153
|
4.2
|
33.6
|
1.0
|
O
|
T:CYS122
|
4.4
|
30.1
|
1.0
|
SG
|
T:CYS108
|
4.4
|
35.3
|
1.0
|
CA
|
T:CYS122
|
4.4
|
30.1
|
1.0
|
N
|
T:CYS104
|
4.5
|
35.5
|
1.0
|
C
|
T:CYS122
|
4.5
|
30.1
|
1.0
|
C
|
T:CYS150
|
4.5
|
30.1
|
1.0
|
SG
|
T:CYS145
|
4.5
|
31.2
|
1.0
|
N
|
T:GLY152
|
4.6
|
32.1
|
1.0
|
CA
|
T:CYS153
|
4.6
|
33.6
|
1.0
|
N
|
T:CYS150
|
4.6
|
30.1
|
1.0
|
C
|
T:GLY152
|
4.7
|
32.1
|
1.0
|
N
|
T:ARG151
|
4.7
|
32.9
|
1.0
|
SG
|
T:CYS148
|
4.8
|
26.3
|
1.0
|
CB
|
T:CYS108
|
4.8
|
35.3
|
1.0
|
CB
|
n:PRO68
|
4.9
|
33.4
|
1.0
|
CA
|
T:GLY152
|
5.0
|
32.1
|
1.0
|
|
Zinc binding site 6 out
of 7 in 6j6q
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Zinc Binding Sites List in 6j6q
Zinc binding site 6 out
of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
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 Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Zn1002
b:45.6
occ:1.00
|
SG
|
T:CYS122
|
2.3
|
30.1
|
1.0
|
SG
|
T:CYS120
|
2.3
|
32.1
|
1.0
|
SG
|
T:CYS108
|
2.3
|
35.3
|
1.0
|
SG
|
T:CYS145
|
2.3
|
31.2
|
1.0
|
CB
|
T:CYS145
|
3.0
|
31.2
|
1.0
|
CB
|
T:CYS120
|
3.2
|
32.1
|
1.0
|
CB
|
T:CYS108
|
3.5
|
35.3
|
1.0
|
CB
|
T:CYS122
|
3.5
|
30.1
|
1.0
|
ZN
|
T:ZN1000
|
3.8
|
42.6
|
1.0
|
ZN
|
T:ZN1001
|
3.8
|
44.3
|
1.0
|
N
|
T:CYS122
|
4.3
|
30.1
|
1.0
|
SG
|
T:CYS148
|
4.4
|
26.3
|
1.0
|
CD2
|
T:HIS147
|
4.4
|
29.9
|
1.0
|
SG
|
T:CYS104
|
4.4
|
35.5
|
1.0
|
CB
|
T:CYS150
|
4.4
|
30.1
|
1.0
|
CA
|
T:CYS122
|
4.5
|
30.1
|
1.0
|
CA
|
T:CYS145
|
4.5
|
31.2
|
1.0
|
CA
|
T:CYS108
|
4.6
|
35.3
|
1.0
|
CA
|
T:CYS120
|
4.6
|
32.1
|
1.0
|
CB
|
T:HIS147
|
4.7
|
29.9
|
1.0
|
CG
|
T:HIS147
|
4.9
|
29.9
|
1.0
|
C
|
T:CYS120
|
5.0
|
32.1
|
1.0
|
|
Zinc binding site 7 out
of 7 in 6j6q
Go back to
Zinc Binding Sites List in 6j6q
Zinc binding site 7 out
of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom
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 Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn300
b:97.6
occ:1.00
|
SG
|
F:CYS54
|
2.3
|
71.5
|
1.0
|
SG
|
F:CYS88
|
2.3
|
65.8
|
1.0
|
SG
|
F:CYS91
|
2.3
|
77.0
|
1.0
|
SG
|
F:CYS51
|
2.3
|
69.3
|
1.0
|
CB
|
F:CYS51
|
3.3
|
69.3
|
1.0
|
CB
|
F:CYS88
|
3.4
|
65.8
|
1.0
|
CB
|
F:CYS91
|
3.6
|
77.0
|
1.0
|
CB
|
F:CYS54
|
3.7
|
71.5
|
1.0
|
N
|
F:CYS54
|
3.9
|
71.5
|
1.0
|
N
|
F:CYS91
|
3.9
|
77.0
|
1.0
|
CA
|
F:CYS91
|
4.3
|
77.0
|
1.0
|
CA
|
F:CYS54
|
4.3
|
71.5
|
1.0
|
CB
|
F:GLU56
|
4.6
|
66.8
|
1.0
|
O
|
F:CYS91
|
4.6
|
77.0
|
1.0
|
CB
|
F:ARG90
|
4.7
|
85.7
|
1.0
|
C
|
F:CYS91
|
4.7
|
77.0
|
1.0
|
C
|
F:CYS54
|
4.8
|
71.5
|
1.0
|
CA
|
F:CYS51
|
4.8
|
69.3
|
1.0
|
CA
|
F:CYS88
|
4.8
|
65.8
|
1.0
|
CB
|
F:GLU53
|
4.8
|
72.2
|
1.0
|
CB
|
F:ASN93
|
4.9
|
59.2
|
1.0
|
N
|
F:GLU56
|
4.9
|
66.8
|
1.0
|
C
|
F:ARG90
|
5.0
|
85.7
|
1.0
|
N
|
F:ARG90
|
5.0
|
85.7
|
1.0
|
C
|
F:GLU53
|
5.0
|
72.2
|
1.0
|
N
|
F:GLU53
|
5.0
|
72.2
|
1.0
|
N
|
F:ASN55
|
5.0
|
65.2
|
1.0
|
|
Reference:
R.Wan,
R.Bai,
C.Yan,
J.Lei,
Y.Shi.
Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Cell V. 177 339 2019.
ISSN: ISSN 1097-4172
PubMed: 30879786
DOI: 10.1016/J.CELL.2019.02.006
Page generated: Tue Oct 29 00:55:23 2024
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