Zinc in PDB 5emc: Transcription Factor Grdbd and Smgre Complex
Protein crystallography data
The structure of Transcription Factor Grdbd and Smgre Complex, PDB code: 5emc
was solved by
X.D.Su,
T.Lian,
J.Jin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.26 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.942,
99.643,
112.229,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.5 /
26.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Transcription Factor Grdbd and Smgre Complex
(pdb code 5emc). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Transcription Factor Grdbd and Smgre Complex, PDB code: 5emc:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5emc
Go back to
Zinc Binding Sites List in 5emc
Zinc binding site 1 out
of 4 in the Transcription Factor Grdbd and Smgre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Transcription Factor Grdbd and Smgre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:37.1
occ:1.00
|
SG
|
A:CYS440
|
2.3
|
42.1
|
1.0
|
SG
|
A:CYS443
|
2.3
|
36.5
|
1.0
|
SG
|
A:CYS460
|
2.4
|
37.0
|
1.0
|
SG
|
A:CYS457
|
2.4
|
36.7
|
1.0
|
CB
|
A:CYS460
|
3.2
|
37.8
|
1.0
|
CB
|
A:CYS440
|
3.3
|
34.5
|
1.0
|
CB
|
A:CYS443
|
3.4
|
27.0
|
1.0
|
CB
|
A:CYS457
|
3.6
|
39.6
|
1.0
|
N
|
A:CYS443
|
3.7
|
30.7
|
1.0
|
N
|
A:CYS457
|
3.9
|
43.2
|
1.0
|
CA
|
A:CYS443
|
4.1
|
36.4
|
1.0
|
CA
|
A:CYS457
|
4.3
|
40.3
|
1.0
|
CA
|
A:CYS460
|
4.3
|
36.7
|
1.0
|
N
|
A:CYS460
|
4.3
|
28.1
|
1.0
|
CB
|
A:VAL442
|
4.4
|
37.1
|
1.0
|
NH2
|
A:ARG489
|
4.4
|
37.3
|
1.0
|
OG
|
A:SER459
|
4.5
|
39.4
|
1.0
|
C
|
A:VAL442
|
4.7
|
37.1
|
1.0
|
CB
|
A:ASP445
|
4.7
|
29.5
|
1.0
|
CA
|
A:CYS440
|
4.7
|
40.9
|
1.0
|
C
|
A:CYS443
|
4.7
|
36.4
|
1.0
|
N
|
A:SER444
|
4.9
|
36.8
|
1.0
|
CA
|
A:VAL442
|
4.9
|
36.4
|
1.0
|
N
|
A:ASP445
|
4.9
|
46.7
|
1.0
|
CD
|
A:ARG489
|
5.0
|
24.4
|
1.0
|
C
|
A:CYS457
|
5.0
|
35.8
|
1.0
|
CG1
|
A:VAL442
|
5.0
|
30.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5emc
Go back to
Zinc Binding Sites List in 5emc
Zinc binding site 2 out
of 4 in the Transcription Factor Grdbd and Smgre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Transcription Factor Grdbd and Smgre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn602
b:22.4
occ:1.00
|
SG
|
A:CYS492
|
2.3
|
23.1
|
1.0
|
SG
|
A:CYS482
|
2.3
|
20.6
|
1.0
|
SG
|
A:CYS476
|
2.4
|
25.2
|
1.0
|
SG
|
A:CYS495
|
2.4
|
27.8
|
1.0
|
CB
|
A:CYS482
|
3.2
|
20.1
|
1.0
|
CB
|
A:CYS476
|
3.3
|
20.5
|
1.0
|
CB
|
A:CYS495
|
3.3
|
21.5
|
1.0
|
CB
|
A:CYS492
|
3.4
|
20.4
|
1.0
|
O
|
A:HOH713
|
3.8
|
19.4
|
1.0
|
N
|
A:CYS482
|
3.9
|
23.5
|
1.0
|
CA
|
A:CYS476
|
4.0
|
20.4
|
1.0
|
O
|
A:HOH742
|
4.0
|
25.6
|
1.0
|
CA
|
A:CYS482
|
4.1
|
26.9
|
1.0
|
O
|
A:HOH702
|
4.3
|
22.1
|
1.0
|
N
|
A:CYS495
|
4.3
|
22.2
|
1.0
|
CA
|
A:ASN480
|
4.3
|
21.1
|
1.0
|
CA
|
A:CYS495
|
4.4
|
22.2
|
1.0
|
N
|
A:ASP481
|
4.5
|
30.7
|
1.0
|
N
|
A:ASN480
|
4.5
|
29.9
|
1.0
|
C
|
A:ASN480
|
4.7
|
21.3
|
1.0
|
N
|
A:ALA477
|
4.7
|
22.1
|
1.0
|
NH1
|
A:ARG498
|
4.7
|
35.4
|
1.0
|
N
|
A:GLY478
|
4.8
|
18.9
|
1.0
|
CA
|
A:CYS492
|
4.8
|
34.9
|
1.0
|
C
|
A:CYS476
|
4.8
|
19.9
|
1.0
|
OD1
|
A:ASN480
|
4.9
|
21.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5emc
Go back to
Zinc Binding Sites List in 5emc
Zinc binding site 3 out
of 4 in the Transcription Factor Grdbd and Smgre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Transcription Factor Grdbd and Smgre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn601
b:29.1
occ:1.00
|
SG
|
B:CYS443
|
2.3
|
32.6
|
1.0
|
SG
|
B:CYS460
|
2.3
|
30.4
|
1.0
|
SG
|
B:CYS440
|
2.4
|
23.6
|
1.0
|
SG
|
B:CYS457
|
2.5
|
28.5
|
1.0
|
CB
|
B:CYS460
|
3.1
|
26.2
|
1.0
|
CB
|
B:CYS440
|
3.2
|
22.1
|
1.0
|
CB
|
B:CYS443
|
3.2
|
22.4
|
1.0
|
CB
|
B:CYS457
|
3.5
|
23.1
|
1.0
|
N
|
B:CYS443
|
3.8
|
34.3
|
1.0
|
N
|
B:CYS457
|
3.9
|
31.0
|
1.0
|
CA
|
B:CYS443
|
4.0
|
29.4
|
1.0
|
CA
|
B:CYS457
|
4.2
|
23.3
|
1.0
|
NH1
|
B:ARG489
|
4.2
|
30.7
|
1.0
|
N
|
B:CYS460
|
4.3
|
23.3
|
1.0
|
CA
|
B:CYS460
|
4.3
|
28.5
|
1.0
|
OG
|
B:SER459
|
4.4
|
33.2
|
1.0
|
CB
|
B:VAL442
|
4.5
|
39.4
|
1.0
|
C
|
B:CYS443
|
4.6
|
33.9
|
1.0
|
CB
|
B:ASP445
|
4.6
|
41.0
|
1.0
|
CA
|
B:CYS440
|
4.6
|
34.8
|
1.0
|
O
|
B:CYS457
|
4.7
|
22.9
|
1.0
|
N
|
B:SER444
|
4.7
|
25.8
|
1.0
|
C
|
B:VAL442
|
4.7
|
38.3
|
1.0
|
N
|
B:ASP445
|
4.8
|
28.4
|
1.0
|
C
|
B:CYS457
|
4.8
|
25.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5emc
Go back to
Zinc Binding Sites List in 5emc
Zinc binding site 4 out
of 4 in the Transcription Factor Grdbd and Smgre Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Transcription Factor Grdbd and Smgre Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn602
b:24.2
occ:1.00
|
SG
|
B:CYS492
|
2.2
|
25.0
|
1.0
|
SG
|
B:CYS482
|
2.3
|
26.6
|
1.0
|
SG
|
B:CYS476
|
2.3
|
24.9
|
1.0
|
SG
|
B:CYS495
|
2.5
|
22.5
|
1.0
|
CB
|
B:CYS482
|
3.1
|
17.5
|
1.0
|
CB
|
B:CYS476
|
3.2
|
17.9
|
1.0
|
CB
|
B:CYS492
|
3.3
|
21.3
|
1.0
|
CB
|
B:CYS495
|
3.3
|
17.1
|
1.0
|
O
|
B:HOH723
|
3.6
|
20.2
|
1.0
|
CA
|
B:CYS476
|
3.9
|
26.5
|
1.0
|
N
|
B:CYS482
|
4.0
|
17.2
|
1.0
|
CA
|
B:CYS482
|
4.1
|
20.1
|
1.0
|
N
|
B:CYS495
|
4.3
|
25.6
|
1.0
|
CA
|
B:CYS495
|
4.4
|
23.0
|
1.0
|
CA
|
B:ASN480
|
4.5
|
36.2
|
1.0
|
N
|
B:ASP481
|
4.6
|
24.5
|
1.0
|
N
|
B:ALA477
|
4.6
|
28.2
|
1.0
|
N
|
B:ASN480
|
4.6
|
29.1
|
1.0
|
C
|
B:CYS476
|
4.7
|
30.0
|
1.0
|
O
|
B:HOH711
|
4.7
|
20.4
|
1.0
|
CA
|
B:CYS492
|
4.7
|
38.4
|
1.0
|
N
|
B:GLY478
|
4.8
|
21.0
|
1.0
|
C
|
B:ASN480
|
4.8
|
29.0
|
1.0
|
O
|
B:HOH718
|
4.9
|
41.2
|
1.0
|
|
Reference:
J.Jin,
T.Lian,
X.D.Su.
The Effects of Cytosine Methylation on General Transcription Factors To Be Published.
Page generated: Sun Oct 27 15:23:20 2024
|