Zinc in PDB 7jtz: Yeast GLO3 Gap Domain
Protein crystallography data
The structure of Yeast GLO3 Gap Domain, PDB code: 7jtz
was solved by
B.Xie,
L.P.Jackson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.20 /
2.07
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.369,
74.031,
77.902,
90,
105.34,
90
|
R / Rfree (%)
|
18.1 /
23.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Yeast GLO3 Gap Domain
(pdb code 7jtz). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Yeast GLO3 Gap Domain, PDB code: 7jtz:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7jtz
Go back to
Zinc Binding Sites List in 7jtz
Zinc binding site 1 out
of 4 in the Yeast GLO3 Gap Domain
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Yeast GLO3 Gap Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:40.5
occ:1.00
|
SG
|
B:CYS54
|
2.3
|
45.0
|
1.0
|
SG
|
B:CYS51
|
2.3
|
38.7
|
1.0
|
SG
|
B:CYS34
|
2.4
|
38.3
|
1.0
|
SG
|
B:CYS31
|
2.5
|
34.2
|
1.0
|
CB
|
B:CYS31
|
3.2
|
33.6
|
1.0
|
CB
|
B:CYS54
|
3.3
|
36.9
|
1.0
|
CB
|
B:CYS34
|
3.3
|
41.4
|
1.0
|
CB
|
B:CYS51
|
3.6
|
35.3
|
1.0
|
N
|
B:CYS34
|
3.7
|
43.3
|
1.0
|
CA
|
B:CYS34
|
4.0
|
48.1
|
1.0
|
N
|
B:CYS51
|
4.0
|
34.2
|
1.0
|
OE1
|
B:GLN53
|
4.1
|
60.1
|
1.0
|
N
|
B:CYS54
|
4.1
|
38.9
|
1.0
|
CA
|
B:CYS54
|
4.3
|
42.0
|
1.0
|
CA
|
B:CYS51
|
4.4
|
32.8
|
1.0
|
CB
|
B:ASP33
|
4.5
|
33.1
|
1.0
|
C
|
B:ASP33
|
4.6
|
44.8
|
1.0
|
C
|
B:CYS34
|
4.6
|
44.6
|
1.0
|
CB
|
B:ASN36
|
4.7
|
59.1
|
1.0
|
CA
|
B:CYS31
|
4.7
|
33.1
|
1.0
|
N
|
B:GLY35
|
4.8
|
44.6
|
1.0
|
N
|
B:ASP33
|
4.9
|
39.6
|
1.0
|
CA
|
B:ASP33
|
4.9
|
39.0
|
1.0
|
C
|
B:CYS51
|
5.0
|
44.9
|
1.0
|
O
|
B:CYS51
|
5.0
|
34.9
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7jtz
Go back to
Zinc Binding Sites List in 7jtz
Zinc binding site 2 out
of 4 in the Yeast GLO3 Gap Domain
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Yeast GLO3 Gap Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:44.8
occ:1.00
|
SG
|
A:CYS51
|
2.2
|
40.2
|
1.0
|
SG
|
A:CYS34
|
2.4
|
41.6
|
1.0
|
SG
|
A:CYS31
|
2.4
|
34.9
|
1.0
|
SG
|
A:CYS54
|
2.5
|
48.7
|
1.0
|
CB
|
A:CYS34
|
3.2
|
45.3
|
1.0
|
CB
|
A:CYS31
|
3.2
|
30.1
|
1.0
|
CB
|
A:CYS54
|
3.2
|
38.0
|
1.0
|
CB
|
A:CYS51
|
3.5
|
35.5
|
1.0
|
N
|
A:CYS34
|
3.7
|
33.7
|
1.0
|
O
|
A:HOH339
|
3.8
|
57.5
|
1.0
|
N
|
A:CYS51
|
3.9
|
30.5
|
1.0
|
CA
|
A:CYS34
|
4.0
|
43.0
|
1.0
|
N
|
A:CYS54
|
4.1
|
35.4
|
1.0
|
CA
|
A:CYS51
|
4.2
|
27.1
|
1.0
|
CA
|
A:CYS54
|
4.3
|
41.2
|
1.0
|
C
|
A:CYS34
|
4.5
|
39.3
|
1.0
|
ND2
|
A:ASN36
|
4.5
|
59.7
|
1.0
|
CB
|
A:ASN36
|
4.6
|
55.6
|
1.0
|
CA
|
A:CYS31
|
4.6
|
24.7
|
1.0
|
N
|
A:GLY35
|
4.7
|
37.2
|
1.0
|
CB
|
A:ASP33
|
4.7
|
41.6
|
1.0
|
C
|
A:ASP33
|
4.8
|
45.9
|
1.0
|
N
|
A:ASN36
|
4.8
|
42.4
|
1.0
|
C
|
A:CYS51
|
4.8
|
39.9
|
1.0
|
CG
|
A:ASN36
|
4.9
|
65.4
|
1.0
|
O
|
A:CYS51
|
5.0
|
32.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7jtz
Go back to
Zinc Binding Sites List in 7jtz
Zinc binding site 3 out
of 4 in the Yeast GLO3 Gap Domain
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Yeast GLO3 Gap Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:42.0
occ:1.00
|
SG
|
C:CYS54
|
2.2
|
43.3
|
1.0
|
SG
|
C:CYS34
|
2.3
|
43.4
|
1.0
|
SG
|
C:CYS31
|
2.4
|
32.5
|
1.0
|
SG
|
C:CYS51
|
2.5
|
46.3
|
1.0
|
CB
|
C:CYS54
|
3.1
|
43.2
|
1.0
|
CB
|
C:CYS31
|
3.2
|
35.3
|
1.0
|
CB
|
C:CYS34
|
3.5
|
39.1
|
1.0
|
CB
|
C:CYS51
|
3.6
|
42.7
|
1.0
|
N
|
C:CYS34
|
3.8
|
44.4
|
1.0
|
N
|
C:CYS54
|
4.0
|
42.7
|
1.0
|
N
|
C:CYS51
|
4.0
|
32.8
|
1.0
|
CA
|
C:CYS34
|
4.2
|
44.1
|
1.0
|
CA
|
C:CYS54
|
4.2
|
46.5
|
1.0
|
ND2
|
C:ASN36
|
4.3
|
44.2
|
1.0
|
CA
|
C:CYS51
|
4.3
|
34.9
|
1.0
|
CB
|
C:ASN36
|
4.4
|
47.8
|
1.0
|
C
|
C:ASP33
|
4.5
|
46.3
|
1.0
|
CB
|
C:ASP33
|
4.6
|
39.1
|
1.0
|
N
|
C:ASN36
|
4.7
|
58.4
|
1.0
|
CA
|
C:CYS31
|
4.7
|
39.3
|
1.0
|
C
|
C:CYS34
|
4.7
|
50.6
|
1.0
|
CG
|
C:ASN36
|
4.8
|
50.6
|
1.0
|
N
|
C:ASP33
|
4.8
|
34.4
|
1.0
|
C
|
C:CYS51
|
4.9
|
37.2
|
1.0
|
CA
|
C:ASP33
|
4.9
|
35.7
|
1.0
|
O
|
C:CYS51
|
4.9
|
35.9
|
1.0
|
N
|
C:GLY35
|
5.0
|
35.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7jtz
Go back to
Zinc Binding Sites List in 7jtz
Zinc binding site 4 out
of 4 in the Yeast GLO3 Gap Domain
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Yeast GLO3 Gap Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn201
b:58.6
occ:1.00
|
SG
|
D:CYS54
|
2.1
|
59.2
|
1.0
|
SG
|
D:CYS31
|
2.4
|
45.5
|
1.0
|
SG
|
D:CYS34
|
2.5
|
65.7
|
1.0
|
SG
|
D:CYS51
|
2.5
|
58.4
|
1.0
|
CB
|
D:CYS54
|
3.2
|
47.1
|
1.0
|
CB
|
D:CYS31
|
3.3
|
48.0
|
1.0
|
CB
|
D:CYS34
|
3.4
|
67.5
|
1.0
|
CB
|
D:CYS51
|
3.6
|
50.4
|
1.0
|
N
|
D:CYS34
|
3.7
|
55.3
|
1.0
|
N
|
D:CYS51
|
4.0
|
44.8
|
1.0
|
CA
|
D:CYS34
|
4.1
|
64.2
|
1.0
|
N
|
D:CYS54
|
4.1
|
48.2
|
1.0
|
CA
|
D:CYS54
|
4.3
|
47.9
|
1.0
|
CA
|
D:CYS51
|
4.4
|
44.7
|
1.0
|
ND2
|
D:ASN36
|
4.4
|
71.0
|
1.0
|
CB
|
D:ASP33
|
4.4
|
47.2
|
1.0
|
C
|
D:ASP33
|
4.6
|
46.0
|
1.0
|
C
|
D:CYS34
|
4.7
|
61.4
|
1.0
|
CA
|
D:CYS31
|
4.7
|
40.9
|
1.0
|
N
|
D:GLY35
|
4.8
|
59.7
|
1.0
|
CB
|
D:ASN36
|
4.8
|
66.4
|
1.0
|
C
|
D:CYS51
|
4.8
|
48.5
|
1.0
|
CA
|
D:ASP33
|
4.9
|
42.0
|
1.0
|
N
|
D:ASP33
|
4.9
|
44.5
|
1.0
|
CG
|
D:ASN36
|
4.9
|
71.2
|
1.0
|
N
|
D:ASN36
|
4.9
|
58.4
|
1.0
|
O
|
D:CYS51
|
5.0
|
49.2
|
1.0
|
|
Reference:
B.Xie,
C.Jung,
M.Chandra,
A.Engel,
A.K.Kendall,
L.P.Jackson.
The GLO3 Gap Crystal Structure Supports the Molecular Niche Model For Arfgaps in Copi Coats Advances in Biological V. 79 2021REGULATION.
DOI: HTTPS://DOI.ORG/10.1016/J.JBIOR.2020.100781
Page generated: Tue Oct 29 21:05:14 2024
|