Zinc in PDB 7lm3: Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe
Protein crystallography data
The structure of Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe, PDB code: 7lm3
was solved by
R.Shrestha,
C.Das,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.04 /
2.70
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.531,
121.338,
57.145,
90,
129.58,
90
|
R / Rfree (%)
|
20.1 /
25.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe
(pdb code 7lm3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe, PDB code: 7lm3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7lm3
Go back to
Zinc Binding Sites List in 7lm3
Zinc binding site 1 out
of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe
![](/pictures/ZN/pdb/lm/7lm3-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/lm/7lm3-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 Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:81.8
occ:1.00
|
NE2
|
A:HIS406
|
2.0
|
65.7
|
1.0
|
NE2
|
A:HIS404
|
2.0
|
81.3
|
1.0
|
NE2
|
A:HIS356
|
2.1
|
74.3
|
1.0
|
SG
|
A:CYS397
|
2.3
|
67.6
|
1.0
|
CD2
|
A:HIS404
|
2.6
|
82.4
|
1.0
|
CE1
|
A:HIS406
|
2.9
|
70.1
|
1.0
|
CD2
|
A:HIS356
|
3.0
|
65.2
|
1.0
|
CE1
|
A:HIS356
|
3.0
|
73.6
|
1.0
|
CD2
|
A:HIS406
|
3.1
|
70.3
|
1.0
|
CE1
|
A:HIS404
|
3.2
|
83.2
|
1.0
|
CB
|
A:CYS397
|
3.5
|
73.0
|
1.0
|
CG
|
A:HIS404
|
3.8
|
78.2
|
1.0
|
ND1
|
A:HIS406
|
4.1
|
71.7
|
1.0
|
ND1
|
A:HIS404
|
4.1
|
86.7
|
1.0
|
ND1
|
A:HIS356
|
4.1
|
67.8
|
1.0
|
CG
|
A:HIS356
|
4.1
|
60.6
|
1.0
|
O
|
A:CYS397
|
4.2
|
83.8
|
1.0
|
CG
|
A:HIS406
|
4.2
|
73.1
|
1.0
|
OG
|
A:SER352
|
4.4
|
71.2
|
1.0
|
CA
|
A:CYS397
|
4.7
|
74.1
|
1.0
|
C
|
A:CYS397
|
4.7
|
81.0
|
1.0
|
CD1
|
A:ILE394
|
4.7
|
59.8
|
1.0
|
O
|
A:HIS404
|
4.8
|
79.9
|
1.0
|
O
|
A:LYS399
|
4.8
|
87.2
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7lm3
Go back to
Zinc Binding Sites List in 7lm3
Zinc binding site 2 out
of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe
![](/pictures/ZN/pdb/lm/7lm3-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/lm/7lm3-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 Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:66.2
occ:1.00
|
OD2
|
A:ASP354
|
1.9
|
57.3
|
1.0
|
NE2
|
A:HIS343
|
2.2
|
56.5
|
1.0
|
NE2
|
A:HIS341
|
2.3
|
62.4
|
1.0
|
CG
|
A:ASP354
|
2.6
|
58.8
|
1.0
|
OD1
|
A:ASP354
|
2.6
|
59.1
|
1.0
|
CD2
|
A:HIS343
|
3.0
|
63.3
|
1.0
|
CD2
|
A:HIS341
|
3.2
|
63.1
|
1.0
|
CE1
|
A:HIS343
|
3.3
|
64.3
|
1.0
|
CE1
|
A:HIS341
|
3.3
|
58.9
|
1.0
|
OE1
|
A:GLU286
|
3.4
|
90.5
|
1.0
|
CB
|
A:ASP354
|
4.0
|
58.7
|
1.0
|
CG
|
A:HIS343
|
4.2
|
66.0
|
1.0
|
CB
|
A:SER351
|
4.3
|
61.3
|
1.0
|
ND1
|
A:HIS343
|
4.3
|
68.6
|
1.0
|
CD
|
A:GLU286
|
4.3
|
93.4
|
1.0
|
OG
|
A:SER351
|
4.4
|
64.5
|
1.0
|
CG
|
A:HIS341
|
4.4
|
63.4
|
1.0
|
ND1
|
A:HIS341
|
4.4
|
67.8
|
1.0
|
OE2
|
A:GLU286
|
4.6
|
96.5
|
1.0
|
N
|
A:SER351
|
4.6
|
62.8
|
1.0
|
O
|
A:PHE349
|
4.8
|
63.3
|
1.0
|
O
|
A:ASP315
|
4.9
|
86.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7lm3
Go back to
Zinc Binding Sites List in 7lm3
Zinc binding site 3 out
of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe
![](/pictures/ZN/pdb/lm/7lm3-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/lm/7lm3-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 Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:76.4
occ:1.00
|
NE2
|
B:HIS406
|
2.0
|
64.6
|
1.0
|
NE2
|
B:HIS356
|
2.0
|
69.7
|
1.0
|
NE2
|
B:HIS404
|
2.1
|
79.9
|
1.0
|
SG
|
B:CYS397
|
2.3
|
75.1
|
1.0
|
CD2
|
B:HIS404
|
2.6
|
80.4
|
1.0
|
CE1
|
B:HIS406
|
2.9
|
68.9
|
1.0
|
CE1
|
B:HIS356
|
3.0
|
70.9
|
1.0
|
CD2
|
B:HIS356
|
3.0
|
61.0
|
1.0
|
CD2
|
B:HIS406
|
3.1
|
68.7
|
1.0
|
CE1
|
B:HIS404
|
3.2
|
82.7
|
1.0
|
CB
|
B:CYS397
|
3.4
|
75.7
|
1.0
|
CG
|
B:HIS404
|
3.9
|
76.6
|
1.0
|
ND1
|
B:HIS406
|
4.1
|
70.5
|
1.0
|
ND1
|
B:HIS356
|
4.1
|
63.0
|
1.0
|
ND1
|
B:HIS404
|
4.1
|
84.5
|
1.0
|
CG
|
B:HIS356
|
4.1
|
56.2
|
1.0
|
CG
|
B:HIS406
|
4.2
|
67.9
|
1.0
|
O
|
B:CYS397
|
4.3
|
82.0
|
1.0
|
OG
|
B:SER352
|
4.6
|
77.4
|
1.0
|
CD1
|
B:ILE394
|
4.6
|
59.5
|
1.0
|
CA
|
B:CYS397
|
4.7
|
77.1
|
1.0
|
C
|
B:CYS397
|
4.7
|
80.6
|
1.0
|
CG
|
B:LYS399
|
4.8
|
90.2
|
1.0
|
O
|
B:HIS404
|
4.9
|
77.9
|
1.0
|
O
|
B:LYS399
|
5.0
|
87.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7lm3
Go back to
Zinc Binding Sites List in 7lm3
Zinc binding site 4 out
of 4 in the Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe
![](/pictures/ZN/pdb/lm/7lm3-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/lm/7lm3-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 Crystal Structure of THR316ALA Mutant of Jamm Domain of S. Pombe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:58.0
occ:1.00
|
OD2
|
B:ASP354
|
1.9
|
56.5
|
1.0
|
NE2
|
B:HIS343
|
2.2
|
58.2
|
1.0
|
NE2
|
B:HIS341
|
2.3
|
61.0
|
1.0
|
CG
|
B:ASP354
|
2.7
|
58.0
|
1.0
|
OD1
|
B:ASP354
|
2.8
|
56.1
|
1.0
|
CD2
|
B:HIS343
|
3.0
|
61.8
|
1.0
|
CD2
|
B:HIS341
|
3.2
|
65.0
|
1.0
|
CE1
|
B:HIS341
|
3.4
|
60.9
|
1.0
|
CE1
|
B:HIS343
|
3.4
|
62.9
|
1.0
|
OE2
|
B:GLU286
|
3.8
|
89.3
|
1.0
|
CB
|
B:ASP354
|
4.1
|
60.1
|
1.0
|
CG
|
B:HIS343
|
4.2
|
68.1
|
1.0
|
OE1
|
B:GLU286
|
4.2
|
87.0
|
1.0
|
CB
|
B:SER351
|
4.2
|
61.8
|
1.0
|
OG
|
B:SER351
|
4.2
|
65.1
|
1.0
|
CG
|
B:HIS341
|
4.4
|
59.0
|
1.0
|
CD
|
B:GLU286
|
4.4
|
87.5
|
1.0
|
ND1
|
B:HIS343
|
4.4
|
68.3
|
1.0
|
ND1
|
B:HIS341
|
4.4
|
64.3
|
1.0
|
N
|
B:SER351
|
4.7
|
66.1
|
1.0
|
O
|
B:PHE349
|
4.7
|
65.2
|
1.0
|
|
Reference:
R.Shrestha,
C.Das.
Crystal Structure of the THR316ALA Mutant of A Yeast Jamm Deubiquitinase: Implication of Active-Site Loop Dynamics in Catalysis. Acta Crystallogr.,Sect.F V. 77 163 2021.
ISSN: ESSN 2053-230X
PubMed: 34100774
DOI: 10.1107/S2053230X21005124
Page generated: Mon Jul 12 17:20:33 2021
|