Zinc in PDB 4eo4: Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate
Enzymatic activity of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate
All present enzymatic activity of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate:
6.1.1.3;
Protein crystallography data
The structure of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate, PDB code: 4eo4
was solved by
K.M.Peterson,
J.Ling,
I.Simonovic,
D.Soll,
M.Simonovic,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.72 /
2.87
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
213.233,
107.498,
153.391,
90.00,
130.05,
90.00
|
R / Rfree (%)
|
17.5 /
22.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate
(pdb code 4eo4). 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 the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate, PDB code: 4eo4:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4eo4
Go back to
Zinc Binding Sites List in 4eo4
Zinc binding site 1 out
of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1003
b:36.3
occ:1.00
|
NE2
|
A:HIS184
|
2.5
|
22.2
|
1.0
|
ND1
|
A:HIS319
|
2.5
|
28.0
|
1.0
|
N10
|
A:SSA1001
|
2.7
|
54.0
|
1.0
|
SG
|
A:CYS133
|
2.9
|
46.8
|
1.0
|
CA
|
A:SSA1001
|
2.9
|
35.4
|
1.0
|
OG
|
A:SSA1001
|
3.0
|
39.4
|
1.0
|
CB
|
A:SSA1001
|
3.4
|
36.2
|
1.0
|
CE1
|
A:HIS319
|
3.4
|
41.7
|
1.0
|
CD2
|
A:HIS184
|
3.4
|
25.2
|
1.0
|
CB
|
A:CYS133
|
3.4
|
25.4
|
1.0
|
CG
|
A:HIS319
|
3.4
|
39.3
|
1.0
|
CE1
|
A:HIS184
|
3.5
|
32.0
|
1.0
|
CB
|
A:HIS319
|
3.7
|
29.4
|
1.0
|
OH
|
A:TYR270
|
4.1
|
29.8
|
1.0
|
O
|
A:HOH1101
|
4.2
|
48.3
|
1.0
|
N
|
A:CYS133
|
4.2
|
29.5
|
1.0
|
OD2
|
A:ASP182
|
4.2
|
31.6
|
1.0
|
CA
|
A:CYS133
|
4.3
|
33.9
|
1.0
|
OD1
|
A:ASP182
|
4.3
|
40.3
|
1.0
|
C9
|
A:SSA1001
|
4.4
|
38.0
|
1.0
|
NE2
|
A:HIS319
|
4.5
|
45.5
|
1.0
|
CD2
|
A:HIS319
|
4.6
|
46.0
|
1.0
|
SD
|
A:MET131
|
4.6
|
37.2
|
1.0
|
CG
|
A:HIS184
|
4.6
|
31.8
|
1.0
|
ND1
|
A:HIS184
|
4.6
|
40.8
|
1.0
|
OE1
|
A:GLN292
|
4.6
|
41.0
|
1.0
|
CA
|
A:HIS319
|
4.7
|
30.9
|
1.0
|
CG
|
A:ASP182
|
4.7
|
43.2
|
1.0
|
CZ
|
A:TYR270
|
4.7
|
42.4
|
1.0
|
CB
|
A:MET131
|
4.8
|
30.8
|
1.0
|
O9
|
A:SSA1001
|
5.0
|
44.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4eo4
Go back to
Zinc Binding Sites List in 4eo4
Zinc binding site 2 out
of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1003
b:62.2
occ:1.00
|
ND1
|
B:HIS319
|
2.6
|
49.4
|
1.0
|
NE2
|
B:HIS184
|
2.6
|
39.4
|
1.0
|
N10
|
B:SSA1001
|
2.7
|
58.3
|
1.0
|
OG
|
B:SSA1001
|
2.8
|
41.2
|
1.0
|
SG
|
B:CYS133
|
2.8
|
44.2
|
1.0
|
CA
|
B:SSA1001
|
3.0
|
48.6
|
1.0
|
CB
|
B:HIS319
|
3.1
|
38.7
|
1.0
|
CG
|
B:HIS319
|
3.1
|
51.3
|
1.0
|
CD2
|
B:HIS184
|
3.2
|
38.5
|
1.0
|
CB
|
B:SSA1001
|
3.3
|
45.7
|
1.0
|
CE1
|
B:HIS319
|
3.6
|
63.5
|
1.0
|
CE1
|
B:HIS184
|
3.7
|
46.7
|
1.0
|
CB
|
B:CYS133
|
4.0
|
49.7
|
1.0
|
CA
|
B:HIS319
|
4.1
|
35.4
|
1.0
|
OD1
|
B:ASP182
|
4.2
|
64.2
|
1.0
|
CD2
|
B:HIS319
|
4.2
|
66.4
|
1.0
|
OD2
|
B:ASP182
|
4.2
|
39.9
|
1.0
|
O
|
B:HOH1107
|
4.3
|
52.0
|
1.0
|
CG
|
B:HIS184
|
4.4
|
46.8
|
1.0
|
C9
|
B:SSA1001
|
4.5
|
49.1
|
1.0
|
NE2
|
B:HIS319
|
4.5
|
76.8
|
1.0
|
CA
|
B:CYS133
|
4.5
|
39.4
|
1.0
|
N
|
B:CYS133
|
4.6
|
44.0
|
1.0
|
ND1
|
B:HIS184
|
4.6
|
47.0
|
1.0
|
OH
|
B:TYR270
|
4.7
|
65.3
|
1.0
|
CG
|
B:ASP182
|
4.7
|
55.3
|
1.0
|
OE1
|
B:GLN292
|
4.7
|
61.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4eo4
Go back to
Zinc Binding Sites List in 4eo4
Zinc binding site 3 out
of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1003
b:61.5
occ:1.00
|
OG
|
C:SSA1001
|
2.3
|
47.8
|
1.0
|
ND1
|
C:HIS319
|
2.4
|
64.3
|
1.0
|
NE2
|
C:HIS184
|
2.5
|
44.7
|
1.0
|
N10
|
C:SSA1001
|
2.8
|
69.6
|
1.0
|
CA
|
C:SSA1001
|
3.0
|
43.0
|
1.0
|
CB
|
C:SSA1001
|
3.1
|
48.9
|
1.0
|
CG
|
C:HIS319
|
3.2
|
56.8
|
1.0
|
CB
|
C:HIS319
|
3.3
|
45.6
|
1.0
|
CE1
|
C:HIS184
|
3.4
|
49.6
|
1.0
|
CD2
|
C:HIS184
|
3.4
|
48.0
|
1.0
|
CE1
|
C:HIS319
|
3.4
|
65.5
|
1.0
|
SG
|
C:CYS133
|
3.5
|
55.4
|
1.0
|
CB
|
C:CYS133
|
3.6
|
48.5
|
1.0
|
O
|
C:HOH1135
|
4.1
|
54.5
|
1.0
|
OD1
|
C:ASP182
|
4.1
|
53.9
|
1.0
|
OD2
|
C:ASP182
|
4.2
|
51.6
|
1.0
|
CA
|
C:HIS319
|
4.2
|
42.6
|
1.0
|
OH
|
C:TYR270
|
4.3
|
59.0
|
1.0
|
CD2
|
C:HIS319
|
4.4
|
64.7
|
1.0
|
CA
|
C:CYS133
|
4.4
|
52.9
|
1.0
|
N
|
C:CYS133
|
4.4
|
54.3
|
1.0
|
ND1
|
C:HIS184
|
4.5
|
51.1
|
1.0
|
NE2
|
C:HIS319
|
4.5
|
77.7
|
1.0
|
OE1
|
C:GLN292
|
4.5
|
52.5
|
1.0
|
C9
|
C:SSA1001
|
4.5
|
55.6
|
1.0
|
CG
|
C:HIS184
|
4.5
|
47.2
|
1.0
|
CG
|
C:ASP182
|
4.6
|
61.2
|
1.0
|
SD
|
C:MET131
|
5.0
|
66.1
|
1.0
|
CZ
|
C:TYR270
|
5.0
|
76.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4eo4
Go back to
Zinc Binding Sites List in 4eo4
Zinc binding site 4 out
of 4 in the Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Yeast Mitochondrial Threonyl-Trna Synthetase (MST1) in Complex with Seryl Sulfamoyl Adenylate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1003
b:75.4
occ:1.00
|
SG
|
D:CYS133
|
1.9
|
40.8
|
1.0
|
N10
|
D:SSA1001
|
2.0
|
64.6
|
1.0
|
NE2
|
D:HIS184
|
2.6
|
62.5
|
1.0
|
ND1
|
D:HIS319
|
2.7
|
62.7
|
1.0
|
CA
|
D:SSA1001
|
2.8
|
57.5
|
1.0
|
OG
|
D:SSA1001
|
3.0
|
59.7
|
1.0
|
CB
|
D:SSA1001
|
3.3
|
50.2
|
1.0
|
CE1
|
D:HIS184
|
3.4
|
66.7
|
1.0
|
CD2
|
D:HIS184
|
3.5
|
63.8
|
1.0
|
CB
|
D:CYS133
|
3.5
|
46.8
|
1.0
|
CG
|
D:HIS319
|
3.6
|
54.1
|
1.0
|
O
|
D:HOH1129
|
3.6
|
44.9
|
1.0
|
CE1
|
D:HIS319
|
3.7
|
56.1
|
1.0
|
CB
|
D:HIS319
|
3.7
|
46.6
|
1.0
|
OD1
|
D:ASP182
|
4.1
|
51.9
|
1.0
|
CA
|
D:CYS133
|
4.1
|
48.7
|
1.0
|
OD2
|
D:ASP182
|
4.2
|
54.3
|
1.0
|
C9
|
D:SSA1001
|
4.2
|
53.0
|
1.0
|
N
|
D:CYS133
|
4.2
|
64.6
|
1.0
|
OH
|
D:TYR270
|
4.4
|
60.8
|
1.0
|
ND1
|
D:HIS184
|
4.5
|
64.2
|
1.0
|
CA
|
D:HIS319
|
4.5
|
40.8
|
1.0
|
CG
|
D:HIS184
|
4.5
|
66.3
|
1.0
|
CG
|
D:ASP182
|
4.6
|
50.8
|
1.0
|
O9
|
D:SSA1001
|
4.6
|
58.2
|
1.0
|
CD2
|
D:HIS319
|
4.7
|
63.0
|
1.0
|
NE2
|
D:HIS319
|
4.8
|
77.3
|
1.0
|
SD
|
D:MET131
|
4.8
|
98.8
|
1.0
|
OE1
|
D:GLN292
|
4.8
|
66.4
|
1.0
|
CB
|
D:MET131
|
4.9
|
63.6
|
1.0
|
|
Reference:
J.Ling,
K.M.Peterson,
I.Simonovic,
D.Soll,
M.Simonovic.
The Mechanism of Pre-Transfer Editing in Yeast Mitochondrial Threonyl-Trna Synthetase. J.Biol.Chem. V. 287 28518 2012.
ISSN: ISSN 0021-9258
PubMed: 22773845
DOI: 10.1074/JBC.M112.372920
Page generated: Sat Oct 26 22:02:52 2024
|