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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

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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

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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

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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

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