Magnesium in PDB 1t3t: Structure of Formylglycinamide Synthetase
Enzymatic activity of Structure of Formylglycinamide Synthetase
All present enzymatic activity of Structure of Formylglycinamide Synthetase:
6.3.5.3;
Protein crystallography data
The structure of Structure of Formylglycinamide Synthetase, PDB code: 1t3t
was solved by
S.E.Ealick,
R.Anand,
A.A.Hoskin,
J.Stubbe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.73 /
1.90
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.806,
145.806,
141.353,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.8 /
20.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Formylglycinamide Synthetase
(pdb code 1t3t). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Structure of Formylglycinamide Synthetase, PDB code: 1t3t:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 1t3t
Go back to
Magnesium Binding Sites List in 1t3t
Magnesium binding site 1 out
of 3 in the Structure of Formylglycinamide Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Formylglycinamide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2006
b:15.6
occ:1.00
|
O1B
|
A:ADP2005
|
2.0
|
1.6
|
0.5
|
OD1
|
A:ASP884
|
2.2
|
12.5
|
1.0
|
OD1
|
A:ASN722
|
2.2
|
9.7
|
1.0
|
OD1
|
A:ASP679
|
2.2
|
14.3
|
1.0
|
O
|
A:HOH3089
|
2.4
|
24.9
|
1.0
|
O
|
A:HOH3086
|
2.5
|
14.8
|
1.0
|
CG
|
A:ASP884
|
3.1
|
13.8
|
1.0
|
PB
|
A:ADP2005
|
3.1
|
1.6
|
0.5
|
CG
|
A:ASP679
|
3.1
|
16.0
|
1.0
|
CG
|
A:ASN722
|
3.2
|
13.1
|
1.0
|
OD2
|
A:ASP884
|
3.4
|
13.2
|
1.0
|
O2B
|
A:ADP2005
|
3.6
|
1.6
|
0.5
|
ND2
|
A:ASN722
|
3.6
|
12.1
|
1.0
|
O3B
|
A:ADP2005
|
3.7
|
1.6
|
0.5
|
CB
|
A:ASP679
|
3.8
|
14.5
|
1.0
|
O
|
A:HOH2041
|
3.9
|
22.5
|
1.0
|
OD2
|
A:ASP679
|
4.0
|
15.5
|
1.0
|
O
|
A:HOH2061
|
4.0
|
14.8
|
1.0
|
OG
|
A:SER886
|
4.0
|
15.4
|
1.0
|
CA
|
A:ASP679
|
4.3
|
14.1
|
1.0
|
O
|
A:ASP884
|
4.3
|
17.3
|
1.0
|
NE2
|
A:HIS883
|
4.4
|
16.8
|
1.0
|
O
|
A:HOH2682
|
4.4
|
28.1
|
1.0
|
CD2
|
A:HIS883
|
4.4
|
11.0
|
1.0
|
O3A
|
A:ADP2005
|
4.4
|
1.6
|
0.5
|
CB
|
A:ASP884
|
4.5
|
11.2
|
1.0
|
CB
|
A:ASN722
|
4.6
|
11.8
|
1.0
|
N
|
A:ASP884
|
4.7
|
13.5
|
1.0
|
C
|
A:ASP884
|
4.8
|
15.5
|
1.0
|
OE2
|
A:GLU718
|
4.8
|
15.3
|
1.0
|
CA
|
A:ASN722
|
4.8
|
12.6
|
1.0
|
CA
|
A:ASP884
|
4.9
|
13.6
|
1.0
|
CB
|
A:SER886
|
4.9
|
14.2
|
1.0
|
O
|
A:HOH2273
|
5.0
|
24.8
|
1.0
|
O
|
A:ASP679
|
5.0
|
14.2
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 1t3t
Go back to
Magnesium Binding Sites List in 1t3t
Magnesium binding site 2 out
of 3 in the Structure of Formylglycinamide Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Formylglycinamide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2007
b:21.3
occ:1.00
|
O3B
|
A:ADP2005
|
2.1
|
1.6
|
0.5
|
OE2
|
A:GLU718
|
2.1
|
15.3
|
1.0
|
O
|
A:HOH3091
|
2.2
|
91.5
|
1.0
|
O
|
A:HOH3090
|
2.4
|
28.0
|
1.0
|
O
|
A:HOH2054
|
2.5
|
40.6
|
1.0
|
O
|
A:HOH2023
|
2.5
|
32.5
|
1.0
|
CD
|
A:GLU718
|
3.2
|
18.6
|
1.0
|
PB
|
A:ADP2005
|
3.4
|
1.6
|
0.5
|
O2B
|
A:ADP2005
|
3.5
|
1.6
|
0.5
|
OE1
|
A:GLU718
|
3.6
|
18.0
|
1.0
|
O
|
A:HOH2140
|
3.8
|
21.5
|
1.0
|
O
|
A:HOH3086
|
3.9
|
14.8
|
1.0
|
ND2
|
A:ASN722
|
4.2
|
12.1
|
1.0
|
O
|
A:HOH2458
|
4.2
|
28.0
|
1.0
|
O1A
|
A:ADP2005
|
4.2
|
1.6
|
0.5
|
O3A
|
A:ADP2005
|
4.2
|
1.6
|
0.5
|
OD2
|
A:ASP887
|
4.3
|
20.9
|
1.0
|
O
|
A:ILE697
|
4.4
|
13.7
|
1.0
|
CG
|
A:GLU718
|
4.5
|
15.2
|
1.0
|
O
|
A:HOH2103
|
4.5
|
91.5
|
1.0
|
O
|
A:HOH3088
|
4.5
|
19.6
|
1.0
|
O1B
|
A:ADP2005
|
4.5
|
1.6
|
0.5
|
OG
|
A:SER886
|
4.5
|
15.4
|
1.0
|
CB
|
A:SER886
|
4.6
|
14.2
|
1.0
|
PA
|
A:ADP2005
|
4.8
|
2.5
|
0.5
|
O
|
A:GLU699
|
4.8
|
13.9
|
1.0
|
O
|
A:HOH2381
|
5.0
|
24.9
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 1t3t
Go back to
Magnesium Binding Sites List in 1t3t
Magnesium binding site 3 out
of 3 in the Structure of Formylglycinamide Synthetase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Formylglycinamide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2008
b:19.8
occ:1.00
|
O2A
|
A:ADP2005
|
2.2
|
1.6
|
0.5
|
O2B
|
A:ADP2005
|
2.2
|
1.6
|
0.5
|
O
|
A:HOH3087
|
2.5
|
21.5
|
1.0
|
O
|
A:HOH3088
|
2.5
|
19.6
|
1.0
|
O
|
A:HOH3085
|
2.5
|
17.5
|
1.0
|
O
|
A:HOH2041
|
2.6
|
22.5
|
1.0
|
PA
|
A:ADP2005
|
3.2
|
2.5
|
0.5
|
PB
|
A:ADP2005
|
3.3
|
1.6
|
0.5
|
O3A
|
A:ADP2005
|
3.5
|
1.6
|
0.5
|
O
|
A:HOH3090
|
3.8
|
28.0
|
1.0
|
O1A
|
A:ADP2005
|
3.9
|
1.6
|
0.5
|
OG
|
A:SER886
|
4.0
|
15.4
|
1.0
|
O
|
A:HOH3089
|
4.1
|
24.9
|
1.0
|
O
|
A:HOH2156
|
4.1
|
19.6
|
1.0
|
O1B
|
A:ADP2005
|
4.1
|
1.6
|
0.5
|
OE1
|
A:GLU896
|
4.2
|
14.4
|
1.0
|
OE2
|
A:GLU896
|
4.2
|
12.4
|
1.0
|
O
|
A:HOH2061
|
4.4
|
14.8
|
1.0
|
O3B
|
A:ADP2005
|
4.5
|
1.6
|
0.5
|
O
|
A:HOH2273
|
4.5
|
24.8
|
1.0
|
O
|
A:THR645
|
4.5
|
11.7
|
1.0
|
O5'
|
A:ADP2005
|
4.5
|
1.6
|
0.5
|
O
|
A:ASP887
|
4.6
|
15.6
|
1.0
|
OD2
|
A:ASP887
|
4.7
|
20.9
|
1.0
|
CD
|
A:GLU896
|
4.7
|
13.5
|
1.0
|
O
|
A:VAL646
|
4.7
|
12.7
|
1.0
|
CB
|
A:ASP887
|
4.8
|
17.3
|
1.0
|
C5'
|
A:ADP2005
|
4.9
|
3.6
|
0.5
|
|
Reference:
R.Anand,
A.A.Hoskin,
J.Stubbe,
S.E.Ealick.
Domain Organization of Salmonella Typhimurium Formylglycinamide Ribonucleotide Amidotransferase Revealed By X-Ray Crystallography Biochemistry V. 43 10328 2004.
ISSN: ISSN 0006-2960
PubMed: 15301531
DOI: 10.1021/BI0491301
Page generated: Tue Aug 13 14:25:03 2024
|