Magnesium in PDB 1kj8: Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar
Protein crystallography data
The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar, PDB code: 1kj8
was solved by
J.B.Thoden,
S.M.Firestine,
S.J.Benkovic,
H.M.Holden,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.60
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.100,
179.300,
75.800,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1kj8:
The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar
(pdb code 1kj8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar, PDB code: 1kj8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1kj8
Go back to
Magnesium Binding Sites List in 1kj8
Magnesium binding site 1 out
of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg393
b:16.8
occ:1.00
|
O3G
|
A:ATP1
|
2.0
|
17.1
|
1.0
|
O
|
A:HOH410
|
2.0
|
14.7
|
1.0
|
O2B
|
A:ATP1
|
2.0
|
14.2
|
1.0
|
O
|
A:HOH533
|
2.2
|
21.7
|
1.0
|
OE2
|
A:GLU279
|
2.3
|
14.0
|
1.0
|
OE1
|
A:GLU279
|
2.3
|
14.2
|
1.0
|
CD
|
A:GLU279
|
2.6
|
17.4
|
1.0
|
PG
|
A:ATP1
|
3.2
|
19.3
|
1.0
|
PB
|
A:ATP1
|
3.3
|
16.4
|
1.0
|
O3B
|
A:ATP1
|
3.5
|
16.1
|
1.0
|
O2G
|
A:ATP1
|
3.7
|
15.0
|
1.0
|
MG
|
A:MG394
|
3.8
|
12.9
|
1.0
|
O
|
A:HOH527
|
4.0
|
20.5
|
1.0
|
O
|
A:HOH508
|
4.0
|
25.3
|
1.0
|
NH1
|
A:ARG114
|
4.0
|
13.7
|
1.0
|
CG
|
A:GLU279
|
4.1
|
12.4
|
1.0
|
O2A
|
A:ATP1
|
4.1
|
19.8
|
1.0
|
O
|
A:SER159
|
4.2
|
25.3
|
1.0
|
O3A
|
A:ATP1
|
4.2
|
21.1
|
1.0
|
OE2
|
A:GLU84
|
4.3
|
19.8
|
1.0
|
O1B
|
A:ATP1
|
4.3
|
14.8
|
1.0
|
OE1
|
A:GLU84
|
4.3
|
25.6
|
1.0
|
O
|
A:HOH461
|
4.4
|
16.0
|
1.0
|
NH2
|
A:ARG114
|
4.4
|
17.7
|
1.0
|
O1G
|
A:ATP1
|
4.5
|
18.3
|
1.0
|
PA
|
A:ATP1
|
4.6
|
16.4
|
1.0
|
CZ
|
A:ARG114
|
4.6
|
13.9
|
1.0
|
O1A
|
A:ATP1
|
4.7
|
18.6
|
1.0
|
CB
|
A:SER160
|
4.7
|
39.8
|
1.0
|
CA
|
A:SER160
|
4.7
|
20.4
|
1.0
|
CD
|
A:GLU84
|
4.8
|
43.4
|
1.0
|
OE1
|
A:GLU267
|
4.8
|
20.5
|
1.0
|
CB
|
A:GLU279
|
4.9
|
10.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1kj8
Go back to
Magnesium Binding Sites List in 1kj8
Magnesium binding site 2 out
of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg394
b:12.9
occ:1.00
|
O2A
|
A:ATP1
|
2.0
|
19.8
|
1.0
|
OE1
|
A:GLU279
|
2.0
|
14.2
|
1.0
|
OE1
|
A:GLU267
|
2.1
|
20.5
|
1.0
|
O2G
|
A:ATP1
|
2.1
|
15.0
|
1.0
|
O
|
A:HOH404
|
2.2
|
12.6
|
1.0
|
OE2
|
A:GLU267
|
2.2
|
18.6
|
1.0
|
CD
|
A:GLU267
|
2.5
|
17.8
|
1.0
|
CD
|
A:GLU279
|
3.1
|
17.4
|
1.0
|
PG
|
A:ATP1
|
3.2
|
19.3
|
1.0
|
PA
|
A:ATP1
|
3.4
|
16.4
|
1.0
|
O3B
|
A:ATP1
|
3.5
|
16.1
|
1.0
|
CG
|
A:GLU279
|
3.7
|
12.4
|
1.0
|
MG
|
A:MG393
|
3.8
|
16.8
|
1.0
|
O3G
|
A:ATP1
|
3.8
|
17.1
|
1.0
|
CG
|
A:GLU267
|
4.0
|
14.9
|
1.0
|
O3A
|
A:ATP1
|
4.0
|
21.1
|
1.0
|
O
|
A:HOH402
|
4.0
|
8.4
|
1.0
|
O2B
|
A:ATP1
|
4.0
|
14.2
|
1.0
|
O
|
A:HOH455
|
4.1
|
19.3
|
1.0
|
PB
|
A:ATP1
|
4.1
|
16.4
|
1.0
|
OE2
|
A:GLU279
|
4.2
|
14.0
|
1.0
|
O
|
A:HOH423
|
4.2
|
13.6
|
1.0
|
O1A
|
A:ATP1
|
4.3
|
18.6
|
1.0
|
O5'
|
A:ATP1
|
4.4
|
14.7
|
1.0
|
O3'
|
A:ATP1
|
4.5
|
14.7
|
1.0
|
O1G
|
A:ATP1
|
4.5
|
18.3
|
1.0
|
C5'
|
A:ATP1
|
4.5
|
15.4
|
1.0
|
NE2
|
A:HIS285
|
4.6
|
13.7
|
1.0
|
O
|
A:HOH508
|
4.6
|
25.3
|
1.0
|
O
|
A:HOH533
|
4.7
|
21.7
|
1.0
|
CB
|
A:GLU267
|
4.8
|
14.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1kj8
Go back to
Magnesium Binding Sites List in 1kj8
Magnesium binding site 3 out
of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg393
b:51.5
occ:1.00
|
O3G
|
B:ATP397
|
2.0
|
91.6
|
1.0
|
O
|
B:HOH684
|
2.6
|
40.0
|
1.0
|
OE2
|
B:GLU279
|
2.7
|
32.9
|
1.0
|
OE1
|
B:GLU279
|
2.9
|
31.5
|
1.0
|
O2B
|
B:ATP397
|
3.0
|
54.6
|
1.0
|
CD
|
B:GLU279
|
3.1
|
35.6
|
1.0
|
PG
|
B:ATP397
|
3.4
|
95.9
|
1.0
|
NH2
|
B:ARG114
|
3.8
|
0.0
|
1.0
|
PB
|
B:ATP397
|
3.9
|
62.0
|
1.0
|
O
|
B:HOH740
|
3.9
|
42.8
|
1.0
|
O3B
|
B:ATP397
|
4.0
|
97.2
|
1.0
|
O
|
B:HOH556
|
4.0
|
41.8
|
1.0
|
O2G
|
B:ATP397
|
4.0
|
77.5
|
1.0
|
OE1
|
B:GLU84
|
4.1
|
62.9
|
1.0
|
O3A
|
B:ATP397
|
4.1
|
39.5
|
1.0
|
O
|
B:SER159
|
4.2
|
0.0
|
1.0
|
O
|
B:HOH482
|
4.4
|
35.5
|
1.0
|
MG
|
B:MG394
|
4.5
|
39.7
|
1.0
|
O1G
|
B:ATP397
|
4.6
|
92.8
|
1.0
|
CG
|
B:GLU279
|
4.6
|
31.7
|
1.0
|
CZ
|
B:ARG114
|
4.6
|
93.2
|
1.0
|
O
|
B:HOH708
|
4.7
|
51.2
|
1.0
|
CA
|
B:SER160
|
4.9
|
95.0
|
1.0
|
CD
|
B:GLU84
|
4.9
|
88.2
|
1.0
|
NE
|
B:ARG114
|
5.0
|
38.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1kj8
Go back to
Magnesium Binding Sites List in 1kj8
Magnesium binding site 4 out
of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg394
b:39.7
occ:1.00
|
O2G
|
B:ATP397
|
2.2
|
77.5
|
1.0
|
O2A
|
B:ATP397
|
2.2
|
61.7
|
1.0
|
O
|
B:HOH605
|
2.2
|
37.2
|
1.0
|
OE2
|
B:GLU267
|
2.3
|
46.0
|
1.0
|
OE1
|
B:GLU279
|
2.3
|
31.5
|
1.0
|
O3B
|
B:ATP397
|
2.8
|
97.2
|
1.0
|
OE1
|
B:GLU267
|
2.8
|
64.8
|
1.0
|
CD
|
B:GLU267
|
2.9
|
95.5
|
1.0
|
PG
|
B:ATP397
|
3.0
|
95.9
|
1.0
|
CD
|
B:GLU279
|
3.3
|
35.6
|
1.0
|
PA
|
B:ATP397
|
3.3
|
46.1
|
1.0
|
O3A
|
B:ATP397
|
3.5
|
39.5
|
1.0
|
PB
|
B:ATP397
|
3.7
|
62.0
|
1.0
|
O3G
|
B:ATP397
|
3.8
|
91.6
|
1.0
|
CG
|
B:GLU279
|
4.0
|
31.7
|
1.0
|
C5'
|
B:ATP397
|
4.1
|
42.3
|
1.0
|
O
|
B:HOH489
|
4.2
|
25.2
|
1.0
|
O1G
|
B:ATP397
|
4.2
|
92.8
|
1.0
|
O3'
|
B:ATP397
|
4.3
|
30.9
|
1.0
|
O5'
|
B:ATP397
|
4.3
|
68.6
|
1.0
|
OE2
|
B:GLU279
|
4.3
|
32.9
|
1.0
|
CG
|
B:GLU267
|
4.4
|
21.2
|
1.0
|
O
|
B:HOH677
|
4.4
|
42.1
|
1.0
|
O1A
|
B:ATP397
|
4.4
|
37.2
|
1.0
|
O
|
B:HOH740
|
4.4
|
42.8
|
1.0
|
MG
|
B:MG393
|
4.5
|
51.5
|
1.0
|
O2B
|
B:ATP397
|
4.6
|
54.6
|
1.0
|
C3'
|
B:ATP397
|
4.7
|
31.6
|
1.0
|
O1B
|
B:ATP397
|
4.9
|
0.0
|
1.0
|
C4'
|
B:ATP397
|
5.0
|
43.8
|
1.0
|
|
Reference:
J.B.Thoden,
S.M.Firestine,
S.J.Benkovic,
H.M.Holden.
Purt-Encoded Glycinamide Ribonucleotide Transformylase. Accommodation of Adenosine Nucleotide Analogs Within the Active Site. J.Biol.Chem. V. 277 23898 2002.
ISSN: ISSN 0021-9258
PubMed: 11953435
DOI: 10.1074/JBC.M202251200
Page generated: Tue Aug 13 07:44:50 2024
|