Magnesium in PDB 1kj9: Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp
Protein crystallography data
The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp, PDB code: 1kj9
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 (°)
|
62.300,
179.500,
75.700,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1kj9:
The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp 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 Complexed with Mg-Atp
(pdb code 1kj9). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp, PDB code: 1kj9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 1kj9
Go back to
Magnesium Binding Sites List in 1kj9
Magnesium binding site 1 out
of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp
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 Complexed with Mg-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg393
b:11.6
occ:1.00
|
O3G
|
A:ATP1
|
1.9
|
9.9
|
1.0
|
O
|
A:HOH417
|
2.0
|
13.7
|
1.0
|
O1
|
A:EDO403
|
2.1
|
16.0
|
1.0
|
O2B
|
A:ATP1
|
2.1
|
11.8
|
1.0
|
OE2
|
A:GLU279
|
2.2
|
12.9
|
1.0
|
OE1
|
A:GLU279
|
2.2
|
10.8
|
1.0
|
CD
|
A:GLU279
|
2.5
|
11.7
|
1.0
|
C1
|
A:EDO403
|
3.1
|
17.4
|
1.0
|
PG
|
A:ATP1
|
3.1
|
13.1
|
1.0
|
PB
|
A:ATP1
|
3.3
|
13.2
|
1.0
|
O3B
|
A:ATP1
|
3.5
|
15.4
|
1.0
|
O2G
|
A:ATP1
|
3.6
|
9.6
|
1.0
|
C2
|
A:EDO403
|
3.7
|
13.3
|
1.0
|
MG
|
A:MG394
|
3.8
|
10.8
|
1.0
|
O
|
A:HOH434
|
4.0
|
13.2
|
1.0
|
CG
|
A:GLU279
|
4.0
|
9.1
|
1.0
|
O2A
|
A:ATP1
|
4.2
|
12.2
|
1.0
|
NH1
|
A:ARG114
|
4.2
|
11.3
|
1.0
|
OE1
|
A:GLU84
|
4.3
|
18.8
|
1.0
|
O1B
|
A:ATP1
|
4.3
|
14.1
|
1.0
|
OE2
|
A:GLU84
|
4.3
|
17.1
|
1.0
|
O
|
A:SER159
|
4.3
|
21.2
|
1.0
|
O3A
|
A:ATP1
|
4.3
|
13.3
|
1.0
|
O2
|
A:EDO403
|
4.4
|
21.5
|
1.0
|
O
|
A:HOH459
|
4.4
|
14.7
|
1.0
|
O1G
|
A:ATP1
|
4.4
|
14.6
|
1.0
|
NH2
|
A:ARG114
|
4.5
|
11.7
|
1.0
|
PA
|
A:ATP1
|
4.6
|
12.0
|
1.0
|
CD
|
A:GLU84
|
4.7
|
30.1
|
1.0
|
CZ
|
A:ARG114
|
4.8
|
13.5
|
1.0
|
CA
|
A:SER160
|
4.8
|
14.7
|
1.0
|
O1A
|
A:ATP1
|
4.8
|
12.3
|
1.0
|
OE1
|
A:GLU267
|
4.8
|
16.9
|
1.0
|
CB
|
A:GLU279
|
4.8
|
8.3
|
1.0
|
CB
|
A:SER160
|
4.9
|
23.5
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 1kj9
Go back to
Magnesium Binding Sites List in 1kj9
Magnesium binding site 2 out
of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp
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 Complexed with Mg-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg394
b:10.8
occ:1.00
|
O2A
|
A:ATP1
|
2.0
|
12.2
|
1.0
|
OE1
|
A:GLU279
|
2.0
|
10.8
|
1.0
|
O2G
|
A:ATP1
|
2.0
|
9.6
|
1.0
|
O
|
A:HOH419
|
2.1
|
11.3
|
1.0
|
OE2
|
A:GLU267
|
2.1
|
9.7
|
1.0
|
OE1
|
A:GLU267
|
2.2
|
16.9
|
1.0
|
CD
|
A:GLU267
|
2.5
|
9.4
|
1.0
|
CD
|
A:GLU279
|
3.0
|
11.7
|
1.0
|
PG
|
A:ATP1
|
3.2
|
13.1
|
1.0
|
PA
|
A:ATP1
|
3.5
|
12.0
|
1.0
|
O3B
|
A:ATP1
|
3.5
|
15.4
|
1.0
|
CG
|
A:GLU279
|
3.7
|
9.1
|
1.0
|
O3G
|
A:ATP1
|
3.8
|
9.9
|
1.0
|
MG
|
A:MG393
|
3.8
|
11.6
|
1.0
|
CG
|
A:GLU267
|
4.0
|
11.9
|
1.0
|
C2
|
A:EDO403
|
4.1
|
13.3
|
1.0
|
O2B
|
A:ATP1
|
4.1
|
11.8
|
1.0
|
OE2
|
A:GLU279
|
4.1
|
12.9
|
1.0
|
O3A
|
A:ATP1
|
4.1
|
13.3
|
1.0
|
O
|
A:HOH474
|
4.2
|
19.2
|
1.0
|
PB
|
A:ATP1
|
4.2
|
13.2
|
1.0
|
O
|
A:HOH455
|
4.2
|
13.9
|
1.0
|
O
|
A:HOH509
|
4.2
|
20.3
|
1.0
|
O1A
|
A:ATP1
|
4.3
|
12.3
|
1.0
|
O5'
|
A:ATP1
|
4.4
|
13.3
|
1.0
|
O3'
|
A:ATP1
|
4.4
|
11.5
|
1.0
|
O1G
|
A:ATP1
|
4.5
|
14.6
|
1.0
|
C5'
|
A:ATP1
|
4.5
|
12.9
|
1.0
|
O
|
A:HOH576
|
4.6
|
31.6
|
1.0
|
C1
|
A:EDO403
|
4.6
|
17.4
|
1.0
|
NE2
|
A:HIS285
|
4.7
|
10.0
|
1.0
|
CB
|
A:GLU267
|
4.7
|
11.4
|
1.0
|
O1
|
A:EDO403
|
4.8
|
16.0
|
1.0
|
C3'
|
A:ATP1
|
5.0
|
12.5
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 1kj9
Go back to
Magnesium Binding Sites List in 1kj9
Magnesium binding site 3 out
of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp
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 Complexed with Mg-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg395
b:18.2
occ:1.00
|
O
|
A:HOH478
|
2.1
|
16.4
|
1.0
|
OD2
|
A:ASP286
|
2.1
|
15.9
|
1.0
|
O
|
A:HOH549
|
2.2
|
21.1
|
1.0
|
O
|
A:HOH474
|
2.2
|
19.2
|
1.0
|
O
|
A:HOH482
|
2.2
|
19.9
|
1.0
|
O1G
|
A:ATP1
|
2.2
|
14.6
|
1.0
|
CG
|
A:ASP286
|
3.1
|
18.1
|
1.0
|
PG
|
A:ATP1
|
3.4
|
13.1
|
1.0
|
OD1
|
A:ASP286
|
3.4
|
12.4
|
1.0
|
O2G
|
A:ATP1
|
3.5
|
9.6
|
1.0
|
O
|
A:HOH435
|
4.0
|
13.8
|
1.0
|
O
|
A:HOH509
|
4.1
|
20.3
|
1.0
|
O
|
A:HOH434
|
4.2
|
13.2
|
1.0
|
O
|
A:HOH451
|
4.3
|
21.7
|
1.0
|
OD1
|
A:ASP229
|
4.3
|
27.6
|
1.0
|
NH2
|
A:ARG363
|
4.3
|
16.4
|
1.0
|
O3G
|
A:ATP1
|
4.4
|
9.9
|
1.0
|
OG
|
A:SER161
|
4.4
|
24.0
|
1.0
|
CB
|
A:ASP286
|
4.4
|
10.2
|
1.0
|
O
|
A:HOH576
|
4.4
|
31.6
|
1.0
|
O3B
|
A:ATP1
|
4.5
|
15.4
|
1.0
|
N
|
A:SER161
|
4.5
|
14.1
|
1.0
|
CA
|
A:SER161
|
4.6
|
21.2
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 1kj9
Go back to
Magnesium Binding Sites List in 1kj9
Magnesium binding site 4 out
of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp
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 Complexed with Mg-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg393
b:25.3
occ:1.00
|
O
|
B:HOH502
|
1.7
|
22.5
|
1.0
|
O3G
|
B:ATP395
|
2.0
|
25.3
|
1.0
|
O2B
|
B:ATP395
|
2.1
|
29.1
|
1.0
|
O
|
B:HOH447
|
2.2
|
23.3
|
1.0
|
OE2
|
B:GLU279
|
2.3
|
21.4
|
1.0
|
OE1
|
B:GLU279
|
2.4
|
24.9
|
1.0
|
CD
|
B:GLU279
|
2.6
|
23.8
|
1.0
|
PG
|
B:ATP395
|
3.2
|
29.8
|
1.0
|
PB
|
B:ATP395
|
3.3
|
35.4
|
1.0
|
O3B
|
B:ATP395
|
3.6
|
34.7
|
1.0
|
O
|
B:HOH684
|
3.6
|
47.9
|
1.0
|
O2G
|
B:ATP395
|
3.7
|
19.7
|
1.0
|
O
|
B:HOH473
|
4.0
|
23.1
|
1.0
|
MG
|
B:MG394
|
4.0
|
19.8
|
1.0
|
OE2
|
B:GLU84
|
4.1
|
45.3
|
1.0
|
CG
|
B:GLU279
|
4.1
|
17.0
|
1.0
|
NH2
|
B:ARG114
|
4.1
|
34.9
|
1.0
|
NH1
|
B:ARG114
|
4.2
|
25.9
|
1.0
|
O2A
|
B:ATP395
|
4.2
|
31.8
|
1.0
|
O3A
|
B:ATP395
|
4.3
|
18.5
|
1.0
|
O
|
B:SER159
|
4.3
|
42.6
|
1.0
|
O1B
|
B:ATP395
|
4.3
|
35.9
|
1.0
|
O
|
B:HOH489
|
4.4
|
33.4
|
1.0
|
O
|
B:HOH504
|
4.4
|
30.6
|
1.0
|
O1G
|
B:ATP395
|
4.5
|
38.5
|
1.0
|
CZ
|
B:ARG114
|
4.5
|
32.6
|
1.0
|
PA
|
B:ATP395
|
4.7
|
28.6
|
1.0
|
O1A
|
B:ATP395
|
4.8
|
25.4
|
1.0
|
CA
|
B:SER160
|
4.9
|
46.2
|
1.0
|
CB
|
B:GLU279
|
4.9
|
15.2
|
1.0
|
O
|
B:HOH529
|
4.9
|
30.3
|
1.0
|
CB
|
B:SER160
|
4.9
|
39.8
|
1.0
|
OE1
|
B:GLU267
|
5.0
|
19.8
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 1kj9
Go back to
Magnesium Binding Sites List in 1kj9
Magnesium binding site 5 out
of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg394
b:19.8
occ:1.00
|
O2G
|
B:ATP395
|
1.9
|
19.7
|
1.0
|
O2A
|
B:ATP395
|
2.0
|
31.8
|
1.0
|
OE2
|
B:GLU267
|
2.1
|
19.7
|
1.0
|
OE1
|
B:GLU279
|
2.1
|
24.9
|
1.0
|
O
|
B:HOH557
|
2.1
|
21.6
|
1.0
|
OE1
|
B:GLU267
|
2.3
|
19.8
|
1.0
|
CD
|
B:GLU267
|
2.5
|
21.0
|
1.0
|
CD
|
B:GLU279
|
3.1
|
23.8
|
1.0
|
PG
|
B:ATP395
|
3.2
|
29.8
|
1.0
|
PA
|
B:ATP395
|
3.5
|
28.6
|
1.0
|
O3B
|
B:ATP395
|
3.7
|
34.7
|
1.0
|
CG
|
B:GLU279
|
3.8
|
17.0
|
1.0
|
O3G
|
B:ATP395
|
3.9
|
25.3
|
1.0
|
O
|
B:HOH473
|
3.9
|
23.1
|
1.0
|
CG
|
B:GLU267
|
4.0
|
11.1
|
1.0
|
MG
|
B:MG393
|
4.0
|
25.3
|
1.0
|
O3A
|
B:ATP395
|
4.1
|
18.5
|
1.0
|
OE2
|
B:GLU279
|
4.2
|
21.4
|
1.0
|
PB
|
B:ATP395
|
4.2
|
35.4
|
1.0
|
O
|
B:HOH476
|
4.3
|
20.0
|
1.0
|
C5'
|
B:ATP395
|
4.3
|
33.0
|
1.0
|
O
|
B:HOH522
|
4.3
|
37.2
|
1.0
|
O2B
|
B:ATP395
|
4.3
|
29.1
|
1.0
|
O3'
|
B:ATP395
|
4.3
|
33.5
|
1.0
|
O5'
|
B:ATP395
|
4.3
|
27.1
|
1.0
|
O1A
|
B:ATP395
|
4.3
|
25.4
|
1.0
|
O1G
|
B:ATP395
|
4.4
|
38.5
|
1.0
|
C3'
|
B:ATP395
|
4.7
|
27.2
|
1.0
|
NE2
|
B:HIS285
|
4.7
|
16.9
|
1.0
|
CB
|
B:GLU267
|
4.8
|
13.5
|
1.0
|
O
|
B:HOH447
|
4.9
|
23.3
|
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 07:45:06 2024
|