Magnesium in PDB 7mxb: Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
Protein crystallography data
The structure of Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp, PDB code: 7mxb
was solved by
M.N.Lisa,
P.M.Alzari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.02 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.663,
42.741,
175.327,
90,
95.31,
90
|
R / Rfree (%)
|
20.9 /
24.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
(pdb code 7mxb). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp, PDB code: 7mxb:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7mxb
Go back to
Magnesium Binding Sites List in 7mxb
Magnesium binding site 1 out
of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
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 the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg901
b:31.3
occ:1.00
|
MG
|
A:MAP901
|
0.0
|
31.3
|
1.0
|
O1B
|
A:MAP901
|
2.0
|
23.1
|
1.0
|
O2A
|
A:MAP901
|
2.0
|
25.2
|
1.0
|
O
|
A:HOH1164
|
2.0
|
21.3
|
1.0
|
O
|
A:HOH1060
|
2.2
|
28.2
|
1.0
|
OE2
|
A:GLU305
|
2.2
|
24.2
|
1.0
|
O1G
|
A:MAP901
|
2.3
|
23.3
|
1.0
|
PB
|
A:MAP901
|
2.8
|
29.3
|
1.0
|
PA
|
A:MAP901
|
3.1
|
26.3
|
1.0
|
O3A
|
A:MAP901
|
3.1
|
27.4
|
1.0
|
PG
|
A:MAP901
|
3.2
|
28.8
|
1.0
|
N3B
|
A:MAP901
|
3.3
|
30.6
|
1.0
|
CD
|
A:GLU305
|
3.4
|
29.0
|
1.0
|
O2G
|
A:MAP901
|
3.8
|
28.2
|
1.0
|
C5'
|
A:MAP901
|
3.8
|
21.8
|
1.0
|
O5'
|
A:MAP901
|
3.9
|
26.8
|
1.0
|
O
|
A:HOH1093
|
4.1
|
19.9
|
1.0
|
OE1
|
A:GLU305
|
4.2
|
38.0
|
1.0
|
O1A
|
A:MAP901
|
4.2
|
23.8
|
1.0
|
CG
|
A:GLU305
|
4.3
|
22.8
|
1.0
|
O
|
A:HOH1224
|
4.3
|
27.6
|
1.0
|
O2B
|
A:MAP901
|
4.3
|
31.3
|
1.0
|
NZ
|
A:LYS303
|
4.3
|
20.1
|
1.0
|
N
|
A:GLY185
|
4.4
|
29.7
|
1.0
|
O
|
A:HOH1009
|
4.5
|
37.3
|
1.0
|
CA
|
A:GLY184
|
4.6
|
29.9
|
1.0
|
O3G
|
A:MAP901
|
4.6
|
26.8
|
1.0
|
CE
|
A:LYS303
|
4.8
|
18.4
|
1.0
|
O
|
A:HOH1233
|
4.8
|
44.7
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7mxb
Go back to
Magnesium Binding Sites List in 7mxb
Magnesium binding site 2 out
of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
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 the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg902
b:29.3
occ:1.00
|
OD2
|
A:ASP301
|
2.0
|
13.9
|
1.0
|
OD2
|
A:ASP318
|
2.0
|
19.6
|
1.0
|
O
|
A:HOH1141
|
2.0
|
19.3
|
1.0
|
O
|
A:HOH1093
|
2.1
|
19.9
|
1.0
|
O3G
|
A:MAP901
|
2.1
|
26.8
|
1.0
|
O
|
A:HOH1066
|
2.2
|
26.6
|
1.0
|
CG
|
A:ASP318
|
3.0
|
22.9
|
1.0
|
CG
|
A:ASP301
|
3.2
|
18.5
|
1.0
|
PG
|
A:MAP901
|
3.2
|
28.8
|
1.0
|
N3B
|
A:MAP901
|
3.4
|
30.6
|
1.0
|
OD1
|
A:ASP318
|
3.5
|
24.9
|
1.0
|
O1G
|
A:MAP901
|
3.6
|
23.3
|
1.0
|
CB
|
A:ASP301
|
3.9
|
16.9
|
1.0
|
OD1
|
A:ASP301
|
4.1
|
23.2
|
1.0
|
CB
|
A:ASP318
|
4.3
|
21.6
|
1.0
|
O1A
|
A:MAP901
|
4.4
|
23.8
|
1.0
|
CE
|
A:LYS303
|
4.4
|
18.4
|
1.0
|
ND2
|
A:ASN306
|
4.4
|
17.6
|
1.0
|
O2G
|
A:MAP901
|
4.6
|
28.2
|
1.0
|
NZ
|
A:LYS303
|
4.6
|
20.1
|
1.0
|
O
|
A:TYR332
|
4.7
|
29.0
|
1.0
|
O2A
|
A:MAP901
|
4.9
|
25.2
|
1.0
|
NZ
|
A:LYS205
|
4.9
|
34.8
|
1.0
|
CB
|
A:ALA321
|
4.9
|
19.9
|
1.0
|
CE
|
A:MET208
|
5.0
|
55.5
|
1.0
|
PB
|
A:MAP901
|
5.0
|
29.3
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7mxb
Go back to
Magnesium Binding Sites List in 7mxb
Magnesium binding site 3 out
of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
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 the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg903
b:27.4
occ:1.00
|
O
|
A:HOH1058
|
2.0
|
15.9
|
1.0
|
O
|
A:HOH1088
|
2.0
|
22.0
|
1.0
|
O
|
A:HOH1126
|
2.1
|
18.8
|
1.0
|
O
|
A:GLY199
|
2.2
|
21.3
|
1.0
|
O
|
A:HOH1333
|
2.2
|
23.4
|
1.0
|
O
|
A:HOH1192
|
2.3
|
20.5
|
1.0
|
C
|
A:GLY199
|
3.3
|
24.0
|
1.0
|
CA
|
A:GLY199
|
3.8
|
20.8
|
1.0
|
OE1
|
A:GLU145
|
3.8
|
36.9
|
1.0
|
OE2
|
A:GLU145
|
4.0
|
39.6
|
1.0
|
CD
|
A:GLU145
|
4.3
|
39.4
|
1.0
|
O
|
A:HOH1272
|
4.4
|
26.7
|
1.0
|
O
|
A:HOH1150
|
4.4
|
23.7
|
1.0
|
N
|
A:ARG200
|
4.4
|
20.0
|
1.0
|
O
|
A:HOH1219
|
4.5
|
23.8
|
1.0
|
CA
|
A:ARG200
|
4.8
|
24.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7mxb
Go back to
Magnesium Binding Sites List in 7mxb
Magnesium binding site 4 out
of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
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 the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg901
b:27.4
occ:1.00
|
MG
|
B:MAP901
|
0.0
|
27.4
|
1.0
|
O1B
|
B:MAP901
|
1.9
|
21.4
|
1.0
|
O2A
|
B:MAP901
|
2.0
|
24.2
|
1.0
|
O
|
B:HOH1056
|
2.1
|
27.5
|
1.0
|
OE2
|
B:GLU305
|
2.2
|
27.3
|
1.0
|
O
|
B:HOH1171
|
2.2
|
23.7
|
1.0
|
O1G
|
B:MAP901
|
2.4
|
22.2
|
1.0
|
PB
|
B:MAP901
|
2.8
|
28.0
|
1.0
|
PA
|
B:MAP901
|
3.1
|
32.8
|
1.0
|
O3A
|
B:MAP901
|
3.1
|
21.8
|
1.0
|
CD
|
B:GLU305
|
3.3
|
33.7
|
1.0
|
PG
|
B:MAP901
|
3.4
|
23.4
|
1.0
|
N3B
|
B:MAP901
|
3.5
|
32.3
|
1.0
|
C5'
|
B:MAP901
|
3.8
|
26.7
|
1.0
|
O5'
|
B:MAP901
|
3.9
|
27.0
|
1.0
|
O3G
|
B:MAP901
|
4.0
|
28.8
|
1.0
|
O
|
B:HOH1198
|
4.0
|
27.6
|
1.0
|
O
|
B:HOH1015
|
4.1
|
32.4
|
1.0
|
OE1
|
B:GLU305
|
4.1
|
42.4
|
1.0
|
O
|
B:HOH1066
|
4.2
|
17.6
|
1.0
|
O1A
|
B:MAP901
|
4.2
|
29.3
|
1.0
|
CG
|
B:GLU305
|
4.2
|
30.6
|
1.0
|
O2B
|
B:MAP901
|
4.3
|
29.3
|
1.0
|
O
|
B:HOH1284
|
4.4
|
44.7
|
1.0
|
NZ
|
B:LYS303
|
4.4
|
26.0
|
1.0
|
N
|
B:GLY185
|
4.7
|
40.5
|
1.0
|
CA
|
B:GLY184
|
4.8
|
34.0
|
1.0
|
O2G
|
B:MAP901
|
4.8
|
26.5
|
1.0
|
CE
|
B:LYS303
|
4.9
|
24.2
|
1.0
|
O
|
B:HOH1170
|
5.0
|
32.3
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7mxb
Go back to
Magnesium Binding Sites List in 7mxb
Magnesium binding site 5 out
of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
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 the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg902
b:27.4
occ:1.00
|
OD2
|
B:ASP301
|
2.0
|
19.2
|
1.0
|
OD2
|
B:ASP318
|
2.1
|
22.2
|
1.0
|
O2G
|
B:MAP901
|
2.1
|
26.5
|
1.0
|
O
|
B:HOH1066
|
2.1
|
17.6
|
1.0
|
O
|
B:HOH1095
|
2.1
|
22.7
|
1.0
|
O
|
B:HOH1120
|
2.3
|
20.9
|
1.0
|
CG
|
B:ASP318
|
3.1
|
22.2
|
1.0
|
CG
|
B:ASP301
|
3.1
|
25.1
|
1.0
|
PG
|
B:MAP901
|
3.3
|
23.4
|
1.0
|
OD1
|
B:ASP318
|
3.5
|
27.1
|
1.0
|
N3B
|
B:MAP901
|
3.6
|
32.3
|
1.0
|
O1G
|
B:MAP901
|
3.7
|
22.2
|
1.0
|
CB
|
B:ASP301
|
3.8
|
22.1
|
1.0
|
O
|
B:HOH1366
|
3.9
|
31.2
|
1.0
|
O
|
B:TYR332
|
4.1
|
34.4
|
1.0
|
OD1
|
B:ASP301
|
4.1
|
24.6
|
1.0
|
O
|
B:HOH1165
|
4.2
|
30.0
|
1.0
|
CB
|
B:ASP318
|
4.4
|
21.7
|
1.0
|
O1A
|
B:MAP901
|
4.4
|
29.3
|
1.0
|
CE
|
B:LYS303
|
4.5
|
24.2
|
1.0
|
ND2
|
B:ASN306
|
4.6
|
19.7
|
1.0
|
O3G
|
B:MAP901
|
4.6
|
28.8
|
1.0
|
NZ
|
B:LYS303
|
4.7
|
26.0
|
1.0
|
CB
|
B:ALA321
|
4.8
|
24.3
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7mxb
Go back to
Magnesium Binding Sites List in 7mxb
Magnesium binding site 6 out
of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg903
b:29.2
occ:1.00
|
O
|
B:HOH1214
|
2.0
|
19.5
|
1.0
|
O
|
B:HOH1126
|
2.0
|
21.2
|
1.0
|
O
|
B:GLY199
|
2.1
|
12.8
|
1.0
|
O
|
B:HOH1106
|
2.1
|
16.5
|
1.0
|
O
|
B:HOH1274
|
2.2
|
14.8
|
1.0
|
O
|
B:HOH1136
|
2.2
|
19.6
|
1.0
|
C
|
B:GLY199
|
3.1
|
16.2
|
1.0
|
CA
|
B:GLY199
|
3.6
|
17.6
|
1.0
|
OE1
|
B:GLU145
|
3.7
|
33.8
|
1.0
|
OE2
|
B:GLU145
|
3.8
|
33.6
|
1.0
|
CD
|
B:GLU145
|
4.2
|
31.4
|
1.0
|
N
|
B:ARG200
|
4.3
|
14.9
|
1.0
|
O
|
B:HOH1205
|
4.3
|
21.3
|
1.0
|
O
|
B:HOH1381
|
4.4
|
34.2
|
1.0
|
O
|
B:HOH1153
|
4.5
|
21.0
|
1.0
|
CA
|
B:ARG200
|
4.7
|
20.6
|
1.0
|
O
|
B:HOH1351
|
4.9
|
23.9
|
1.0
|
N
|
B:ILE201
|
4.9
|
12.7
|
1.0
|
|
Reference:
M.N.Lisa,
A.Sogues,
N.Barilone,
M.Baumgart,
M.Gil,
M.Grana,
R.Duran,
R.M.Biondi,
M.Bellinzoni,
M.Bott,
P.M.Alzari.
A Tetratricopeptide Repeat Scaffold Couples Signal Detection to Odhi Phosphorylation in Metabolic Control By the Protein Kinase Pkng Mbio 2021.
ISSN: ESSN 2150-7511
PubMed: 34607462
DOI: 10.1128/MBIO.01717-21
Page generated: Thu Oct 3 01:09:03 2024
|