Magnesium in PDB 6vcl: Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-
Enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-
All present enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-:
5.1.1.7;
Protein crystallography data
The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-, PDB code: 6vcl
was solved by
A.Gao,
N.Vasilyev,
A.Kaushik,
W.Duan,
A.Serganov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.06
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
162.444,
190.649,
51.336,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
22.7
|
Other elements in 6vcl:
The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-
(pdb code 6vcl). 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 E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-, PDB code: 6vcl:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6vcl
Go back to
Magnesium Binding Sites List in 6vcl
Magnesium binding site 1 out
of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-
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 E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg201
b:38.6
occ:1.00
|
O
|
B:HOH405
|
1.9
|
35.8
|
1.0
|
O
|
B:HOH304
|
2.0
|
29.7
|
1.0
|
OE2
|
B:GLU53
|
2.0
|
31.7
|
1.0
|
O
|
B:HOH307
|
2.1
|
35.3
|
1.0
|
O
|
B:HOH446
|
2.2
|
39.4
|
1.0
|
O
|
B:HOH357
|
2.3
|
38.1
|
1.0
|
MG
|
B:MG204
|
3.0
|
34.3
|
1.0
|
CD
|
B:GLU53
|
3.0
|
34.2
|
1.0
|
MG
|
B:MG202
|
3.3
|
35.5
|
1.0
|
OE1
|
B:GLU53
|
3.5
|
30.9
|
1.0
|
F
|
B:F208
|
3.6
|
32.9
|
1.0
|
O
|
B:HOH425
|
3.7
|
42.1
|
1.0
|
N
|
B:GLY39
|
3.8
|
32.0
|
1.0
|
O
|
B:HOH437
|
3.9
|
51.9
|
1.0
|
NH2
|
B:ARG52
|
3.9
|
31.0
|
1.0
|
O
|
B:GLY39
|
4.1
|
34.7
|
1.0
|
OE1
|
B:GLU56
|
4.1
|
39.8
|
1.0
|
O
|
B:HOH313
|
4.3
|
49.8
|
1.0
|
O
|
B:HOH325
|
4.3
|
34.5
|
1.0
|
CG
|
B:GLU53
|
4.4
|
30.3
|
1.0
|
O2G
|
B:0O2209
|
4.5
|
38.5
|
1.0
|
CA
|
B:GLY38
|
4.6
|
31.9
|
1.0
|
CA
|
B:GLY39
|
4.6
|
35.1
|
1.0
|
C
|
B:GLY38
|
4.6
|
30.6
|
1.0
|
O
|
B:HOH396
|
4.7
|
64.0
|
1.0
|
O
|
B:HOH370
|
4.7
|
41.2
|
1.0
|
NH1
|
B:ARG52
|
4.8
|
32.4
|
1.0
|
CZ
|
B:ARG52
|
4.8
|
38.0
|
1.0
|
C
|
B:GLY39
|
4.8
|
34.7
|
1.0
|
NH1
|
B:ARG8
|
4.9
|
39.5
|
1.0
|
OE2
|
B:GLU120
|
4.9
|
32.3
|
1.0
|
OD1
|
B:ASN41
|
4.9
|
46.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6vcl
Go back to
Magnesium Binding Sites List in 6vcl
Magnesium binding site 2 out
of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-
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 E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg202
b:35.5
occ:1.00
|
F
|
B:F208
|
2.0
|
32.9
|
1.0
|
OE1
|
B:GLU53
|
2.0
|
30.9
|
1.0
|
O
|
B:HOH405
|
2.1
|
35.8
|
1.0
|
O
|
B:HOH325
|
2.1
|
34.5
|
1.0
|
OE2
|
B:GLU120
|
2.1
|
32.3
|
1.0
|
OE2
|
B:GLU57
|
2.4
|
35.5
|
1.0
|
CD
|
B:GLU53
|
3.0
|
34.2
|
1.0
|
CD
|
B:GLU120
|
3.1
|
40.2
|
1.0
|
MG
|
B:MG204
|
3.2
|
34.3
|
1.0
|
MG
|
B:MG203
|
3.3
|
34.7
|
1.0
|
OE2
|
B:GLU53
|
3.3
|
31.7
|
1.0
|
MG
|
B:MG201
|
3.3
|
38.6
|
1.0
|
CD
|
B:GLU57
|
3.3
|
32.9
|
1.0
|
OE1
|
B:GLU120
|
3.4
|
35.3
|
1.0
|
CG
|
B:GLU57
|
3.6
|
32.3
|
1.0
|
O
|
B:HOH370
|
3.7
|
41.2
|
1.0
|
O
|
B:HOH304
|
3.7
|
29.7
|
1.0
|
OE1
|
B:GLU56
|
4.0
|
39.8
|
1.0
|
O
|
B:HOH357
|
4.1
|
38.1
|
1.0
|
O
|
B:GLN37
|
4.2
|
29.5
|
1.0
|
O
|
B:HOH437
|
4.3
|
51.9
|
1.0
|
O
|
B:HOH371
|
4.3
|
55.5
|
1.0
|
CG
|
B:GLU53
|
4.4
|
30.3
|
1.0
|
CG
|
B:GLU120
|
4.4
|
42.6
|
1.0
|
CA
|
B:GLY38
|
4.5
|
31.9
|
1.0
|
OE1
|
B:GLU57
|
4.5
|
32.8
|
1.0
|
O2G
|
B:0O2209
|
4.6
|
38.5
|
1.0
|
O1G
|
B:0O2209
|
4.7
|
33.0
|
1.0
|
CB
|
B:GLU53
|
4.8
|
25.6
|
1.0
|
O
|
B:HOH387
|
4.9
|
45.0
|
1.0
|
O
|
B:HOH446
|
4.9
|
39.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6vcl
Go back to
Magnesium Binding Sites List in 6vcl
Magnesium binding site 3 out
of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-
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 E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg203
b:34.7
occ:1.00
|
O
|
B:GLN37
|
1.9
|
29.5
|
1.0
|
F
|
B:F208
|
2.0
|
32.9
|
1.0
|
O1G
|
B:0O2209
|
2.1
|
33.0
|
1.0
|
OE2
|
B:GLU57
|
2.1
|
35.5
|
1.0
|
OE1
|
B:GLU120
|
2.1
|
35.3
|
1.0
|
O
|
B:HOH361
|
2.3
|
31.5
|
1.0
|
CD
|
B:GLU120
|
3.1
|
40.2
|
1.0
|
CD
|
B:GLU57
|
3.1
|
32.9
|
1.0
|
C
|
B:GLN37
|
3.1
|
30.0
|
1.0
|
MG
|
B:MG202
|
3.3
|
35.5
|
1.0
|
PG
|
B:0O2209
|
3.3
|
37.7
|
1.0
|
OE2
|
B:GLU120
|
3.4
|
32.3
|
1.0
|
OE1
|
B:GLU57
|
3.4
|
32.8
|
1.0
|
O2G
|
B:0O2209
|
3.5
|
38.5
|
1.0
|
MG
|
B:MG204
|
3.6
|
34.3
|
1.0
|
O
|
B:HOH370
|
3.7
|
41.2
|
1.0
|
CA
|
B:GLY38
|
3.8
|
31.9
|
1.0
|
O
|
B:HOH306
|
3.9
|
45.8
|
1.0
|
N
|
B:GLY38
|
3.9
|
32.9
|
1.0
|
O
|
B:HOH340
|
4.0
|
36.6
|
1.0
|
N
|
B:GLN37
|
4.1
|
24.8
|
1.0
|
O
|
B:HOH400
|
4.1
|
37.7
|
1.0
|
OE1
|
B:GLU53
|
4.1
|
30.9
|
1.0
|
O3G
|
B:0O2209
|
4.1
|
32.3
|
1.0
|
CA
|
B:GLN37
|
4.2
|
28.0
|
1.0
|
CG
|
B:GLN37
|
4.3
|
30.9
|
1.0
|
CG
|
B:GLU120
|
4.4
|
42.6
|
1.0
|
O3B
|
B:0O2209
|
4.4
|
41.9
|
1.0
|
CG
|
B:GLU57
|
4.5
|
32.3
|
1.0
|
O
|
B:HOH405
|
4.6
|
35.8
|
1.0
|
O
|
B:HOH304
|
4.7
|
29.7
|
1.0
|
CB
|
B:GLU120
|
4.8
|
35.0
|
1.0
|
CB
|
B:GLN37
|
4.9
|
26.9
|
1.0
|
CD
|
B:GLU53
|
5.0
|
34.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6vcl
Go back to
Magnesium Binding Sites List in 6vcl
Magnesium binding site 4 out
of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-
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 E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg204
b:34.3
occ:1.00
|
F
|
B:F208
|
1.9
|
32.9
|
1.0
|
O
|
B:HOH304
|
1.9
|
29.7
|
1.0
|
O2G
|
B:0O2209
|
1.9
|
38.5
|
1.0
|
O
|
B:HOH370
|
2.1
|
41.2
|
1.0
|
O
|
B:HOH405
|
2.4
|
35.8
|
1.0
|
O
|
B:HOH425
|
2.5
|
42.1
|
1.0
|
MG
|
B:MG201
|
3.0
|
38.6
|
1.0
|
MG
|
B:MG202
|
3.2
|
35.5
|
1.0
|
PG
|
B:0O2209
|
3.2
|
37.7
|
1.0
|
O1G
|
B:0O2209
|
3.5
|
33.0
|
1.0
|
O
|
B:HOH446
|
3.6
|
39.4
|
1.0
|
MG
|
B:MG203
|
3.6
|
34.7
|
1.0
|
NH2
|
B:ARG8
|
3.8
|
40.3
|
1.0
|
O3B
|
B:0O2209
|
3.8
|
41.9
|
1.0
|
OE2
|
B:GLU120
|
3.8
|
32.3
|
1.0
|
OE1
|
B:GLU120
|
3.9
|
35.3
|
1.0
|
CA
|
B:GLY38
|
4.0
|
31.9
|
1.0
|
N
|
B:GLY39
|
4.1
|
32.0
|
1.0
|
CD
|
B:GLU120
|
4.2
|
40.2
|
1.0
|
OE2
|
B:GLU53
|
4.2
|
31.7
|
1.0
|
OE1
|
B:GLU53
|
4.3
|
30.9
|
1.0
|
O3G
|
B:0O2209
|
4.4
|
32.3
|
1.0
|
NH1
|
B:ARG8
|
4.4
|
39.5
|
1.0
|
OE2
|
B:GLU57
|
4.5
|
35.5
|
1.0
|
CZ
|
B:ARG8
|
4.5
|
48.6
|
1.0
|
O
|
B:HOH307
|
4.6
|
35.3
|
1.0
|
CD
|
B:GLU53
|
4.6
|
34.2
|
1.0
|
O
|
B:GLN37
|
4.6
|
29.5
|
1.0
|
C
|
B:GLY38
|
4.6
|
30.6
|
1.0
|
O
|
B:HOH357
|
4.8
|
38.1
|
1.0
|
|
Reference:
A.Gao,
N.Vasilyev,
A.Kaushik,
W.Duan,
A.Serganov.
Principles of Rna and Nucleotide Discrimination By the Rna Processing Enzyme Rpph. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 31960065
DOI: 10.1093/NAR/GKAA024
Page generated: Tue Oct 1 21:59:10 2024
|