Magnesium in PDB 8s87: Kod-H4 Dna Polymerase Mutant - Apo Structure
Enzymatic activity of Kod-H4 Dna Polymerase Mutant - Apo Structure
All present enzymatic activity of Kod-H4 Dna Polymerase Mutant - Apo Structure:
2.7.7.7;
Protein crystallography data
The structure of Kod-H4 Dna Polymerase Mutant - Apo Structure, PDB code: 8s87
was solved by
C.Gutfreund,
K.Betz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.40 /
1.82
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.424,
110.629,
111.363,
90,
90,
90
|
|
R / Rfree (%)
|
23 /
27.1
|
Other elements in 8s87:
The structure of Kod-H4 Dna Polymerase Mutant - Apo Structure also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Kod-H4 Dna Polymerase Mutant - Apo Structure
(pdb code 8s87). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Kod-H4 Dna Polymerase Mutant - Apo Structure, PDB code: 8s87:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 1 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg801
b:56.0
occ:1.00
|
HH22
|
A:ARG17
|
2.4
|
52.5
|
1.0
|
|
OD2
|
A:ASP235
|
2.6
|
42.6
|
1.0
|
|
HB3
|
A:SER237
|
3.1
|
57.3
|
1.0
|
|
NH2
|
A:ARG17
|
3.1
|
43.6
|
1.0
|
|
HD3
|
A:LYS253
|
3.3
|
69.0
|
1.0
|
|
HG
|
A:SER237
|
3.3
|
53.1
|
1.0
|
|
HH12
|
A:ARG17
|
3.4
|
51.4
|
1.0
|
|
HG3
|
A:LYS253
|
3.5
|
64.6
|
1.0
|
|
HH21
|
A:ARG17
|
3.6
|
52.5
|
1.0
|
|
CG
|
A:ASP235
|
3.7
|
46.9
|
1.0
|
|
CB
|
A:SER237
|
3.8
|
47.6
|
1.0
|
|
HD2
|
A:LYS253
|
3.8
|
69.0
|
1.0
|
|
CD
|
A:LYS253
|
3.9
|
57.4
|
1.0
|
|
OG
|
A:SER237
|
3.9
|
44.2
|
1.0
|
|
HB2
|
A:SER237
|
3.9
|
57.3
|
1.0
|
|
CZ
|
A:ARG17
|
3.9
|
48.2
|
1.0
|
|
NH1
|
A:ARG17
|
4.0
|
42.7
|
1.0
|
|
OD1
|
A:ASP235
|
4.1
|
42.8
|
1.0
|
|
CG
|
A:LYS253
|
4.1
|
53.8
|
1.0
|
|
HB2
|
A:LYS253
|
4.4
|
58.2
|
1.0
|
|
HG22
|
A:ILE8
|
4.5
|
53.7
|
1.0
|
|
HB3
|
A:LYS253
|
4.5
|
58.2
|
1.0
|
|
HG21
|
A:ILE8
|
4.6
|
53.7
|
1.0
|
|
CB
|
A:LYS253
|
4.6
|
48.5
|
1.0
|
|
HH11
|
A:ARG17
|
4.7
|
51.4
|
1.0
|
|
HG2
|
A:LYS253
|
5.0
|
64.6
|
1.0
|
|
CG2
|
A:ILE8
|
5.0
|
44.7
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 2 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:46.4
occ:1.00
|
HG
|
A:SER345
|
2.3
|
46.9
|
1.0
|
|
H
|
A:ASP259
|
2.4
|
41.5
|
1.0
|
|
OG
|
A:SER345
|
2.8
|
39.0
|
1.0
|
|
O
|
A:ASP259
|
2.8
|
44.3
|
1.0
|
|
HB2
|
A:SER345
|
2.8
|
55.2
|
1.0
|
|
N
|
A:ASP259
|
3.0
|
34.5
|
1.0
|
|
HB3
|
A:ASP259
|
3.1
|
46.3
|
1.0
|
|
HA
|
A:PHE258
|
3.2
|
46.0
|
1.0
|
|
NH1
|
A:ARG346
|
3.2
|
34.0
|
1.0
|
|
HH12
|
A:ARG346
|
3.3
|
40.4
|
1.0
|
|
CB
|
A:SER345
|
3.3
|
46.0
|
1.0
|
|
HG2
|
A:ARG346
|
3.3
|
54.6
|
1.0
|
|
HG2
|
A:PRO262
|
3.3
|
57.8
|
1.0
|
|
CZ
|
A:ARG346
|
3.4
|
42.7
|
1.0
|
|
C
|
A:ASP259
|
3.5
|
45.7
|
1.0
|
|
HH11
|
A:ARG346
|
3.5
|
40.4
|
1.0
|
|
HG3
|
A:ARG346
|
3.5
|
54.6
|
1.0
|
|
CA
|
A:ASP259
|
3.6
|
34.6
|
1.0
|
|
HG23
|
A:VAL263
|
3.6
|
60.5
|
1.0
|
|
NH2
|
A:ARG346
|
3.7
|
41.0
|
1.0
|
|
HH22
|
A:ARG346
|
3.7
|
49.3
|
1.0
|
|
CB
|
A:ASP259
|
3.8
|
38.5
|
1.0
|
|
HD1
|
A:PHE258
|
3.8
|
57.7
|
1.0
|
|
HB3
|
A:SER345
|
3.8
|
55.2
|
1.0
|
|
C
|
A:PHE258
|
3.8
|
38.2
|
1.0
|
|
CG
|
A:ARG346
|
3.8
|
45.4
|
1.0
|
|
HG3
|
A:PRO262
|
3.8
|
57.8
|
1.0
|
|
CA
|
A:PHE258
|
3.9
|
38.2
|
1.0
|
|
NE
|
A:ARG346
|
4.0
|
40.7
|
1.0
|
|
CG
|
A:PRO262
|
4.0
|
48.1
|
1.0
|
|
CD1
|
A:PHE258
|
4.1
|
48.0
|
1.0
|
|
HB2
|
A:ASP259
|
4.2
|
46.3
|
1.0
|
|
O
|
A:HIS257
|
4.2
|
36.3
|
1.0
|
|
HH21
|
A:ARG346
|
4.2
|
49.3
|
1.0
|
|
O
|
A:SER345
|
4.3
|
44.6
|
1.0
|
|
CG2
|
A:VAL263
|
4.3
|
50.4
|
1.0
|
|
HD2
|
A:PRO262
|
4.3
|
59.3
|
1.0
|
|
HG21
|
A:VAL263
|
4.4
|
60.5
|
1.0
|
|
C
|
A:SER345
|
4.4
|
41.5
|
1.0
|
|
HE
|
A:ARG346
|
4.4
|
48.9
|
1.0
|
|
CA
|
A:SER345
|
4.5
|
42.1
|
1.0
|
|
HG22
|
A:VAL263
|
4.5
|
60.5
|
1.0
|
|
CD
|
A:ARG346
|
4.5
|
44.5
|
1.0
|
|
HA
|
A:ASP259
|
4.5
|
41.6
|
1.0
|
|
CE1
|
A:PHE258
|
4.5
|
50.9
|
1.0
|
|
HE1
|
A:PHE258
|
4.6
|
61.1
|
1.0
|
|
CG
|
A:PHE258
|
4.6
|
44.2
|
1.0
|
|
N
|
A:LEU260
|
4.7
|
43.7
|
1.0
|
|
CD
|
A:PRO262
|
4.7
|
49.3
|
1.0
|
|
H
|
A:VAL263
|
4.8
|
59.7
|
1.0
|
|
CB
|
A:PHE258
|
4.9
|
41.7
|
1.0
|
|
O
|
A:PHE258
|
4.9
|
36.3
|
1.0
|
|
HD2
|
A:ARG346
|
4.9
|
53.5
|
1.0
|
|
N
|
A:ARG346
|
4.9
|
42.1
|
1.0
|
|
N
|
A:PHE258
|
4.9
|
36.8
|
1.0
|
|
C
|
A:HIS257
|
5.0
|
36.9
|
1.0
|
|
O
|
A:TRP342
|
5.0
|
40.2
|
1.0
|
|
OD2
|
A:ASP212
|
5.0
|
47.9
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 3 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:58.1
occ:1.00
|
H
|
A:ILE142
|
2.1
|
47.9
|
1.0
|
|
HB1
|
A:ALA141
|
2.9
|
49.0
|
1.0
|
|
OD2
|
A:ASP215
|
2.9
|
41.3
|
1.0
|
|
O
|
A:HOH1001
|
2.9
|
60.3
|
1.0
|
|
N
|
A:ILE142
|
2.9
|
39.9
|
1.0
|
|
HA
|
A:ALA141
|
3.1
|
47.4
|
1.0
|
|
O
|
A:ILE142
|
3.1
|
46.1
|
1.0
|
|
HG12
|
A:ILE142
|
3.1
|
48.6
|
1.0
|
|
O3
|
A:SO4817
|
3.1
|
108.1
|
1.0
|
|
CB
|
A:ALA141
|
3.6
|
40.8
|
1.0
|
|
CA
|
A:ALA141
|
3.6
|
39.5
|
1.0
|
|
CG
|
A:ASP215
|
3.7
|
49.1
|
1.0
|
|
C
|
A:ALA141
|
3.7
|
42.0
|
1.0
|
|
O2
|
A:SO4817
|
3.8
|
143.2
|
1.0
|
|
C
|
A:ILE142
|
3.9
|
42.5
|
1.0
|
|
CA
|
A:ILE142
|
3.9
|
44.5
|
1.0
|
|
HB2
|
A:ALA141
|
3.9
|
49.0
|
1.0
|
|
O
|
A:HOH947
|
3.9
|
36.6
|
1.0
|
|
CG1
|
A:ILE142
|
4.0
|
40.5
|
1.0
|
|
S
|
A:SO4817
|
4.0
|
166.4
|
1.0
|
|
OD1
|
A:ASP215
|
4.0
|
53.8
|
1.0
|
|
HG13
|
A:ILE142
|
4.2
|
48.6
|
1.0
|
|
HD2
|
A:PHE214
|
4.2
|
65.7
|
1.0
|
|
O
|
A:HOH972
|
4.3
|
51.9
|
1.0
|
|
O
|
A:HOH989
|
4.3
|
42.0
|
1.0
|
|
O1
|
A:SO4817
|
4.3
|
87.7
|
1.0
|
|
HB3
|
A:ALA141
|
4.4
|
49.0
|
1.0
|
|
HG23
|
A:ILE142
|
4.5
|
46.6
|
1.0
|
|
CB
|
A:ILE142
|
4.5
|
40.1
|
1.0
|
|
HE2
|
A:PHE214
|
4.5
|
59.8
|
1.0
|
|
OD2
|
A:ASP315
|
4.7
|
49.7
|
1.0
|
|
HA
|
A:ILE142
|
4.7
|
53.5
|
1.0
|
|
HB3
|
A:ASP215
|
4.9
|
49.3
|
1.0
|
|
CD2
|
A:PHE214
|
4.9
|
54.7
|
1.0
|
|
CB
|
A:ASP215
|
4.9
|
41.0
|
1.0
|
|
O
|
A:ALA141
|
5.0
|
43.0
|
1.0
|
|
HB3
|
A:ASP315
|
5.0
|
58.4
|
1.0
|
|
N
|
A:ALA141
|
5.0
|
38.5
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 4 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg804
b:83.4
occ:1.00
|
OE2
|
A:GLU580
|
2.4
|
75.6
|
1.0
|
|
OD1
|
A:ASP404
|
3.0
|
66.8
|
1.0
|
|
O
|
A:PHE405
|
3.2
|
52.0
|
1.0
|
|
HA
|
A:ARG406
|
3.2
|
70.0
|
1.0
|
|
OD2
|
A:ASP404
|
3.5
|
63.6
|
1.0
|
|
CG
|
A:ASP404
|
3.5
|
59.7
|
1.0
|
|
CD
|
A:GLU580
|
3.6
|
86.7
|
1.0
|
|
OE1
|
A:GLU578
|
3.7
|
78.6
|
1.0
|
|
C
|
A:PHE405
|
3.9
|
54.9
|
1.0
|
|
HG3
|
A:ARG406
|
3.9
|
105.0
|
1.0
|
|
CA
|
A:ARG406
|
4.0
|
58.2
|
1.0
|
|
HB2
|
A:GLU578
|
4.2
|
78.5
|
1.0
|
|
N
|
A:ARG406
|
4.2
|
59.5
|
1.0
|
|
O
|
A:ASP404
|
4.2
|
51.1
|
1.0
|
|
OE1
|
A:GLU580
|
4.4
|
81.8
|
1.0
|
|
H
|
A:SER407
|
4.4
|
62.9
|
1.0
|
|
HG3
|
A:GLU580
|
4.5
|
105.5
|
1.0
|
|
C
|
A:ASP404
|
4.6
|
49.6
|
1.0
|
|
CG
|
A:ARG406
|
4.6
|
87.4
|
1.0
|
|
CG
|
A:GLU580
|
4.6
|
87.9
|
1.0
|
|
HB2
|
A:ARG406
|
4.7
|
78.3
|
1.0
|
|
CB
|
A:ARG406
|
4.7
|
65.2
|
1.0
|
|
HG2
|
A:ARG406
|
4.7
|
105.0
|
1.0
|
|
CB
|
A:ASP404
|
4.8
|
55.1
|
1.0
|
|
HG2
|
A:GLU580
|
4.8
|
105.5
|
1.0
|
|
CD
|
A:GLU578
|
4.8
|
96.4
|
1.0
|
|
H
|
A:ARG406
|
4.9
|
71.5
|
1.0
|
|
HB2
|
A:ASP404
|
4.9
|
66.2
|
1.0
|
|
N
|
A:PHE405
|
4.9
|
46.0
|
1.0
|
|
O
|
A:HOH956
|
5.0
|
46.6
|
1.0
|
|
CA
|
A:PHE405
|
5.0
|
55.0
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 5 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg811
b:54.8
occ:1.00
|
H
|
A:ALA217
|
2.4
|
45.3
|
1.0
|
|
O
|
A:GLY211
|
2.7
|
46.9
|
1.0
|
|
O
|
A:HOH968
|
2.7
|
49.3
|
1.0
|
|
N
|
A:PHE214
|
2.8
|
45.0
|
1.0
|
|
C
|
A:ASN213
|
2.8
|
46.6
|
1.0
|
|
H
|
A:PHE214
|
2.8
|
54.1
|
1.0
|
|
HB2
|
A:ALA217
|
2.9
|
55.6
|
1.0
|
|
N
|
A:ASN213
|
3.0
|
45.7
|
1.0
|
|
HA
|
A:ASN213
|
3.0
|
57.2
|
1.0
|
|
C
|
A:ASP212
|
3.0
|
45.7
|
1.0
|
|
CA
|
A:ASN213
|
3.0
|
47.6
|
1.0
|
|
H
|
A:PHE216
|
3.1
|
54.8
|
1.0
|
|
N
|
A:ALA217
|
3.1
|
37.6
|
1.0
|
|
O
|
A:ASP212
|
3.1
|
43.1
|
1.0
|
|
HB2
|
A:PHE216
|
3.2
|
52.1
|
1.0
|
|
HB3
|
A:ALA217
|
3.3
|
55.6
|
1.0
|
|
O
|
A:ASN213
|
3.4
|
48.0
|
1.0
|
|
H
|
A:ASN213
|
3.4
|
54.9
|
1.0
|
|
CB
|
A:ALA217
|
3.5
|
46.2
|
1.0
|
|
C
|
A:PHE214
|
3.5
|
46.5
|
1.0
|
|
CA
|
A:PHE214
|
3.5
|
50.3
|
1.0
|
|
N
|
A:PHE216
|
3.6
|
45.6
|
1.0
|
|
C
|
A:GLY211
|
3.6
|
49.8
|
1.0
|
|
O
|
A:PHE214
|
3.7
|
44.8
|
1.0
|
|
HA
|
A:PHE214
|
3.7
|
60.5
|
1.0
|
|
N
|
A:ASP215
|
3.8
|
45.0
|
1.0
|
|
CA
|
A:ALA217
|
3.9
|
42.8
|
1.0
|
|
H
|
A:ASP215
|
3.9
|
54.1
|
1.0
|
|
HG21
|
A:VAL250
|
3.9
|
54.9
|
1.0
|
|
O
|
A:HOH1038
|
4.0
|
53.0
|
1.0
|
|
CB
|
A:PHE216
|
4.0
|
43.4
|
1.0
|
|
CA
|
A:ASP212
|
4.0
|
49.1
|
1.0
|
|
C
|
A:PHE216
|
4.0
|
42.2
|
1.0
|
|
HA
|
A:ASP212
|
4.1
|
59.0
|
1.0
|
|
CA
|
A:PHE216
|
4.1
|
46.7
|
1.0
|
|
HG23
|
A:VAL250
|
4.1
|
54.9
|
1.0
|
|
N
|
A:ASP212
|
4.2
|
45.4
|
1.0
|
|
HB1
|
A:ALA217
|
4.4
|
55.6
|
1.0
|
|
HA
|
A:ALA217
|
4.4
|
51.4
|
1.0
|
|
HA2
|
A:GLY211
|
4.4
|
58.2
|
1.0
|
|
HB3
|
A:PHE216
|
4.4
|
52.1
|
1.0
|
|
C
|
A:ASP215
|
4.4
|
49.4
|
1.0
|
|
CG2
|
A:VAL250
|
4.5
|
45.7
|
1.0
|
|
HD2
|
A:PHE216
|
4.5
|
52.2
|
1.0
|
|
CB
|
A:ASN213
|
4.6
|
52.0
|
1.0
|
|
O
|
A:ASN210
|
4.6
|
45.0
|
1.0
|
|
CA
|
A:GLY211
|
4.7
|
48.4
|
1.0
|
|
H
|
A:TYR218
|
4.7
|
59.1
|
1.0
|
|
CA
|
A:ASP215
|
4.7
|
43.2
|
1.0
|
|
HB3
|
A:ASN213
|
4.9
|
62.5
|
1.0
|
|
HB2
|
A:ASN213
|
4.9
|
62.5
|
1.0
|
|
CB
|
A:PHE214
|
5.0
|
52.4
|
1.0
|
|
H
|
A:ASP212
|
5.0
|
54.5
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 6 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg812
b:69.3
occ:1.00
|
HH22
|
A:ARG255
|
2.4
|
51.8
|
1.0
|
|
HA
|
A:LYS199
|
2.7
|
71.7
|
1.0
|
|
OD1
|
A:ASP202
|
3.0
|
46.6
|
1.0
|
|
O
|
A:LYS199
|
3.1
|
62.0
|
1.0
|
|
HB2
|
A:ASP202
|
3.1
|
62.6
|
1.0
|
|
HA
|
A:ASP202
|
3.1
|
65.5
|
1.0
|
|
HG2
|
A:LYS199
|
3.1
|
97.4
|
1.0
|
|
HH12
|
A:ARG255
|
3.1
|
55.6
|
1.0
|
|
NH2
|
A:ARG255
|
3.2
|
43.1
|
1.0
|
|
CG
|
A:ASP202
|
3.2
|
51.5
|
1.0
|
|
CB
|
A:ASP202
|
3.5
|
52.1
|
1.0
|
|
CA
|
A:LYS199
|
3.5
|
59.6
|
1.0
|
|
C
|
A:LYS199
|
3.7
|
62.2
|
1.0
|
|
CA
|
A:ASP202
|
3.7
|
54.5
|
1.0
|
|
HH21
|
A:ARG255
|
3.8
|
51.8
|
1.0
|
|
NH1
|
A:ARG255
|
3.8
|
46.2
|
1.0
|
|
CG
|
A:LYS199
|
3.9
|
81.1
|
1.0
|
|
HG2
|
A:ARG234
|
3.9
|
60.5
|
1.0
|
|
OD2
|
A:ASP202
|
4.0
|
53.7
|
1.0
|
|
CZ
|
A:ARG255
|
4.0
|
51.6
|
1.0
|
|
HG3
|
A:LYS199
|
4.0
|
97.4
|
1.0
|
|
O
|
A:VAL198
|
4.1
|
53.7
|
1.0
|
|
H
|
A:ASP202
|
4.2
|
63.3
|
1.0
|
|
CB
|
A:LYS199
|
4.3
|
67.3
|
1.0
|
|
HE
|
A:ARG234
|
4.4
|
54.3
|
1.0
|
|
HB3
|
A:ASP202
|
4.4
|
62.6
|
1.0
|
|
N
|
A:ASP202
|
4.4
|
52.7
|
1.0
|
|
HG3
|
A:ARG234
|
4.6
|
60.5
|
1.0
|
|
N
|
A:LYS199
|
4.6
|
53.1
|
1.0
|
|
HH11
|
A:ARG255
|
4.6
|
55.6
|
1.0
|
|
HA
|
A:ARG234
|
4.7
|
57.4
|
1.0
|
|
CG
|
A:ARG234
|
4.7
|
50.3
|
1.0
|
|
HB2
|
A:LYS199
|
4.7
|
80.8
|
1.0
|
|
C
|
A:VAL198
|
4.8
|
56.9
|
1.0
|
|
HG12
|
A:VAL198
|
4.9
|
61.8
|
1.0
|
|
HD2
|
A:PRO203
|
4.9
|
58.2
|
1.0
|
|
C
|
A:ASP202
|
4.9
|
53.8
|
1.0
|
|
N
|
A:GLU200
|
5.0
|
58.4
|
1.0
|
|
HE3
|
A:LYS199
|
5.0
|
97.9
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 7 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg814
b:44.6
occ:1.00
|
HE21
|
A:GLN339
|
2.3
|
54.1
|
1.0
|
|
HE
|
A:ARG359
|
2.3
|
54.5
|
1.0
|
|
HB2
|
A:ARG359
|
2.7
|
42.9
|
1.0
|
|
O
|
A:ILE337
|
2.8
|
41.5
|
1.0
|
|
O
|
A:TRP355
|
2.9
|
40.1
|
1.0
|
|
HG2
|
A:GLN339
|
3.0
|
60.4
|
1.0
|
|
NE2
|
A:GLN339
|
3.1
|
45.0
|
1.0
|
|
NE
|
A:ARG359
|
3.1
|
45.3
|
1.0
|
|
HG12
|
A:ILE122
|
3.2
|
42.4
|
1.0
|
|
HB3
|
A:TRP355
|
3.2
|
52.4
|
1.0
|
|
O
|
A:GLY338
|
3.2
|
39.0
|
1.0
|
|
HH21
|
A:ARG359
|
3.4
|
45.8
|
1.0
|
|
HD11
|
A:ILE122
|
3.4
|
42.4
|
1.0
|
|
HA3
|
A:GLY338
|
3.5
|
53.3
|
1.0
|
|
HE22
|
A:GLN339
|
3.6
|
54.1
|
1.0
|
|
C
|
A:TRP355
|
3.6
|
43.5
|
1.0
|
|
CB
|
A:ARG359
|
3.7
|
36.1
|
1.0
|
|
HD2
|
A:ARG359
|
3.7
|
48.7
|
1.0
|
|
C
|
A:GLY338
|
3.7
|
44.6
|
1.0
|
|
CG
|
A:GLN339
|
3.8
|
50.3
|
1.0
|
|
HB3
|
A:ARG359
|
3.9
|
42.9
|
1.0
|
|
HA
|
A:PHE356
|
3.9
|
50.1
|
1.0
|
|
CD
|
A:GLN339
|
3.9
|
57.8
|
1.0
|
|
CG1
|
A:ILE122
|
3.9
|
35.7
|
1.0
|
|
CD
|
A:ARG359
|
3.9
|
40.5
|
1.0
|
|
C
|
A:ILE337
|
4.0
|
42.9
|
1.0
|
|
NH2
|
A:ARG359
|
4.0
|
38.1
|
1.0
|
|
CZ
|
A:ARG359
|
4.0
|
44.5
|
1.0
|
|
HG13
|
A:ILE122
|
4.0
|
42.4
|
1.0
|
|
CD1
|
A:ILE122
|
4.0
|
35.7
|
1.0
|
|
HG22
|
A:ILE337
|
4.0
|
52.7
|
1.0
|
|
CA
|
A:GLY338
|
4.0
|
44.3
|
1.0
|
|
H
|
A:ARG359
|
4.0
|
43.0
|
1.0
|
|
CB
|
A:TRP355
|
4.1
|
43.6
|
1.0
|
|
HG3
|
A:GLN339
|
4.1
|
60.4
|
1.0
|
|
HD13
|
A:ILE122
|
4.2
|
42.4
|
1.0
|
|
CA
|
A:TRP355
|
4.3
|
47.1
|
1.0
|
|
N
|
A:PHE356
|
4.3
|
40.7
|
1.0
|
|
CG
|
A:ARG359
|
4.4
|
36.2
|
1.0
|
|
HA
|
A:TRP355
|
4.4
|
56.6
|
1.0
|
|
N
|
A:GLY338
|
4.5
|
38.4
|
1.0
|
|
CA
|
A:PHE356
|
4.6
|
41.7
|
1.0
|
|
HB2
|
A:TRP355
|
4.6
|
52.4
|
1.0
|
|
N
|
A:ARG359
|
4.6
|
36.2
|
1.0
|
|
N
|
A:GLN339
|
4.6
|
42.5
|
1.0
|
|
HG3
|
A:ARG359
|
4.6
|
43.0
|
1.0
|
|
HG23
|
A:ILE337
|
4.6
|
52.7
|
1.0
|
|
CA
|
A:ARG359
|
4.6
|
36.4
|
1.0
|
|
CG2
|
A:ILE337
|
4.8
|
43.9
|
1.0
|
|
HD3
|
A:ARG359
|
4.8
|
48.7
|
1.0
|
|
HA
|
A:ARG359
|
4.8
|
43.2
|
1.0
|
|
HH22
|
A:ARG359
|
4.8
|
45.8
|
1.0
|
|
HD12
|
A:ILE122
|
4.9
|
42.4
|
1.0
|
|
HA2
|
A:GLY338
|
4.9
|
53.3
|
1.0
|
|
CB
|
A:GLN339
|
5.0
|
43.8
|
1.0
|
|
H
|
A:PHE356
|
5.0
|
49.0
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 8 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg815
b:59.0
occ:1.00
|
HH11
|
A:ARG625
|
2.0
|
71.2
|
1.0
|
|
HG1
|
A:THR622
|
2.7
|
53.8
|
1.0
|
|
HD3
|
A:ARG625
|
2.7
|
67.0
|
1.0
|
|
NH1
|
A:ARG625
|
2.8
|
59.2
|
1.0
|
|
OG1
|
A:THR622
|
2.8
|
44.7
|
1.0
|
|
HG21
|
A:VAL646
|
2.9
|
54.5
|
1.0
|
|
HA
|
A:THR622
|
2.9
|
61.9
|
1.0
|
|
OE1
|
A:GLU621
|
3.0
|
73.7
|
1.0
|
|
HH12
|
A:ARG625
|
3.1
|
71.2
|
1.0
|
|
HG22
|
A:VAL646
|
3.2
|
54.5
|
1.0
|
|
HB3
|
A:GLU621
|
3.4
|
66.8
|
1.0
|
|
HD12
|
A:ILE618
|
3.4
|
64.9
|
1.0
|
|
CG2
|
A:VAL646
|
3.5
|
45.8
|
1.0
|
|
CD
|
A:GLU621
|
3.5
|
79.2
|
1.0
|
|
CD
|
A:ARG625
|
3.5
|
55.8
|
1.0
|
|
HD2
|
A:ARG625
|
3.5
|
67.0
|
1.0
|
|
CA
|
A:THR622
|
3.5
|
51.5
|
1.0
|
|
N
|
A:THR622
|
3.6
|
47.7
|
1.0
|
|
CB
|
A:THR622
|
3.7
|
46.5
|
1.0
|
|
H
|
A:THR622
|
3.8
|
57.4
|
1.0
|
|
HD11
|
A:ILE618
|
3.9
|
64.9
|
1.0
|
|
CZ
|
A:ARG625
|
3.9
|
51.4
|
1.0
|
|
C
|
A:GLU621
|
3.9
|
54.2
|
1.0
|
|
HG23
|
A:VAL646
|
3.9
|
54.5
|
1.0
|
|
HG23
|
A:THR622
|
4.0
|
54.8
|
1.0
|
|
HG2
|
A:GLU621
|
4.1
|
86.4
|
1.0
|
|
CD1
|
A:ILE618
|
4.1
|
54.0
|
1.0
|
|
OE2
|
A:GLU621
|
4.1
|
95.2
|
1.0
|
|
CB
|
A:GLU621
|
4.1
|
55.6
|
1.0
|
|
CG
|
A:GLU621
|
4.1
|
72.0
|
1.0
|
|
NE
|
A:ARG625
|
4.1
|
53.8
|
1.0
|
|
HG11
|
A:VAL646
|
4.2
|
61.7
|
1.0
|
|
O
|
A:GLU621
|
4.2
|
50.5
|
1.0
|
|
O
|
A:ILE618
|
4.3
|
46.9
|
1.0
|
|
CG2
|
A:THR622
|
4.4
|
45.6
|
1.0
|
|
HB2
|
A:ARG625
|
4.5
|
66.0
|
1.0
|
|
HB
|
A:THR622
|
4.5
|
55.9
|
1.0
|
|
HG13
|
A:VAL646
|
4.6
|
61.7
|
1.0
|
|
HG23
|
A:ILE642
|
4.6
|
62.8
|
1.0
|
|
CG
|
A:ARG625
|
4.7
|
55.0
|
1.0
|
|
CG1
|
A:VAL646
|
4.7
|
51.4
|
1.0
|
|
HG3
|
A:ARG625
|
4.7
|
66.1
|
1.0
|
|
HD13
|
A:ILE618
|
4.7
|
64.9
|
1.0
|
|
CA
|
A:GLU621
|
4.7
|
50.7
|
1.0
|
|
CB
|
A:VAL646
|
4.7
|
46.0
|
1.0
|
|
HG21
|
A:THR622
|
4.7
|
54.8
|
1.0
|
|
HG13
|
A:ILE618
|
4.8
|
61.7
|
1.0
|
|
HA
|
A:ILE618
|
4.9
|
58.5
|
1.0
|
|
HB2
|
A:GLU621
|
4.9
|
66.8
|
1.0
|
|
C
|
A:THR622
|
4.9
|
47.0
|
1.0
|
|
HG22
|
A:ILE642
|
4.9
|
62.8
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 8s87
Go back to
Magnesium Binding Sites List in 8s87
Magnesium binding site 9 out
of 9 in the Kod-H4 Dna Polymerase Mutant - Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg816
b:55.7
occ:1.00
|
HH11
|
A:ARG482
|
2.3
|
66.3
|
1.0
|
|
OE1
|
A:GLN332
|
2.5
|
61.1
|
1.0
|
|
HG3
|
A:ARG482
|
2.7
|
64.3
|
1.0
|
|
O
|
A:GLN332
|
2.8
|
46.4
|
1.0
|
|
HB3
|
A:GLN332
|
2.9
|
55.8
|
1.0
|
|
HD2
|
A:ARG482
|
3.0
|
62.6
|
1.0
|
|
NH1
|
A:ARG482
|
3.0
|
55.2
|
1.0
|
|
HA
|
A:GLN332
|
3.1
|
57.4
|
1.0
|
|
HH11
|
A:ARG335
|
3.1
|
77.9
|
1.0
|
|
HB2
|
A:ARG482
|
3.1
|
62.8
|
1.0
|
|
HB2
|
A:LEU336
|
3.2
|
49.7
|
1.0
|
|
HB3
|
A:ARG335
|
3.2
|
54.5
|
1.0
|
|
HH12
|
A:ARG482
|
3.3
|
66.3
|
1.0
|
|
CG
|
A:ARG482
|
3.4
|
53.5
|
1.0
|
|
C
|
A:GLN332
|
3.5
|
42.6
|
1.0
|
|
NH1
|
A:ARG335
|
3.5
|
64.9
|
1.0
|
|
HG2
|
A:ARG335
|
3.5
|
65.0
|
1.0
|
|
CA
|
A:GLN332
|
3.5
|
47.8
|
1.0
|
|
CD
|
A:ARG482
|
3.6
|
52.1
|
1.0
|
|
CB
|
A:GLN332
|
3.6
|
46.4
|
1.0
|
|
HA
|
A:ARG482
|
3.6
|
62.0
|
1.0
|
|
HD3
|
A:ARG335
|
3.6
|
67.3
|
1.0
|
|
CD
|
A:GLN332
|
3.6
|
58.1
|
1.0
|
|
HH12
|
A:ARG335
|
3.6
|
77.9
|
1.0
|
|
CB
|
A:ARG482
|
3.7
|
52.2
|
1.0
|
|
H
|
A:LEU336
|
3.7
|
54.8
|
1.0
|
|
CZ
|
A:ARG482
|
4.0
|
60.9
|
1.0
|
|
CB
|
A:ARG335
|
4.0
|
45.4
|
1.0
|
|
N
|
A:LEU336
|
4.0
|
45.6
|
1.0
|
|
CG
|
A:ARG335
|
4.0
|
54.1
|
1.0
|
|
CB
|
A:LEU336
|
4.1
|
41.4
|
1.0
|
|
CG
|
A:GLN332
|
4.1
|
51.2
|
1.0
|
|
CA
|
A:ARG482
|
4.2
|
51.6
|
1.0
|
|
NE
|
A:ARG482
|
4.2
|
55.4
|
1.0
|
|
HD12
|
A:LEU485
|
4.2
|
55.2
|
1.0
|
|
CD
|
A:ARG335
|
4.2
|
56.0
|
1.0
|
|
HG2
|
A:ARG482
|
4.2
|
64.3
|
1.0
|
|
CZ
|
A:ARG335
|
4.3
|
62.3
|
1.0
|
|
HB3
|
A:LEU336
|
4.4
|
49.7
|
1.0
|
|
HD3
|
A:ARG482
|
4.4
|
62.6
|
1.0
|
|
HG3
|
A:GLN332
|
4.4
|
61.6
|
1.0
|
|
HB2
|
A:GLN332
|
4.4
|
55.8
|
1.0
|
|
HA
|
A:LEU336
|
4.5
|
51.4
|
1.0
|
|
CA
|
A:LEU336
|
4.5
|
42.8
|
1.0
|
|
HB3
|
A:ARG482
|
4.5
|
62.8
|
1.0
|
|
NE
|
A:ARG335
|
4.6
|
67.4
|
1.0
|
|
HD13
|
A:LEU336
|
4.6
|
50.0
|
1.0
|
|
HD13
|
A:LEU485
|
4.6
|
55.2
|
1.0
|
|
C
|
A:ARG335
|
4.6
|
45.9
|
1.0
|
|
HB2
|
A:ARG335
|
4.7
|
54.5
|
1.0
|
|
N
|
A:LEU333
|
4.7
|
38.8
|
1.0
|
|
NE2
|
A:GLN332
|
4.7
|
59.7
|
1.0
|
|
HD22
|
A:LEU336
|
4.7
|
59.6
|
1.0
|
|
H
|
A:ARG335
|
4.8
|
48.8
|
1.0
|
|
CA
|
A:ARG335
|
4.8
|
45.0
|
1.0
|
|
HE22
|
A:GLN332
|
4.8
|
71.8
|
1.0
|
|
CD1
|
A:LEU485
|
4.9
|
45.9
|
1.0
|
|
N
|
A:GLN332
|
4.9
|
39.9
|
1.0
|
|
N
|
A:ARG482
|
5.0
|
48.9
|
1.0
|
|
HG3
|
A:ARG335
|
5.0
|
65.0
|
1.0
|
|
HG2
|
A:GLN332
|
5.0
|
61.6
|
1.0
|
|
HA
|
A:LEU333
|
5.0
|
51.3
|
1.0
|
|
Reference:
C.Gutfreund,
K.Betz.
Structural Insights Into A Dna Polymerase Reading the Xeno Nucleic Acid Hna Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
Page generated: Wed Nov 27 18:50:08 2024
|
