Manganese in PDB 8odo: Structure of Human Guanylylated Rtcb in Complex with Archease
Enzymatic activity of Structure of Human Guanylylated Rtcb in Complex with Archease
All present enzymatic activity of Structure of Human Guanylylated Rtcb in Complex with Archease:
6.5.1.8;
Protein crystallography data
The structure of Structure of Human Guanylylated Rtcb in Complex with Archease, PDB code: 8odo
was solved by
J.Kopp,
J.L.Gerber,
J.Peschek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
75.23 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.09,
125.547,
125.733,
90,
108.51,
90
|
R / Rfree (%)
|
19.3 /
21.8
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Structure of Human Guanylylated Rtcb in Complex with Archease
(pdb code 8odo). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Structure of Human Guanylylated Rtcb in Complex with Archease, PDB code: 8odo:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 1 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn602
b:67.2
occ:1.00
|
O1P
|
A:5GP601
|
2.2
|
44.9
|
1.0
|
O
|
A:HOH731
|
2.2
|
56.3
|
1.0
|
NE2
|
A:HIS259
|
2.2
|
49.7
|
1.0
|
NE2
|
A:HIS353
|
2.2
|
49.4
|
1.0
|
SG
|
A:CYS122
|
2.5
|
45.0
|
1.0
|
CE1
|
A:HIS259
|
2.9
|
47.7
|
1.0
|
CE1
|
A:HIS353
|
3.1
|
46.2
|
1.0
|
CD2
|
A:HIS353
|
3.3
|
46.5
|
1.0
|
CD2
|
A:HIS259
|
3.4
|
49.8
|
1.0
|
CB
|
A:CYS122
|
3.5
|
47.4
|
1.0
|
P
|
A:5GP601
|
3.5
|
47.3
|
1.0
|
ND1
|
A:HIS259
|
4.1
|
49.9
|
1.0
|
ND1
|
A:HIS353
|
4.3
|
48.5
|
1.0
|
CD2
|
A:HIS428
|
4.3
|
42.7
|
1.0
|
NE2
|
A:HIS227
|
4.3
|
43.6
|
1.0
|
NE2
|
A:HIS428
|
4.3
|
50.0
|
1.0
|
CG
|
A:HIS353
|
4.4
|
47.6
|
1.0
|
CG
|
A:HIS259
|
4.4
|
45.0
|
1.0
|
CD2
|
A:HIS227
|
4.4
|
51.4
|
1.0
|
C5'
|
A:5GP601
|
4.6
|
48.0
|
1.0
|
O5'
|
A:5GP601
|
4.6
|
49.0
|
1.0
|
O3P
|
A:5GP601
|
4.6
|
44.7
|
1.0
|
O2
|
A:PO4603
|
4.6
|
52.3
|
1.0
|
OD2
|
A:ASP119
|
4.7
|
48.8
|
1.0
|
CA
|
A:CYS122
|
4.7
|
46.2
|
1.0
|
C
|
A:CYS122
|
4.7
|
49.4
|
1.0
|
ND2
|
A:ASN354
|
4.9
|
46.8
|
1.0
|
N
|
A:GLY123
|
5.0
|
46.7
|
1.0
|
O
|
A:CYS122
|
5.0
|
44.8
|
1.0
|
|
Manganese binding site 2 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 2 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn201
b:44.6
occ:1.00
|
O
|
B:HOH326
|
2.1
|
53.9
|
1.0
|
O
|
B:ILE179
|
2.1
|
56.8
|
1.0
|
OD1
|
B:ASP178
|
2.2
|
43.0
|
1.0
|
O
|
B:HOH335
|
2.2
|
43.6
|
1.0
|
O1
|
A:PO4603
|
2.2
|
56.8
|
1.0
|
OD1
|
B:ASP51
|
2.2
|
52.9
|
1.0
|
CG
|
B:ASP51
|
3.2
|
51.6
|
1.0
|
C
|
B:ILE179
|
3.3
|
52.7
|
1.0
|
P
|
A:PO4603
|
3.3
|
47.4
|
1.0
|
CG
|
B:ASP178
|
3.4
|
45.8
|
1.0
|
O4
|
A:PO4603
|
3.4
|
44.6
|
1.0
|
N
|
B:ILE179
|
3.5
|
44.4
|
1.0
|
OD2
|
B:ASP51
|
3.6
|
45.4
|
1.0
|
O3
|
A:PO4603
|
4.0
|
43.5
|
1.0
|
CA
|
B:ILE179
|
4.0
|
45.5
|
1.0
|
OD2
|
B:ASP178
|
4.1
|
45.8
|
1.0
|
O
|
A:HOH837
|
4.1
|
46.1
|
1.0
|
NZ
|
B:LYS156
|
4.1
|
43.5
|
1.0
|
C
|
B:ASP178
|
4.2
|
41.9
|
1.0
|
OXT
|
B:ILE179
|
4.2
|
48.5
|
1.0
|
CA
|
B:ASP178
|
4.3
|
43.1
|
1.0
|
O
|
B:ALA50
|
4.4
|
46.7
|
1.0
|
CD
|
B:LYS156
|
4.4
|
45.2
|
1.0
|
CB
|
B:ASP178
|
4.4
|
41.5
|
1.0
|
O2
|
A:PO4603
|
4.6
|
52.3
|
1.0
|
CB
|
B:ASP51
|
4.6
|
43.3
|
1.0
|
CE2
|
A:TYR92
|
4.6
|
47.1
|
1.0
|
CE
|
B:LYS156
|
4.6
|
47.9
|
1.0
|
CG1
|
B:ILE179
|
4.8
|
48.6
|
1.0
|
|
Manganese binding site 3 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 3 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn602
b:51.6
occ:1.00
|
O3P
|
C:5GP601
|
2.2
|
49.7
|
1.0
|
NE2
|
C:HIS259
|
2.3
|
48.9
|
1.0
|
O
|
C:HOH710
|
2.3
|
55.3
|
1.0
|
NE2
|
C:HIS353
|
2.3
|
51.6
|
1.0
|
SG
|
C:CYS122
|
2.5
|
48.6
|
1.0
|
CE1
|
C:HIS353
|
3.1
|
47.3
|
1.0
|
CE1
|
C:HIS259
|
3.1
|
48.4
|
1.0
|
CD2
|
C:HIS259
|
3.4
|
45.4
|
1.0
|
CD2
|
C:HIS353
|
3.4
|
49.4
|
1.0
|
P
|
C:5GP601
|
3.6
|
49.0
|
1.0
|
CB
|
C:CYS122
|
3.6
|
46.0
|
1.0
|
CD2
|
C:HIS428
|
4.3
|
49.6
|
1.0
|
ND1
|
C:HIS353
|
4.3
|
49.3
|
1.0
|
NE2
|
C:HIS428
|
4.3
|
50.4
|
1.0
|
ND1
|
C:HIS259
|
4.3
|
50.0
|
1.0
|
OD1
|
C:ASN226
|
4.4
|
48.2
|
1.0
|
CG
|
C:HIS259
|
4.4
|
47.4
|
1.0
|
CG
|
C:HIS353
|
4.5
|
46.8
|
1.0
|
O2
|
C:PO4603
|
4.5
|
42.0
|
1.0
|
OD2
|
C:ASP119
|
4.5
|
52.6
|
1.0
|
NE2
|
C:HIS227
|
4.5
|
45.2
|
1.0
|
CD2
|
C:HIS227
|
4.6
|
52.2
|
1.0
|
C5'
|
C:5GP601
|
4.6
|
49.8
|
1.0
|
O1P
|
C:5GP601
|
4.6
|
46.3
|
1.0
|
O5'
|
C:5GP601
|
4.6
|
50.1
|
1.0
|
C
|
C:CYS122
|
4.7
|
49.7
|
1.0
|
CA
|
C:CYS122
|
4.8
|
46.9
|
1.0
|
O
|
C:HOH794
|
4.9
|
49.4
|
1.0
|
O
|
C:CYS122
|
5.0
|
48.6
|
1.0
|
|
Manganese binding site 4 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 4 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn201
b:48.5
occ:1.00
|
OD1
|
D:ASP178
|
2.1
|
55.9
|
1.0
|
O1
|
C:PO4603
|
2.2
|
52.2
|
1.0
|
OD1
|
D:ASP51
|
2.2
|
44.9
|
1.0
|
O
|
C:HOH704
|
2.2
|
54.0
|
1.0
|
O
|
D:ILE179
|
2.2
|
46.6
|
1.0
|
O
|
D:HOH346
|
2.2
|
53.1
|
1.0
|
CG
|
D:ASP51
|
3.1
|
45.4
|
1.0
|
OD2
|
D:ASP51
|
3.3
|
51.0
|
1.0
|
P
|
C:PO4603
|
3.3
|
52.7
|
1.0
|
CG
|
D:ASP178
|
3.3
|
47.1
|
1.0
|
C
|
D:ILE179
|
3.4
|
53.5
|
1.0
|
O4
|
C:PO4603
|
3.4
|
45.9
|
1.0
|
N
|
D:ILE179
|
3.5
|
47.7
|
1.0
|
OD2
|
D:ASP178
|
4.0
|
42.7
|
1.0
|
NZ
|
D:LYS156
|
4.0
|
54.6
|
1.0
|
O
|
C:HOH858
|
4.1
|
50.1
|
1.0
|
CA
|
D:ILE179
|
4.1
|
47.6
|
1.0
|
O3
|
C:PO4603
|
4.2
|
45.5
|
1.0
|
C
|
D:ASP178
|
4.3
|
47.9
|
1.0
|
OXT
|
D:ILE179
|
4.3
|
52.3
|
1.0
|
CA
|
D:ASP178
|
4.4
|
46.2
|
1.0
|
CB
|
D:ASP178
|
4.4
|
45.1
|
1.0
|
O2
|
C:PO4603
|
4.4
|
42.0
|
1.0
|
CD
|
D:LYS156
|
4.5
|
45.8
|
1.0
|
O
|
D:ALA50
|
4.5
|
40.2
|
1.0
|
CB
|
D:ASP51
|
4.5
|
39.9
|
1.0
|
CE2
|
C:TYR92
|
4.6
|
39.8
|
1.0
|
CE
|
D:LYS156
|
4.7
|
47.5
|
1.0
|
CG1
|
D:ILE179
|
4.8
|
48.3
|
1.0
|
|
Manganese binding site 5 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 5 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn602
b:79.9
occ:1.00
|
O3P
|
E:5GP601
|
2.2
|
74.1
|
1.0
|
NE2
|
E:HIS259
|
2.2
|
66.5
|
1.0
|
O
|
E:HOH712
|
2.2
|
73.0
|
1.0
|
NE2
|
E:HIS353
|
2.2
|
80.0
|
1.0
|
SG
|
E:CYS122
|
2.5
|
73.5
|
1.0
|
CE1
|
E:HIS259
|
2.8
|
66.7
|
1.0
|
CE1
|
E:HIS353
|
2.9
|
78.3
|
1.0
|
CD2
|
E:HIS353
|
3.4
|
77.9
|
1.0
|
CD2
|
E:HIS259
|
3.4
|
74.5
|
1.0
|
CB
|
E:CYS122
|
3.6
|
71.5
|
1.0
|
P
|
E:5GP601
|
3.6
|
71.2
|
1.0
|
ND1
|
E:HIS259
|
4.0
|
71.0
|
1.0
|
O4
|
E:PO4603
|
4.1
|
67.3
|
1.0
|
ND1
|
E:HIS353
|
4.1
|
77.7
|
1.0
|
NE2
|
E:HIS428
|
4.3
|
78.4
|
1.0
|
CG
|
E:HIS259
|
4.4
|
72.3
|
1.0
|
O
|
E:HOH705
|
4.4
|
66.6
|
1.0
|
CG
|
E:HIS353
|
4.4
|
79.4
|
1.0
|
NE2
|
E:HIS227
|
4.4
|
74.8
|
1.0
|
CD2
|
E:HIS428
|
4.5
|
78.3
|
1.0
|
CD2
|
E:HIS227
|
4.5
|
74.1
|
1.0
|
OD2
|
E:ASP119
|
4.5
|
69.1
|
1.0
|
O1P
|
E:5GP601
|
4.5
|
70.4
|
1.0
|
O5'
|
E:5GP601
|
4.6
|
65.4
|
1.0
|
C5'
|
E:5GP601
|
4.6
|
67.8
|
1.0
|
C
|
E:CYS122
|
4.8
|
78.0
|
1.0
|
CA
|
E:CYS122
|
4.8
|
73.6
|
1.0
|
ND2
|
E:ASN354
|
4.8
|
78.4
|
1.0
|
O
|
E:CYS122
|
5.0
|
80.5
|
1.0
|
|
Manganese binding site 6 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 6 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn201
b:55.9
occ:1.00
|
O2
|
E:PO4603
|
2.1
|
65.2
|
1.0
|
OD1
|
F:ASP178
|
2.2
|
58.1
|
1.0
|
O
|
F:HOH304
|
2.2
|
59.9
|
1.0
|
OD1
|
F:ASP51
|
2.2
|
57.1
|
1.0
|
O
|
F:ILE179
|
2.2
|
64.7
|
1.0
|
O
|
F:HOH311
|
2.2
|
54.7
|
1.0
|
CG
|
F:ASP51
|
3.1
|
55.4
|
1.0
|
P
|
E:PO4603
|
3.3
|
62.6
|
1.0
|
OD2
|
F:ASP51
|
3.3
|
59.3
|
1.0
|
C
|
F:ILE179
|
3.4
|
62.2
|
1.0
|
O1
|
E:PO4603
|
3.4
|
65.3
|
1.0
|
CG
|
F:ASP178
|
3.4
|
57.9
|
1.0
|
N
|
F:ILE179
|
3.4
|
57.9
|
1.0
|
CA
|
F:ILE179
|
4.0
|
58.5
|
1.0
|
OD2
|
F:ASP178
|
4.1
|
59.3
|
1.0
|
C
|
F:ASP178
|
4.2
|
56.2
|
1.0
|
O3
|
E:PO4603
|
4.2
|
66.7
|
1.0
|
O4
|
E:PO4603
|
4.3
|
67.3
|
1.0
|
OXT
|
F:ILE179
|
4.3
|
64.5
|
1.0
|
CA
|
F:ASP178
|
4.3
|
57.7
|
1.0
|
O
|
F:ALA50
|
4.3
|
55.0
|
1.0
|
NZ
|
F:LYS156
|
4.4
|
69.0
|
1.0
|
CB
|
F:ASP178
|
4.4
|
57.0
|
1.0
|
CE2
|
E:TYR92
|
4.5
|
58.4
|
1.0
|
CB
|
F:ASP51
|
4.5
|
47.3
|
1.0
|
CG1
|
F:ILE179
|
4.7
|
54.1
|
1.0
|
CD
|
F:LYS156
|
4.7
|
63.5
|
1.0
|
CE
|
F:LYS156
|
5.0
|
63.4
|
1.0
|
C
|
F:ALA50
|
5.0
|
55.0
|
1.0
|
|
Manganese binding site 7 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 7 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn602
b:52.9
occ:1.00
|
O3P
|
G:5GP601
|
2.2
|
41.2
|
1.0
|
NE2
|
G:HIS259
|
2.2
|
58.7
|
1.0
|
O
|
G:HOH744
|
2.2
|
60.6
|
1.0
|
NE2
|
G:HIS353
|
2.3
|
55.6
|
1.0
|
SG
|
G:CYS122
|
2.5
|
55.1
|
1.0
|
CE1
|
G:HIS259
|
3.0
|
60.8
|
1.0
|
CD2
|
G:HIS353
|
3.2
|
58.6
|
1.0
|
CD2
|
G:HIS259
|
3.3
|
57.5
|
1.0
|
CE1
|
G:HIS353
|
3.4
|
59.8
|
1.0
|
CB
|
G:CYS122
|
3.5
|
56.9
|
1.0
|
P
|
G:5GP601
|
3.5
|
56.0
|
1.0
|
ND1
|
G:HIS259
|
4.2
|
64.0
|
1.0
|
NE2
|
G:HIS428
|
4.3
|
57.6
|
1.0
|
OD1
|
G:ASN226
|
4.3
|
63.3
|
1.0
|
CD2
|
G:HIS428
|
4.3
|
52.3
|
1.0
|
CG
|
G:HIS353
|
4.4
|
59.5
|
1.0
|
CG
|
G:HIS259
|
4.4
|
61.1
|
1.0
|
O1
|
G:PO4603
|
4.4
|
60.7
|
1.0
|
O1P
|
G:5GP601
|
4.4
|
53.6
|
1.0
|
NE2
|
G:HIS227
|
4.4
|
63.1
|
1.0
|
ND1
|
G:HIS353
|
4.5
|
62.9
|
1.0
|
ND2
|
G:ASN354
|
4.5
|
56.6
|
1.0
|
OD2
|
G:ASP119
|
4.6
|
56.7
|
1.0
|
CD2
|
G:HIS227
|
4.6
|
60.6
|
1.0
|
C5'
|
G:5GP601
|
4.6
|
57.8
|
1.0
|
O5'
|
G:5GP601
|
4.6
|
53.6
|
1.0
|
CA
|
G:CYS122
|
4.7
|
54.8
|
1.0
|
C
|
G:CYS122
|
4.7
|
58.4
|
1.0
|
O
|
G:CYS122
|
4.9
|
57.4
|
1.0
|
CG
|
G:ASN226
|
5.0
|
61.0
|
1.0
|
O
|
G:HOH704
|
5.0
|
54.1
|
1.0
|
|
Manganese binding site 8 out
of 8 in 8odo
Go back to
Manganese Binding Sites List in 8odo
Manganese binding site 8 out
of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn201
b:101.0
occ:1.00
|
O
|
H:HOH308
|
2.1
|
55.7
|
1.0
|
OD1
|
H:ASP178
|
2.1
|
52.0
|
1.0
|
O2
|
G:PO4603
|
2.2
|
63.9
|
1.0
|
O
|
H:ILE179
|
2.2
|
62.1
|
1.0
|
OD1
|
H:ASP51
|
2.2
|
62.2
|
1.0
|
O
|
H:HOH303
|
2.2
|
61.7
|
1.0
|
CG
|
H:ASP51
|
3.1
|
54.7
|
1.0
|
O3
|
G:PO4603
|
3.3
|
49.4
|
1.0
|
P
|
G:PO4603
|
3.3
|
52.0
|
1.0
|
C
|
H:ILE179
|
3.3
|
57.0
|
1.0
|
OD2
|
H:ASP51
|
3.4
|
50.8
|
1.0
|
CG
|
H:ASP178
|
3.4
|
52.0
|
1.0
|
N
|
H:ILE179
|
3.5
|
43.4
|
1.0
|
CA
|
H:ILE179
|
4.0
|
51.8
|
1.0
|
O4
|
G:PO4603
|
4.1
|
48.3
|
1.0
|
OD2
|
H:ASP178
|
4.1
|
49.8
|
1.0
|
C
|
H:ASP178
|
4.2
|
49.0
|
1.0
|
OXT
|
H:ILE179
|
4.3
|
59.6
|
1.0
|
NZ
|
H:LYS156
|
4.3
|
60.5
|
1.0
|
CA
|
H:ASP178
|
4.3
|
51.6
|
1.0
|
O
|
H:ALA50
|
4.4
|
57.2
|
1.0
|
CB
|
H:ASP178
|
4.4
|
50.7
|
1.0
|
O1
|
G:PO4603
|
4.4
|
60.7
|
1.0
|
CE2
|
G:TYR92
|
4.5
|
51.3
|
1.0
|
CB
|
H:ASP51
|
4.5
|
56.1
|
1.0
|
CD
|
H:LYS156
|
4.6
|
53.8
|
1.0
|
CG1
|
H:ILE179
|
4.7
|
57.8
|
1.0
|
CE
|
H:LYS156
|
4.9
|
57.5
|
1.0
|
|
Reference:
J.L.Gerber,
J.Kopp,
J.Peschek.
Structure of Human Rtcb in Complex with Archease To Be Published.
Page generated: Sun Oct 6 13:28:51 2024
|