Potassium in PDB 2i2x: Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Enzymatic activity of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
All present enzymatic activity of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri:
2.1.1.90;
Protein crystallography data
The structure of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri, PDB code: 2i2x
was solved by
C.H.Hagemeier,
M.Kruer,
R.K.Thauer,
E.Warkentin,
U.Ermler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.750,
172.850,
190.540,
90.00,
98.86,
90.00
|
R / Rfree (%)
|
18.2 /
23.1
|
Other elements in 2i2x:
The structure of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
(pdb code 2i2x). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the
Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri, PDB code: 2i2x:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Potassium binding site 1 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 1 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K511
b:23.5
occ:0.70
|
OE2
|
A:GLU86
|
2.3
|
19.5
|
1.0
|
OE2
|
A:GLU164
|
2.4
|
24.6
|
1.0
|
ZN
|
A:ZN501
|
2.9
|
20.9
|
1.0
|
OE1
|
A:GLU313
|
3.2
|
13.9
|
1.0
|
CD
|
A:GLU86
|
3.2
|
17.9
|
1.0
|
CD
|
A:GLU164
|
3.2
|
20.5
|
1.0
|
OE1
|
A:GLU86
|
3.4
|
20.6
|
1.0
|
OE1
|
A:GLU164
|
3.4
|
22.3
|
1.0
|
O
|
A:HOH609
|
3.6
|
8.4
|
1.0
|
NZ
|
A:LYS267
|
4.0
|
14.7
|
1.0
|
CD
|
A:GLU313
|
4.1
|
14.7
|
1.0
|
SG
|
A:CYS269
|
4.3
|
14.2
|
1.0
|
OE2
|
A:GLU313
|
4.3
|
13.8
|
1.0
|
CG
|
A:GLU164
|
4.6
|
15.3
|
1.0
|
CG
|
A:GLU86
|
4.6
|
15.6
|
1.0
|
CE
|
A:LYS267
|
4.7
|
14.4
|
1.0
|
SG
|
A:CYS220
|
4.9
|
14.5
|
1.0
|
O
|
B:HOH501
|
4.9
|
42.7
|
1.0
|
|
Potassium binding site 2 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 2 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K512
b:22.0
occ:0.70
|
OE2
|
C:GLU86
|
2.3
|
22.1
|
1.0
|
OE2
|
C:GLU164
|
2.5
|
17.9
|
1.0
|
O
|
C:HOH679
|
2.8
|
13.8
|
1.0
|
ZN
|
C:ZN502
|
3.0
|
19.9
|
1.0
|
OE1
|
C:GLU313
|
3.1
|
15.3
|
1.0
|
CD
|
C:GLU86
|
3.1
|
19.0
|
1.0
|
OE1
|
C:GLU86
|
3.3
|
21.1
|
1.0
|
CD
|
C:GLU164
|
3.3
|
15.8
|
1.0
|
OE1
|
C:GLU164
|
3.5
|
18.0
|
1.0
|
O
|
C:HOH518
|
3.9
|
9.5
|
1.0
|
CD
|
C:GLU313
|
4.0
|
13.5
|
1.0
|
NZ
|
C:LYS267
|
4.1
|
9.2
|
1.0
|
OE2
|
C:GLU313
|
4.2
|
16.9
|
1.0
|
SG
|
C:CYS269
|
4.4
|
14.3
|
1.0
|
CG
|
C:GLU86
|
4.5
|
14.6
|
1.0
|
O
|
D:HOH501
|
4.6
|
20.5
|
1.0
|
CG
|
C:GLU164
|
4.7
|
13.6
|
1.0
|
CE
|
C:LYS267
|
4.9
|
10.7
|
1.0
|
SG
|
C:CYS220
|
5.0
|
10.5
|
1.0
|
|
Potassium binding site 3 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 3 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K513
b:33.9
occ:0.70
|
OE2
|
E:GLU86
|
2.5
|
42.1
|
1.0
|
OE2
|
E:GLU164
|
2.6
|
38.4
|
1.0
|
OE1
|
E:GLU313
|
2.9
|
37.9
|
1.0
|
ZN
|
E:ZN503
|
3.0
|
37.0
|
0.7
|
CD
|
E:GLU86
|
3.2
|
41.7
|
1.0
|
OE1
|
E:GLU86
|
3.3
|
41.2
|
1.0
|
CD
|
E:GLU164
|
3.5
|
36.3
|
1.0
|
OE1
|
E:GLU164
|
3.6
|
38.0
|
1.0
|
CD
|
E:GLU313
|
3.8
|
37.1
|
1.0
|
OE2
|
E:GLU313
|
4.0
|
38.0
|
1.0
|
NZ
|
E:LYS267
|
4.3
|
26.5
|
1.0
|
SG
|
E:CYS269
|
4.4
|
36.4
|
1.0
|
CG
|
E:GLU86
|
4.7
|
38.2
|
1.0
|
O
|
E:GLU313
|
4.7
|
32.8
|
1.0
|
O
|
F:HOH501
|
4.9
|
17.7
|
0.5
|
CG
|
E:GLU164
|
5.0
|
34.0
|
1.0
|
|
Potassium binding site 4 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 4 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K514
b:40.0
occ:0.70
|
OE2
|
G:GLU86
|
2.5
|
33.7
|
1.0
|
OE2
|
G:GLU164
|
2.5
|
34.1
|
1.0
|
ZN
|
G:ZN504
|
3.0
|
33.2
|
0.7
|
OE1
|
G:GLU313
|
3.2
|
30.7
|
1.0
|
CD
|
G:GLU164
|
3.2
|
33.3
|
1.0
|
OE1
|
G:GLU164
|
3.2
|
34.5
|
1.0
|
CD
|
G:GLU86
|
3.4
|
33.6
|
1.0
|
OE1
|
G:GLU86
|
3.7
|
33.6
|
1.0
|
O
|
H:HOH501
|
4.0
|
18.1
|
0.5
|
CD
|
G:GLU313
|
4.2
|
30.3
|
1.0
|
O
|
G:HOH555
|
4.3
|
20.5
|
1.0
|
NZ
|
G:LYS267
|
4.4
|
29.1
|
1.0
|
SG
|
G:CYS269
|
4.5
|
28.3
|
1.0
|
OE2
|
G:GLU313
|
4.5
|
32.8
|
1.0
|
SG
|
G:CYS220
|
4.6
|
28.3
|
1.0
|
CG
|
G:GLU164
|
4.6
|
32.3
|
1.0
|
CG
|
G:GLU86
|
4.7
|
32.2
|
1.0
|
O39
|
H:B13500
|
4.9
|
61.4
|
1.0
|
|
Potassium binding site 5 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 5 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K515
b:28.7
occ:0.70
|
OE2
|
I:GLU164
|
2.4
|
25.7
|
1.0
|
OE2
|
I:GLU86
|
2.6
|
29.5
|
1.0
|
ZN
|
I:ZN505
|
3.0
|
30.0
|
1.0
|
OE1
|
I:GLU313
|
3.1
|
23.1
|
1.0
|
CD
|
I:GLU164
|
3.3
|
25.1
|
1.0
|
CD
|
I:GLU86
|
3.4
|
28.8
|
1.0
|
OE1
|
I:GLU86
|
3.4
|
30.6
|
1.0
|
OE1
|
I:GLU164
|
3.5
|
28.1
|
1.0
|
CD
|
I:GLU313
|
3.9
|
20.6
|
1.0
|
OE2
|
I:GLU313
|
3.9
|
22.1
|
1.0
|
O
|
I:HOH525
|
4.1
|
13.2
|
1.0
|
NZ
|
I:LYS267
|
4.2
|
21.3
|
1.0
|
SG
|
I:CYS269
|
4.4
|
18.5
|
1.0
|
O
|
J:HOH501
|
4.4
|
2.8
|
0.5
|
CG
|
I:GLU164
|
4.7
|
22.1
|
1.0
|
CG
|
I:GLU86
|
4.7
|
23.4
|
1.0
|
SG
|
I:CYS220
|
5.0
|
21.9
|
1.0
|
CE
|
I:LYS267
|
5.0
|
20.9
|
1.0
|
|
Potassium binding site 6 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 6 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:K516
b:31.9
occ:0.70
|
OE2
|
K:GLU164
|
2.4
|
30.9
|
1.0
|
OE2
|
K:GLU86
|
2.6
|
27.5
|
1.0
|
OE1
|
K:GLU313
|
2.9
|
20.8
|
1.0
|
ZN
|
K:ZN506
|
3.0
|
33.5
|
1.0
|
CD
|
K:GLU164
|
3.2
|
29.8
|
1.0
|
OE1
|
K:GLU164
|
3.3
|
33.9
|
1.0
|
CD
|
K:GLU86
|
3.4
|
26.6
|
1.0
|
OE1
|
K:GLU86
|
3.6
|
28.3
|
1.0
|
CD
|
K:GLU313
|
3.9
|
18.8
|
1.0
|
O
|
K:HOH605
|
3.9
|
19.9
|
1.0
|
NZ
|
K:LYS267
|
4.0
|
20.8
|
1.0
|
OE2
|
K:GLU313
|
4.1
|
19.6
|
1.0
|
SG
|
K:CYS269
|
4.5
|
24.8
|
1.0
|
CG
|
K:GLU86
|
4.5
|
25.2
|
1.0
|
CG
|
K:GLU164
|
4.6
|
25.1
|
1.0
|
SG
|
K:CYS220
|
4.9
|
24.5
|
1.0
|
CE
|
K:LYS267
|
4.9
|
20.1
|
1.0
|
O
|
L:HOH501
|
5.0
|
18.9
|
0.5
|
|
Potassium binding site 7 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 7 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:K517
b:33.7
occ:0.70
|
OE2
|
M:GLU164
|
2.3
|
29.0
|
1.0
|
OE2
|
M:GLU86
|
2.4
|
34.6
|
1.0
|
O
|
M:HOH615
|
2.6
|
27.2
|
1.0
|
ZN
|
M:ZN507
|
3.0
|
33.9
|
1.0
|
OE1
|
M:GLU313
|
3.1
|
22.9
|
1.0
|
CD
|
M:GLU164
|
3.2
|
28.2
|
1.0
|
OE1
|
M:GLU164
|
3.3
|
32.0
|
1.0
|
CD
|
M:GLU86
|
3.4
|
31.7
|
1.0
|
OE1
|
M:GLU86
|
3.8
|
33.7
|
1.0
|
NZ
|
M:LYS267
|
4.0
|
14.2
|
1.0
|
CD
|
M:GLU313
|
4.0
|
21.6
|
1.0
|
O
|
M:HOH563
|
4.3
|
12.4
|
1.0
|
OE2
|
M:GLU313
|
4.3
|
23.2
|
1.0
|
SG
|
M:CYS269
|
4.4
|
22.7
|
1.0
|
O
|
N:HOH501
|
4.5
|
10.9
|
0.5
|
CG
|
M:GLU164
|
4.6
|
24.6
|
1.0
|
CG
|
M:GLU86
|
4.7
|
27.5
|
1.0
|
CE
|
M:LYS267
|
5.0
|
14.6
|
1.0
|
|
Potassium binding site 8 out
of 8 in 2i2x
Go back to
Potassium Binding Sites List in 2i2x
Potassium binding site 8 out
of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:K518
b:35.2
occ:0.70
|
OE2
|
O:GLU86
|
2.3
|
26.5
|
1.0
|
OE2
|
O:GLU164
|
2.5
|
27.9
|
1.0
|
ZN
|
O:ZN508
|
3.0
|
33.9
|
1.0
|
OE1
|
O:GLU313
|
3.1
|
25.0
|
1.0
|
CD
|
O:GLU86
|
3.2
|
25.4
|
1.0
|
CD
|
O:GLU164
|
3.3
|
27.0
|
1.0
|
OE1
|
O:GLU164
|
3.4
|
30.5
|
1.0
|
OE1
|
O:GLU86
|
3.5
|
27.0
|
1.0
|
CD
|
O:GLU313
|
3.9
|
23.7
|
1.0
|
O
|
O:HOH577
|
4.0
|
6.5
|
1.0
|
O
|
P:HOH501
|
4.0
|
2.0
|
0.5
|
OE2
|
O:GLU313
|
4.1
|
25.7
|
1.0
|
NZ
|
O:LYS267
|
4.2
|
17.6
|
1.0
|
CG
|
O:GLU86
|
4.5
|
20.5
|
1.0
|
SG
|
O:CYS269
|
4.6
|
19.2
|
1.0
|
SG
|
O:CYS220
|
4.8
|
21.4
|
1.0
|
CG
|
O:GLU164
|
4.8
|
23.2
|
1.0
|
|
Reference:
C.H.Hagemeier,
M.Krer,
R.K.Thauer,
E.Warkentin,
U.Ermler.
Insight Into the Mechanism of Biological Methanol Activation Based on the Crystal Structure of the Methanol-Cobalamin Methyltransferase Complex Proc.Natl.Acad.Sci.Usa V. 103 18917 2006.
ISSN: ISSN 0027-8424
PubMed: 17142327
DOI: 10.1073/PNAS.0603650103
Page generated: Mon Aug 12 06:38:48 2024
|