Magnesium in PDB 1t57: Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum
Protein crystallography data
The structure of Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum, PDB code: 1t57
was solved by
Y.Kim,
A.Joachimiak,
V.Saridakis,
X.Xu,
C.H.Arrowsmith,
D.Christendat,
A.Edwards,
Midwest Center For Structural Genomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.92 /
2.30
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.983,
69.398,
90.953,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25.2 /
31.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum
(pdb code 1t57). 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 the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum, PDB code: 1t57:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1t57
Go back to
Magnesium Binding Sites List in 1t57
Magnesium binding site 1 out
of 4 in the Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum
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 Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:46.9
occ:1.00
|
O
|
A:VAL122
|
2.5
|
19.1
|
1.0
|
O
|
A:PRO184
|
2.6
|
35.8
|
1.0
|
OXT
|
A:PRO186
|
2.6
|
50.9
|
1.0
|
O
|
B:ILE177
|
2.7
|
28.6
|
1.0
|
O
|
A:ARG185
|
2.8
|
34.0
|
1.0
|
C
|
A:ARG185
|
3.1
|
36.8
|
1.0
|
C
|
A:PRO186
|
3.1
|
48.1
|
1.0
|
O
|
A:PRO186
|
3.6
|
47.2
|
1.0
|
N
|
A:PRO186
|
3.6
|
41.9
|
1.0
|
C
|
A:PRO184
|
3.6
|
37.8
|
1.0
|
C
|
A:VAL122
|
3.7
|
20.3
|
1.0
|
CA
|
A:ARG185
|
3.7
|
32.9
|
1.0
|
C
|
B:ILE177
|
3.8
|
30.6
|
1.0
|
CA
|
A:PRO186
|
3.9
|
46.5
|
1.0
|
NH2
|
B:ARG176
|
4.0
|
18.8
|
1.0
|
N
|
A:ARG185
|
4.1
|
36.4
|
1.0
|
O
|
A:HOH316
|
4.2
|
35.6
|
1.0
|
CA
|
B:HIS178
|
4.3
|
27.9
|
1.0
|
CA
|
A:VAL122
|
4.4
|
21.5
|
1.0
|
N
|
B:HIS178
|
4.5
|
36.6
|
1.0
|
CB
|
A:SER123
|
4.6
|
22.2
|
1.0
|
O
|
B:HIS178
|
4.7
|
30.1
|
1.0
|
N
|
A:SER123
|
4.7
|
18.9
|
1.0
|
CD
|
A:PRO186
|
4.7
|
43.8
|
1.0
|
ND1
|
B:HIS178
|
4.7
|
26.5
|
1.0
|
N
|
B:ILE177
|
4.7
|
27.0
|
1.0
|
CZ
|
B:ARG176
|
4.8
|
18.1
|
1.0
|
CA
|
A:SER123
|
4.8
|
24.6
|
1.0
|
O
|
A:MSE121
|
4.8
|
35.6
|
1.0
|
NE
|
B:ARG176
|
4.9
|
22.6
|
1.0
|
CA
|
B:ILE177
|
4.9
|
28.7
|
1.0
|
C
|
B:HIS178
|
4.9
|
28.3
|
1.0
|
CG1
|
A:VAL122
|
4.9
|
16.4
|
1.0
|
CA
|
A:PRO184
|
4.9
|
36.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1t57
Go back to
Magnesium Binding Sites List in 1t57
Magnesium binding site 2 out
of 4 in the Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum
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 Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:52.1
occ:1.00
|
O2P
|
B:FMN201
|
2.5
|
64.3
|
1.0
|
OE1
|
B:GLU43
|
2.6
|
0.5
|
1.0
|
P
|
B:FMN201
|
3.6
|
62.4
|
1.0
|
N
|
B:GLY157
|
3.6
|
55.0
|
1.0
|
CB
|
B:TRP156
|
3.8
|
70.5
|
1.0
|
CD
|
B:LYS13
|
3.8
|
70.3
|
1.0
|
CD
|
B:GLU43
|
3.8
|
94.5
|
1.0
|
O3P
|
B:FMN201
|
4.0
|
70.1
|
1.0
|
CA
|
B:GLY157
|
4.1
|
54.4
|
1.0
|
O1P
|
B:FMN201
|
4.2
|
68.3
|
1.0
|
C
|
B:TRP156
|
4.2
|
60.8
|
1.0
|
CB
|
B:GLU43
|
4.3
|
69.7
|
1.0
|
CA
|
B:TRP156
|
4.4
|
64.1
|
1.0
|
CE
|
B:LYS13
|
4.5
|
72.0
|
1.0
|
CG
|
B:LYS13
|
4.6
|
67.7
|
1.0
|
OE2
|
B:GLU43
|
4.6
|
98.3
|
1.0
|
CG
|
B:GLU43
|
4.6
|
84.8
|
1.0
|
CG
|
B:TRP156
|
4.9
|
80.2
|
1.0
|
O5'
|
B:FMN201
|
5.0
|
71.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1t57
Go back to
Magnesium Binding Sites List in 1t57
Magnesium binding site 3 out
of 4 in the Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum
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 Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:71.6
occ:1.00
|
O
|
B:VAL122
|
2.3
|
27.6
|
1.0
|
O
|
B:ARG185
|
2.5
|
39.7
|
1.0
|
OXT
|
B:PRO186
|
2.6
|
39.2
|
1.0
|
O
|
B:PRO184
|
2.6
|
37.7
|
1.0
|
O
|
A:ILE177
|
2.6
|
28.2
|
1.0
|
C
|
B:PRO186
|
2.9
|
43.2
|
1.0
|
O
|
A:HOH362
|
2.9
|
34.5
|
1.0
|
C
|
B:ARG185
|
3.1
|
37.6
|
1.0
|
O
|
B:PRO186
|
3.2
|
46.3
|
1.0
|
C
|
B:VAL122
|
3.5
|
30.1
|
1.0
|
N
|
B:PRO186
|
3.7
|
42.5
|
1.0
|
C
|
B:PRO184
|
3.7
|
37.8
|
1.0
|
C
|
A:ILE177
|
3.8
|
29.7
|
1.0
|
NH2
|
A:ARG176
|
3.8
|
20.0
|
1.0
|
CA
|
B:PRO186
|
3.8
|
42.5
|
1.0
|
CA
|
B:ARG185
|
3.9
|
32.6
|
1.0
|
N
|
B:ARG185
|
4.2
|
31.9
|
1.0
|
CA
|
B:VAL122
|
4.3
|
34.0
|
1.0
|
CA
|
A:HIS178
|
4.3
|
36.4
|
1.0
|
N
|
B:SER123
|
4.5
|
28.3
|
1.0
|
N
|
A:HIS178
|
4.5
|
29.8
|
1.0
|
O
|
B:HOH308
|
4.6
|
35.3
|
1.0
|
CB
|
B:SER123
|
4.6
|
30.0
|
1.0
|
CA
|
B:SER123
|
4.7
|
27.6
|
1.0
|
CD2
|
A:HIS178
|
4.7
|
38.0
|
1.0
|
CZ
|
A:ARG176
|
4.7
|
22.0
|
1.0
|
O
|
A:HIS178
|
4.7
|
35.0
|
1.0
|
N
|
A:ILE177
|
4.7
|
26.8
|
1.0
|
CA
|
A:ILE177
|
4.8
|
33.3
|
1.0
|
NE
|
A:ARG176
|
4.8
|
17.8
|
1.0
|
O
|
B:MSE121
|
4.9
|
38.0
|
1.0
|
CA
|
B:PRO184
|
4.9
|
37.8
|
1.0
|
CD
|
B:PRO186
|
4.9
|
40.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1t57
Go back to
Magnesium Binding Sites List in 1t57
Magnesium binding site 4 out
of 4 in the Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum
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 Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg304
b:75.9
occ:1.00
|
O
|
C:PRO184
|
2.6
|
90.6
|
1.0
|
O
|
C:ARG185
|
2.7
|
89.6
|
1.0
|
CG1
|
C:VAL122
|
3.0
|
62.0
|
1.0
|
SE
|
C:MSE183
|
3.3
|
93.5
|
1.0
|
O
|
C:VAL122
|
3.5
|
85.9
|
1.0
|
C
|
C:ARG185
|
3.5
|
92.7
|
1.0
|
O
|
C:PRO186
|
3.5
|
94.0
|
1.0
|
C
|
C:PRO184
|
3.7
|
87.8
|
1.0
|
CA
|
C:ARG185
|
3.8
|
96.0
|
1.0
|
C
|
C:VAL122
|
4.0
|
82.7
|
1.0
|
CA
|
C:VAL122
|
4.2
|
77.1
|
1.0
|
C
|
C:PRO186
|
4.2
|
92.6
|
1.0
|
CG
|
C:MSE183
|
4.2
|
90.8
|
1.0
|
CB
|
C:VAL122
|
4.2
|
69.5
|
1.0
|
N
|
C:ARG185
|
4.3
|
90.8
|
1.0
|
N
|
C:PRO186
|
4.6
|
87.4
|
1.0
|
CB
|
C:MSE183
|
4.7
|
94.1
|
1.0
|
OXT
|
C:PRO186
|
4.7
|
97.0
|
1.0
|
CB
|
C:SER123
|
4.8
|
85.0
|
1.0
|
N
|
C:SER123
|
4.8
|
83.5
|
1.0
|
N
|
C:PRO184
|
4.9
|
78.3
|
1.0
|
CA
|
C:PRO184
|
4.9
|
82.3
|
1.0
|
CA
|
C:PRO186
|
5.0
|
89.6
|
1.0
|
|
Reference:
Y.Kim,
A.Joachimiak,
V.Saridakis,
X.Xu,
C.H.Arrowsmith,
D.Christendat,
A.Edwards.
Crystal Structure of the Conserved Protein MTH1675 From Methanobacterium Thermoautotrophicum To Be Published.
Page generated: Tue Aug 13 14:25:53 2024
|