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Magnesium in PDB 3m2u: Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues

Enzymatic activity of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues

All present enzymatic activity of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues:
2.8.4.1;

Protein crystallography data

The structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2u was solved by P.E.Cedervall, M.Dey, S.W.Ragsdale, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.016, 118.260, 122.387, 90.00, 91.84, 90.00
R / Rfree (%) 13 / 15.5

Other elements in 3m2u:

The structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Zinc (Zn) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues (pdb code 3m2u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 3m2u

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Magnesium binding site 1 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg551

b:17.1
occ:0.60
 O A:HOH1599 2.0 26.8 1.0
O A:HOH3828 2.0 21.9 0.6
OXT A:ACT556 2.1 15.4 0.6
O A:HOH713 2.1 17.1 1.0
O A:HOH2285 2.1 28.7 1.0
O A:HOH3971 2.2 19.6 0.6
C A:ACT556 3.2 14.9 0.6
CH3 A:ACT556 3.7 16.6 0.6
NZ A:LYS531 3.9 25.1 1.0
O A:HOH642 3.9 17.7 0.4
OE2 A:GLU528 4.2 12.3 1.0
O A:ACT556 4.3 16.6 0.6
OE1 A:GLU528 4.3 15.5 1.0
O A:HOH1396 4.3 18.3 0.4
O A:VAL519 4.5 12.1 1.0
CD A:GLU528 4.7 12.3 1.0
CD A:LYS531 5.0 17.8 1.0

Magnesium binding site 2 out of 11 in 3m2u

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Magnesium binding site 2 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg552

b:20.6
occ:0.50
 O A:HOH3761 1.9 20.1 0.5
O A:HOH4217 2.0 20.4 0.5
O A:HOH657 2.0 21.3 1.0
O A:HOH1164 2.0 19.2 1.0
O A:HOH4216 2.2 22.5 0.5
O A:HOH3761 3.0 16.6 0.5
O C:HOH3803 3.6 39.3 1.0
OE1 A:GLU20 3.7 14.0 1.0
OE2 C:GLU164 4.2 27.6 0.5
O A:LYS22 4.3 13.9 1.0
CG A:GLU16 4.3 12.7 1.0
OE2 A:GLU16 4.4 15.5 1.0
O A:HOH1831 4.5 30.0 1.0
CD A:GLU20 4.8 12.2 1.0
CD A:GLU16 4.9 12.3 1.0
CD C:GLU164 4.9 29.0 0.5

Magnesium binding site 3 out of 11 in 3m2u

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Magnesium binding site 3 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg444

b:29.9
occ:1.00
 O B:HOH3549 2.0 38.5 1.0
O B:HOH1305 2.0 24.3 1.0
O B:HOH3548 2.0 41.9 1.0
O B:HOH3550 2.1 39.1 1.0
O B:HOH3714 2.2 36.8 1.0
O B:HOH3547 2.4 27.6 1.0
O B:HOH3225 4.0 35.1 1.0
OD2 B:ASP254 4.1 16.1 1.0
OD1 B:ASP254 4.1 17.9 1.0
ND2 B:ASN250 4.2 18.5 1.0
O B:HOH3031 4.5 40.0 1.0
CG B:ASP254 4.5 14.2 1.0
O B:HOH3325 4.6 31.4 1.0

Magnesium binding site 4 out of 11 in 3m2u

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Magnesium binding site 4 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg445

b:20.6
occ:0.60
 OD1 B:ASP271 2.0 17.4 1.0
O B:HOH4127 2.0 20.4 0.6
O B:HOH811 2.1 20.9 1.0
O B:HOH564 2.1 23.7 0.6
O B:HOH3076 2.1 20.8 0.6
O B:HOH1206 2.2 27.3 0.6
O B:HOH1206 2.8 22.9 0.4
CG B:ASP271 3.0 14.2 1.0
OD2 B:ASP271 3.3 16.7 1.0
OE2 B:GLU274 4.2 38.2 1.0
OE1 B:GLU274 4.3 36.8 1.0
O B:HOH973 4.3 27.4 1.0
CB B:ASP271 4.3 11.7 1.0
O B:SER267 4.5 12.2 1.0
CA B:ASP271 4.6 12.5 1.0
N B:ASP271 4.6 11.5 1.0
CD B:GLU274 4.7 36.7 1.0

Magnesium binding site 5 out of 11 in 3m2u

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Magnesium binding site 5 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg250

b:16.2
occ:1.00
 O C:HOH3558 2.0 18.1 1.0
OE2 C:GLU30 2.1 14.7 1.0
O C:HOH1095 2.1 16.0 1.0
O C:HOH3555 2.1 16.7 1.0
O C:HOH3556 2.1 19.3 1.0
O C:HOH3557 2.2 18.3 1.0
CD C:GLU30 3.1 12.6 1.0
OE1 C:GLU30 3.4 15.0 1.0
O C:HOH722 3.9 18.5 1.0
NZ C:LYS135 3.9 25.8 1.0
O C:HOH2304 4.2 26.1 1.0
O C:ILE31 4.2 15.0 1.0
OE2 C:GLU139 4.2 14.9 1.0
O C:HOH1542 4.3 31.6 1.0
O C:HOH1319 4.4 21.4 1.0
O C:HOH3795 4.4 28.9 1.0
NZ C:LYS27 4.5 15.0 1.0
CG C:GLU30 4.5 12.6 1.0
CE C:LYS135 4.8 21.1 1.0

Magnesium binding site 6 out of 11 in 3m2u

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Magnesium binding site 6 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1

b:23.6
occ:0.80
 O F:HOH3545 2.0 28.0 0.8
O D:HOH3546 2.0 28.8 1.0
O D:HOH3543 2.1 27.5 1.0
O D:HOH3544 2.1 28.9 1.0
O F:HOH3542 2.2 36.5 0.8
NH2 F:ARG225 4.2 26.0 1.0
OE2 D:GLU376 4.3 19.9 1.0
OE1 D:GLU376 4.4 19.5 1.0
O F:HOH807 4.7 25.2 1.0
CD D:GLU376 4.8 16.7 1.0
CZ F:ARG225 5.0 17.2 1.0

Magnesium binding site 7 out of 11 in 3m2u

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Magnesium binding site 7 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg551

b:18.9
occ:0.50
 O D:HOH3559 2.0 27.8 1.0
O D:HOH3562 2.0 32.1 1.0
O D:HOH3560 2.0 26.4 0.5
O D:HOH3561 2.1 28.3 0.5
O D:HOH3563 2.1 25.8 0.5
O D:HOH1116 2.3 25.6 0.5
O D:HOH674 3.9 19.7 1.0
O D:ASP516 4.4 13.6 1.0
OD1 D:ASP516 4.5 27.3 1.0
OD2 D:ASP521 4.6 16.7 1.0
O D:HOH992 4.6 21.4 1.0
CB D:ASP521 4.7 10.6 1.0
CG D:ASP521 4.8 13.1 1.0
CB D:ASP516 4.8 17.2 1.0
O D:HOH733 4.9 28.8 1.0

Magnesium binding site 8 out of 11 in 3m2u

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Magnesium binding site 8 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg552

b:20.2
occ:0.50
 O D:HOH4001 1.9 32.1 1.0
O D:HOH4000 1.9 35.1 1.0
OE1 D:GLU175 2.1 23.3 1.0
O D:HOH4183 2.1 25.2 0.5
CD D:GLU175 3.1 18.0 1.0
OE2 D:GLU175 3.5 21.2 1.0
O D:HOH932 4.0 18.9 1.0
CG D:GLU175 4.4 16.8 1.0
CB D:GLU175 5.0 14.8 1.0

Magnesium binding site 9 out of 11 in 3m2u

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Magnesium binding site 9 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg444

b:21.2
occ:1.00
 O E:HOH3583 1.9 25.3 1.0
O E:HOH3585 2.1 20.0 1.0
O E:HOH2328 2.1 22.8 1.0
O E:HOH2200 2.1 23.9 1.0
O E:HOH3584 2.3 32.7 1.0
O F:HOH3202 3.9 34.3 1.0
O E:HOH3601 4.0 22.5 1.0
OE1 E:GLU287 4.1 24.6 1.0
O E:HOH2118 4.4 40.5 1.0
O E:HOH3758 4.5 39.5 1.0
CD E:GLU287 4.6 25.3 1.0
NZ E:LYS292 4.6 27.2 1.0
OE2 E:GLU287 4.7 21.4 1.0

Magnesium binding site 10 out of 11 in 3m2u

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Magnesium binding site 10 out of 11 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg445

b:20.6
occ:0.50
 O E:HOH4090 1.9 19.6 0.5
O E:HOH1466 2.1 23.5 1.0
O E:HOH1684 2.1 26.7 1.0
OD1 E:ASP271 2.1 20.3 1.0
O E:HOH3695 2.2 28.5 0.5
O E:HOH3695 2.8 27.6 0.5
CG E:ASP271 3.1 16.2 1.0
OD2 E:ASP271 3.4 17.0 1.0
O E:HOH3699 4.0 20.1 0.4
O E:HOH2049 4.3 30.6 1.0
OE2 E:GLU274 4.3 25.9 0.5
OE1 E:GLU274 4.3 28.4 0.5
CB E:ASP271 4.4 15.6 1.0
O E:SER267 4.5 15.4 1.0
N E:ASP271 4.6 14.1 1.0
CA E:ASP271 4.7 14.3 1.0
CB E:ALA270 5.0 16.5 1.0

Reference:

P.E.Cedervall, M.Dey, A.R.Pearson, S.W.Ragsdale, C.M.Wilmot. Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues. Biochemistry V. 49 7683 2010.
ISSN: ISSN 0006-2960
PubMed: 20707311
DOI: 10.1021/BI100458D
Page generated: Wed Aug 14 19:06:57 2024

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