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Magnesium in PDB 3m2r: 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: 3m2r 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) 20.49 / 1.30
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 (%) 14.3 / 16.6

Other elements in 3m2r:

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:

The binding sites of Magnesium atom in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues (pdb code 3m2r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3m2r

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Magnesium binding site 1 out of 9 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:15.4
occ:0.70
 O A:HOH3575 2.0 18.7 0.7
O A:HOH3576 2.0 19.9 0.7
O A:HOH1631 2.1 17.0 0.7
O A:HOH1652 2.1 14.4 0.7
O A:HOH3574 2.2 19.2 0.7
O A:HOH4055 3.5 40.2 1.0
CD A:PRO178 3.7 9.3 0.4
O A:HOH1440 4.1 23.1 1.0
CG A:PRO178 4.2 9.8 0.4
CD A:PRO178 4.3 10.4 0.6
O A:ASP174 4.3 12.8 0.6
O A:GLU175 4.4 12.2 0.6
O A:ASP174 4.4 14.5 0.4
O A:HOH3271 4.4 26.1 1.0
O A:ILE176 4.5 10.3 0.6
O A:HOH1781 4.6 32.2 1.0
CG A:PRO178 5.0 16.8 0.6
C A:GLU175 5.0 13.1 0.6

Magnesium binding site 2 out of 9 in 3m2r

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Magnesium binding site 2 out of 9 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:17.3
occ:0.70
 O A:HOH1356 2.0 22.6 1.0
O A:HOH3581 2.0 23.2 0.7
O A:HOH1590 2.1 20.7 0.7
O A:HOH2583 2.1 22.9 0.7
O A:HOH1599 2.1 19.3 0.7
O A:HOH2603 2.2 25.6 0.7
O A:HOH1599 2.3 15.9 0.3
O A:HOH3971 3.8 17.9 0.3
MG A:MG553 4.1 13.7 0.3
O A:HOH739 4.1 15.8 1.0
CB A:ASP516 4.4 10.2 0.4
O A:ASP516 4.5 12.5 1.0
O A:HOH996 4.5 27.2 1.0
OD2 A:ASP521 4.5 14.2 1.0
O A:HOH716 4.5 15.4 1.0
O A:HOH3828 4.6 13.4 0.3
CB A:ASP521 4.7 9.3 1.0
CG A:ASP521 4.7 9.7 1.0
OD1 A:ASP516 4.8 18.7 0.6
O A:HOH1286 4.8 29.5 1.0
CB A:ASP516 5.0 12.3 0.6

Magnesium binding site 3 out of 9 in 3m2r

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Magnesium binding site 3 out of 9 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
A:Mg553

b:13.7
occ:0.30
 O A:HOH1599 2.0 15.9 0.3
O A:HOH642 2.1 12.5 0.3
O A:HOH716 2.1 15.4 1.0
O A:HOH3828 2.2 13.4 0.3
O A:HOH3971 2.2 17.9 0.3
O A:HOH2285 2.3 31.0 1.0
O A:HOH3581 2.7 23.2 0.7
O A:HOH1599 3.6 19.3 0.7
NZ A:LYS531 3.7 27.5 1.0
O A:HOH2583 3.8 22.9 0.7
O A:HOH642 3.9 15.0 0.7
MG A:MG552 4.1 17.3 0.7
OE2 A:GLU528 4.1 9.7 1.0
O A:HOH1396 4.2 22.7 1.0
OE1 A:GLU528 4.3 14.4 1.0
O A:VAL519 4.5 11.5 1.0
CD A:GLU528 4.6 10.8 1.0
CE A:LYS531 4.9 26.1 1.0
CD A:LYS531 5.0 20.6 1.0
O A:HOH1356 5.0 22.6 1.0

Magnesium binding site 4 out of 9 in 3m2r

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Magnesium binding site 4 out of 9 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:Mg444

b:21.2
occ:1.00
 O B:HOH3550 1.9 33.0 1.0
O B:HOH3548 2.0 28.4 1.0
O B:HOH3549 2.0 24.1 1.0
O B:HOH1305 2.1 18.2 1.0
O B:HOH3547 2.1 19.3 1.0
O B:HOH3714 2.1 35.4 1.0
ND2 B:ASN250 4.0 15.8 1.0
O B:HOH3225 4.1 24.5 1.0
OD2 B:ASP254 4.1 13.6 1.0
OD1 B:ASP254 4.1 14.3 1.0
O B:HOH3031 4.4 31.9 1.0
CG B:ASP254 4.6 13.2 1.0
O B:HOH3325 4.6 33.0 1.0
O B:HOH3430 5.0 33.6 1.0

Magnesium binding site 5 out of 9 in 3m2r

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Magnesium binding site 5 out of 9 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:17.0
occ:1.00
 O C:HOH3558 2.0 19.3 1.0
O C:HOH3555 2.1 16.5 1.0
O C:HOH3556 2.1 18.2 1.0
O C:HOH1095 2.1 18.8 1.0
OE2 C:GLU30 2.1 15.4 1.0
O C:HOH3557 2.1 20.7 1.0
CD C:GLU30 3.1 13.3 1.0
OE1 C:GLU30 3.4 14.6 1.0
NZ C:LYS135 3.9 26.9 1.0
O C:HOH722 3.9 18.2 1.0
O C:HOH2304 4.1 32.0 1.0
O C:HOH1542 4.1 32.8 1.0
O C:ILE31 4.1 16.1 1.0
OE2 C:GLU139 4.3 15.8 1.0
O C:HOH3795 4.3 34.3 1.0
O C:HOH1319 4.4 21.7 1.0
NZ C:LYS27 4.5 16.3 1.0
CG C:GLU30 4.5 14.0 1.0
CE C:LYS135 4.9 24.4 1.0

Magnesium binding site 6 out of 9 in 3m2r

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Magnesium binding site 6 out of 9 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:14.8
occ:1.00
 O D:HOH3546 2.0 16.0 1.0
O F:HOH3545 2.0 17.0 1.0
O F:HOH3542 2.1 18.5 1.0
O D:HOH3544 2.1 15.5 1.0
O D:HOH3543 2.2 17.6 1.0
NH2 F:ARG225 4.1 15.0 1.0
O D:HOH1947 4.3 27.7 1.0
O D:HOH1011 4.4 22.7 1.0
OE2 D:GLU376 4.4 15.2 1.0
OE1 D:GLU376 4.4 13.1 1.0
O F:HOH807 4.5 19.6 1.0
CD D:GLU376 4.9 12.2 1.0
CZ F:ARG225 4.9 11.9 1.0

Magnesium binding site 7 out of 9 in 3m2r

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Magnesium binding site 7 out of 9 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:19.1
occ:1.00
 O D:HOH3559 2.0 17.9 1.0
O D:HOH3563 2.1 23.6 1.0
O D:HOH3561 2.1 28.3 1.0
O D:HOH3562 2.1 22.0 1.0
O D:HOH1116 2.1 23.4 1.0
O D:HOH3560 2.1 25.0 1.0
O D:HOH674 4.0 14.7 1.0
OD1 D:ASP516 4.3 20.2 1.0
OD2 D:ASP521 4.4 13.5 1.0
O D:ASP516 4.4 11.0 1.0
O D:HOH992 4.6 16.9 1.0
CB D:ASP521 4.6 8.0 1.0
CG D:ASP521 4.6 11.4 1.0
CB D:ASP516 4.8 13.7 1.0
CG D:ASP516 4.9 15.4 1.0

Magnesium binding site 8 out of 9 in 3m2r

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Magnesium binding site 8 out of 9 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
E:Mg444

b:24.6
occ:1.00
 O E:HOH3583 1.9 26.6 1.0
O E:HOH3585 2.1 21.8 1.0
O E:HOH2200 2.1 32.6 1.0
O E:HOH2328 2.1 28.7 1.0
O E:HOH3584 2.3 31.9 1.0
OE1 E:GLU287 4.0 26.6 1.0
O E:HOH3202 4.0 31.8 1.0
O E:HOH3601 4.1 23.6 1.0
O E:HOH3758 4.2 34.2 1.0
O E:HOH2118 4.4 26.9 1.0
CD E:GLU287 4.5 27.0 1.0
NZ E:LYS292 4.6 37.2 1.0
OE2 E:GLU287 4.7 26.4 1.0

Magnesium binding site 9 out of 9 in 3m2r

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Magnesium binding site 9 out of 9 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
F:Mg250

b:15.8
occ:1.00
 O F:HOH3554 2.0 18.7 1.0
O F:HOH3552 2.0 15.7 1.0
O F:HOH1294 2.1 15.6 1.0
O F:HOH3553 2.1 17.5 1.0
OE2 F:GLU30 2.1 13.3 1.0
O F:HOH3551 2.1 17.2 1.0
CD F:GLU30 3.1 11.2 1.0
OE1 F:GLU30 3.4 13.9 1.0
O F:HOH752 3.9 16.5 1.0
NZ F:LYS135 4.0 25.0 1.0
O F:ILE31 4.1 14.2 1.0
O F:HOH3665 4.1 33.4 1.0
O F:HOH1096 4.2 28.2 1.0
OE2 F:GLU139 4.3 14.8 1.0
O F:HOH715 4.4 19.0 1.0
NZ F:LYS27 4.4 18.0 1.0
CG F:GLU30 4.4 14.2 1.0
CE F:LYS135 5.0 21.1 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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