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Magnesium in PDB 3m30: 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: 3m30 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) 20.07 / 1.45
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 (%) 13.6 / 16.4

Other elements in 3m30:

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 3m30). 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: 3m30:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3m30

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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:20.3
occ:0.60
 O A:HOH1356 2.0 26.6 1.0
O A:HOH3581 2.0 22.7 0.6
O A:HOH2583 2.1 21.9 0.6
O A:HOH1590 2.1 29.4 1.0
O A:HOH1599 2.2 21.7 0.6
O A:HOH1599 2.2 14.7 0.4
O A:HOH2603 2.4 25.9 0.6
O A:HOH3971 3.7 14.7 0.4
MG A:MG552 3.9 12.6 0.4
O A:HOH739 4.1 17.4 1.0
O A:HOH713 4.4 16.2 1.0
OD2 A:ASP521 4.5 13.4 1.0
O A:HOH3828 4.5 15.8 0.4
O A:HOH996 4.5 29.1 1.0
CB A:ASP516 4.5 11.1 0.4
O A:ASP516 4.5 12.7 1.0
CB A:ASP521 4.5 9.8 1.0
CG A:ASP521 4.6 9.1 1.0
OD1 A:ASP516 4.9 18.7 0.6
O A:HOH1286 4.9 35.4 1.0

Magnesium binding site 2 out of 9 in 3m30

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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:12.6
occ:0.40
 O A:HOH3828 2.0 15.8 0.4
O A:HOH1599 2.0 14.7 0.4
OXT A:ACT556 2.0 13.8 0.4
O A:HOH713 2.1 16.2 1.0
O A:HOH3971 2.2 14.7 0.4
O A:HOH2285 2.4 30.3 1.0
O A:HOH3581 2.5 22.7 0.6
C A:ACT556 3.0 15.4 0.4
CH3 A:ACT556 3.5 16.5 0.4
O A:HOH1599 3.8 21.7 0.6
NZ A:LYS531 3.9 26.1 1.0
O A:HOH2583 3.9 21.9 0.6
MG A:MG551 3.9 20.3 0.6
O A:HOH642 4.1 17.6 0.6
O A:ACT556 4.1 17.0 0.4
OE2 A:GLU528 4.2 11.0 1.0
O A:HOH1396 4.2 17.9 0.6
OE1 A:GLU528 4.4 14.1 1.0
O A:VAL519 4.5 11.8 1.0
CD A:GLU528 4.6 11.7 1.0
O A:HOH1356 4.9 26.6 1.0
CB A:ASP521 5.0 9.8 1.0

Magnesium binding site 3 out of 9 in 3m30

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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
B:Mg444

b:26.3
occ:1.00
 O B:HOH3549 2.0 31.9 1.0
O B:HOH3550 2.1 35.4 1.0
O B:HOH1305 2.1 20.8 1.0
O B:HOH3548 2.1 34.7 1.0
O B:HOH3714 2.1 40.5 1.0
O B:HOH3547 2.2 25.8 1.0
O B:HOH3225 4.0 31.8 1.0
OD2 B:ASP254 4.0 15.5 1.0
OD1 B:ASP254 4.1 16.7 1.0
ND2 B:ASN250 4.1 18.5 1.0
CG B:ASP254 4.5 14.2 1.0
O B:HOH3031 4.5 37.5 1.0
O B:HOH3325 4.7 31.5 1.0

Magnesium binding site 4 out of 9 in 3m30

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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:Mg445

b:34.5
occ:1.00
 OD1 B:ASP271 2.0 15.8 1.0
O B:HOH811 2.1 22.9 1.0
O B:HOH4102 2.1 28.0 1.0
O B:HOH3076 2.2 30.2 1.0
O B:HOH564 2.2 34.4 1.0
O B:HOH1206 2.4 29.7 1.0
CG B:ASP271 3.0 14.1 1.0
OD2 B:ASP271 3.4 16.0 1.0
O B:HOH973 4.2 27.9 1.0
OE2 B:GLU274 4.3 40.6 1.0
CB B:ASP271 4.3 12.3 1.0
OE1 B:GLU274 4.5 36.9 1.0
O B:SER267 4.5 12.7 1.0
CA B:ASP271 4.5 12.0 1.0
N B:ASP271 4.6 11.7 1.0
CD B:GLU274 4.7 36.1 1.0

Magnesium binding site 5 out of 9 in 3m30

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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


Mono view


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:15.8
occ:1.00
 O C:HOH3558 1.9 18.8 1.0
OE2 C:GLU30 2.0 15.3 1.0
O C:HOH3556 2.1 19.6 1.0
O C:HOH3555 2.1 16.4 1.0
O C:HOH1095 2.1 18.5 1.0
O C:HOH3557 2.2 19.7 1.0
CD C:GLU30 3.1 14.2 1.0
OE1 C:GLU30 3.4 16.9 1.0
NZ C:LYS135 3.9 24.2 1.0
O C:HOH722 4.0 16.5 1.0
O C:HOH2304 4.1 28.1 1.0
O C:ILE31 4.2 15.7 1.0
O C:HOH1542 4.2 29.2 1.0
OE2 C:GLU139 4.3 14.9 1.0
O C:HOH3795 4.3 29.9 1.0
NZ C:LYS27 4.5 14.8 1.0
O C:HOH1319 4.5 21.6 1.0
CG C:GLU30 4.5 12.8 1.0
CE C:LYS135 4.9 19.1 1.0

Magnesium binding site 6 out of 9 in 3m30

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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:21.6
occ:1.00
 O D:HOH3544 2.0 21.7 1.0
O F:HOH3545 2.1 23.7 1.0
O D:HOH3546 2.1 23.8 1.0
O F:HOH3542 2.1 25.0 1.0
O D:HOH3543 2.2 21.9 1.0
NH2 F:ARG225 4.1 20.2 1.0
O D:HOH1011 4.3 35.1 1.0
OE2 D:GLU376 4.3 18.2 1.0
OE1 D:GLU376 4.5 17.1 1.0
O F:HOH807 4.6 23.5 1.0
O D:HOH1947 4.8 42.2 1.0
CD D:GLU376 4.8 13.2 1.0
CZ F:ARG225 4.9 15.2 1.0

Magnesium binding site 7 out of 9 in 3m30

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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


Mono view


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:24.4
occ:1.00
 O D:HOH3559 1.9 22.6 1.0
O D:HOH3562 2.0 27.6 1.0
O D:HOH3563 2.1 32.1 1.0
O D:HOH3561 2.1 34.8 1.0
O D:HOH3560 2.1 31.7 1.0
O D:HOH1116 2.3 29.7 1.0
O D:HOH674 3.9 16.4 1.0
O D:ASP516 4.4 11.3 1.0
OD1 D:ASP516 4.4 22.9 1.0
OD2 D:ASP521 4.5 14.4 1.0
O D:HOH992 4.7 18.3 1.0
CB D:ASP521 4.7 7.7 1.0
CG D:ASP521 4.7 11.5 1.0
CB D:ASP516 4.8 14.8 1.0
O D:HOH733 4.9 26.1 1.0
CG D:ASP516 5.0 18.4 1.0

Magnesium binding site 8 out of 9 in 3m30

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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


Mono view


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:21.8
occ:1.00
 O E:HOH3583 2.0 23.6 1.0
O E:HOH3585 2.1 20.4 1.0
O E:HOH2200 2.1 24.7 1.0
O E:HOH2328 2.1 22.4 1.0
O E:HOH3584 2.3 32.1 1.0
O F:HOH3202 4.0 29.6 1.0
O E:HOH3601 4.0 22.3 1.0
OE1 E:GLU287 4.1 24.3 1.0
O E:HOH3758 4.2 41.4 1.0
NZ E:LYS292 4.5 28.5 1.0
O E:HOH2118 4.5 34.8 1.0
CD E:GLU287 4.5 24.5 1.0
OE2 E:GLU287 4.7 22.4 1.0

Magnesium binding site 9 out of 9 in 3m30

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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


Mono view


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:15.6
occ:1.00
 O F:HOH3554 2.0 17.5 1.0
O F:HOH3552 2.0 14.9 1.0
OE2 F:GLU30 2.1 13.6 1.0
O F:HOH1294 2.1 15.2 1.0
O F:HOH3553 2.1 16.6 1.0
O F:HOH3551 2.2 16.1 1.0
CD F:GLU30 3.1 12.0 1.0
OE1 F:GLU30 3.4 13.1 1.0
O F:HOH752 4.0 17.0 1.0
NZ F:LYS135 4.0 24.8 1.0
O F:ILE31 4.1 13.2 1.0
O F:HOH1096 4.2 32.1 1.0
OE2 F:GLU139 4.2 14.6 1.0
O F:HOH3665 4.3 37.4 1.0
CG F:GLU30 4.4 13.5 1.0
NZ F:LYS27 4.4 18.4 1.0
O F:HOH715 4.4 21.5 1.0
CE F:LYS135 5.0 22.1 1.0
C F:ILE31 5.0 12.2 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 19:07:32 2024

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