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Magnesium in PDB 3m32: 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: 3m32 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) 20.28 / 1.35
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 / 15.7

Other elements in 3m32:

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 3m32). 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: 3m32:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3m32

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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:18.1
occ:0.60
 O A:HOH3581 1.9 20.2 0.6
O A:HOH1356 2.0 24.4 1.0
O A:HOH1590 2.1 26.3 1.0
O A:HOH2583 2.1 20.8 0.6
O A:HOH1599 2.2 22.1 0.6
O A:HOH2603 2.3 26.3 0.6
O A:HOH1599 2.4 18.0 0.4
O A:HOH3971 3.7 18.5 0.4
MG A:MG552 4.1 14.9 0.4
O A:HOH739 4.1 16.7 1.0
O A:HOH3907 4.4 21.1 0.5
O A:HOH716 4.5 16.8 1.0
CB A:ASP516 4.5 11.4 0.4
O A:ASP516 4.5 12.8 1.0
OD2 A:ASP521 4.5 13.7 1.0
O A:HOH3828 4.5 15.9 0.4
O A:HOH996 4.6 27.6 1.0
CB A:ASP521 4.7 10.1 1.0
CG A:ASP521 4.7 11.3 1.0
OD1 A:ASP516 4.8 17.1 0.6
O A:HOH1286 4.9 31.2 1.0

Magnesium binding site 2 out of 9 in 3m32

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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:14.9
occ:0.40
 OXT A:ACT556 2.0 15.0 0.4
O A:HOH1599 2.1 18.0 0.4
O A:HOH716 2.1 16.8 1.0
O A:HOH3971 2.2 18.5 0.4
O A:HOH3828 2.2 15.9 0.4
O A:HOH2285 2.3 32.6 1.0
O A:HOH3581 2.7 20.2 0.6
C A:ACT556 3.0 17.1 0.4
CH3 A:ACT556 3.4 19.4 0.4
O A:HOH1599 3.7 22.1 0.6
O A:HOH641 3.8 17.0 0.6
NZ A:LYS531 3.8 26.8 1.0
O A:HOH2583 3.9 20.8 0.6
MG A:MG551 4.1 18.1 0.6
O A:HOH1396 4.1 20.1 0.6
OE2 A:GLU528 4.1 11.2 1.0
O A:ACT556 4.2 16.3 0.4
OE1 A:GLU528 4.3 14.9 1.0
O A:VAL519 4.5 12.2 1.0
CD A:GLU528 4.7 10.9 1.0
CD A:LYS531 4.9 18.5 1.0
CE A:LYS531 4.9 23.4 1.0

Magnesium binding site 3 out of 9 in 3m32

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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:23.2
occ:1.00
 O B:HOH3549 2.0 26.7 1.0
O B:HOH3550 2.0 34.3 1.0
O B:HOH3547 2.0 22.5 1.0
O B:HOH3548 2.1 32.0 1.0
O B:HOH1305 2.1 20.9 1.0
O B:HOH3714 2.2 32.8 1.0
O B:HOH3225 4.1 26.8 1.0
OD2 B:ASP254 4.1 15.5 1.0
ND2 B:ASN250 4.1 17.6 1.0
OD1 B:ASP254 4.1 16.3 1.0
O B:HOH3031 4.4 34.3 1.0
CG B:ASP254 4.5 14.1 1.0
O B:HOH3325 4.6 32.4 1.0
O B:HOH3430 5.0 42.2 1.0

Magnesium binding site 4 out of 9 in 3m32

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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:Mg1

b:21.4
occ:0.40
 O B:HOH4161 2.0 21.4 0.4
O B:HOH811 2.0 17.8 0.4
OD1 B:ASP271 2.0 17.8 1.0
O B:HOH1206 2.0 23.2 0.4
O B:HOH564 2.2 34.4 1.0
O B:HOH3076 2.3 34.0 1.0
O B:HOH811 2.3 21.7 0.6
O B:HOH1206 2.7 26.0 0.6
CG B:ASP271 3.0 15.8 1.0
OD2 B:ASP271 3.4 15.9 1.0
O B:HOH973 4.3 28.4 1.0
OE2 B:GLU274 4.3 28.9 0.5
CB B:ASP271 4.3 12.7 1.0
O B:SER267 4.5 12.9 1.0
CA B:ASP271 4.6 12.8 1.0
N B:ASP271 4.7 12.3 1.0
OE1 B:GLU274 4.7 28.1 0.5
OE1 B:GLU274 4.7 29.8 0.5
CD B:GLU274 4.9 23.8 0.5

Magnesium binding site 5 out of 9 in 3m32

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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:17.2
occ:1.00
 OE2 C:GLU30 2.0 15.6 1.0
O C:HOH3558 2.0 19.9 1.0
O C:HOH3555 2.1 17.8 1.0
O C:HOH1095 2.1 18.6 1.0
O C:HOH3557 2.1 20.0 1.0
O C:HOH3556 2.2 19.9 1.0
CD C:GLU30 3.1 14.2 1.0
OE1 C:GLU30 3.4 16.2 1.0
NZ C:LYS135 3.9 26.8 1.0
O C:HOH722 3.9 18.7 1.0
O C:ILE31 4.1 15.2 1.0
O C:HOH2304 4.1 31.7 1.0
O C:HOH1542 4.2 31.3 1.0
OE2 C:GLU139 4.3 16.7 1.0
O C:HOH3795 4.4 29.8 1.0
O C:HOH1319 4.4 21.4 1.0
CG C:GLU30 4.5 12.5 1.0
NZ C:LYS27 4.5 14.9 1.0
CE C:LYS135 4.9 23.2 1.0

Magnesium binding site 6 out of 9 in 3m32

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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:Mg551

b:18.6
occ:1.00
 O D:HOH3559 2.0 18.0 1.0
O D:HOH3561 2.0 28.3 1.0
O D:HOH3562 2.1 23.5 1.0
O D:HOH3563 2.1 23.4 1.0
O D:HOH3560 2.1 25.3 1.0
O D:HOH1116 2.1 24.5 1.0
O D:HOH674 4.0 15.7 1.0
OD1 D:ASP516 4.3 21.0 1.0
OD2 D:ASP521 4.4 14.4 1.0
O D:ASP516 4.5 11.5 1.0
O D:HOH992 4.6 16.5 1.0
CB D:ASP521 4.6 9.9 1.0
CG D:ASP521 4.7 12.6 1.0
CB D:ASP516 4.8 13.9 1.0
CG D:ASP516 4.9 16.5 1.0

Magnesium binding site 7 out of 9 in 3m32

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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:Mg1

b:20.6
occ:1.00
 O F:HOH3545 2.0 22.3 1.0
O D:HOH3546 2.0 23.7 1.0
O F:HOH3542 2.1 25.8 1.0
O D:HOH3544 2.1 22.6 1.0
O D:HOH3543 2.1 23.5 1.0
NH2 F:ARG225 4.1 19.3 1.0
O D:HOH4148 4.4 27.1 1.0
O D:HOH1011 4.4 31.5 1.0
OE2 D:GLU376 4.4 17.7 1.0
OE1 D:GLU376 4.5 17.4 1.0
O F:HOH807 4.6 24.4 1.0
CD D:GLU376 4.9 14.4 1.0
CZ F:ARG225 5.0 14.5 1.0

Magnesium binding site 8 out of 9 in 3m32

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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:22.1
occ:1.00
 O E:HOH3583 1.9 24.6 1.0
O E:HOH2328 2.0 24.5 1.0
O E:HOH3585 2.1 21.3 1.0
O E:HOH2200 2.1 25.7 1.0
O E:HOH3584 2.2 29.8 1.0
O F:HOH3202 4.0 30.0 1.0
OE1 E:GLU287 4.0 24.8 1.0
O E:HOH3601 4.1 22.0 1.0
O E:HOH3758 4.4 36.7 1.0
O E:HOH2118 4.5 28.3 1.0
NZ E:LYS292 4.5 31.7 1.0
CD E:GLU287 4.5 24.1 1.0
OE2 E:GLU287 4.7 23.2 1.0
CE E:LYS292 5.0 27.5 1.0

Magnesium binding site 9 out of 9 in 3m32

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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:16.1
occ:1.00
 O F:HOH3554 2.0 20.2 1.0
O F:HOH3552 2.1 16.9 1.0
OE2 F:GLU30 2.1 14.1 1.0
O F:HOH1294 2.1 17.6 1.0
O F:HOH3551 2.1 17.4 1.0
O F:HOH3553 2.1 17.6 1.0
CD F:GLU30 3.1 11.9 1.0
OE1 F:GLU30 3.4 13.7 1.0
O F:HOH752 3.9 18.1 1.0
NZ F:LYS135 4.0 26.8 1.0
O F:ILE31 4.1 14.5 1.0
OE2 F:GLU139 4.2 15.1 1.0
O F:HOH3665 4.2 31.9 1.0
O F:HOH1096 4.3 30.8 1.0
CG F:GLU30 4.3 14.3 1.0
O F:HOH715 4.4 19.6 1.0
NZ F:LYS27 4.4 19.4 1.0
CE F:LYS135 4.9 22.3 1.0
C F:ILE31 5.0 13.4 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 19:09:09 2024

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