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Magnesium in PDB 3m2v: 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: 3m2v 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) 19.93 / 1.80
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 (%) 15 / 19.5

Other elements in 3m2v:

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 3m2v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3m2v

Go back to Magnesium Binding Sites List in 3m2v
Magnesium binding site 1 out of 5 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 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:22.1
occ:0.70
 O A:HOH1599 2.0 22.0 0.7
O A:HOH706 2.1 15.3 1.0
O A:HOH2285 2.2 24.6 1.0
OXT A:ACT555 2.2 21.9 0.7
O A:HOH3828 2.2 19.7 0.7
O A:HOH3971 2.2 23.4 0.7
C A:ACT555 3.2 21.4 0.7
CH3 A:ACT555 3.7 22.3 0.7
NZ A:LYS531 4.0 25.6 1.0
OE2 A:GLU528 4.1 11.9 1.0
O2 A:EDO556 4.2 34.8 1.0
O A:HOH4121 4.2 10.8 0.3
OE1 A:GLU528 4.2 14.6 1.0
O A:HOH1396 4.3 21.9 0.3
O A:ACT555 4.3 21.3 0.7
O A:VAL519 4.5 11.7 1.0
CD A:GLU528 4.6 14.0 1.0
C1 A:EDO556 4.7 31.9 1.0
C2 A:EDO556 4.8 31.4 1.0
CD A:LYS531 4.9 21.8 1.0
CB A:ASP521 5.0 10.4 1.0

Magnesium binding site 2 out of 5 in 3m2v

Go back to Magnesium Binding Sites List in 3m2v
Magnesium binding site 2 out of 5 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 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
B:Mg1

b:41.2
occ:1.00
 O B:HOH3548 2.0 37.1 1.0
O B:HOH1305 2.1 26.8 1.0
O B:HOH3549 2.2 40.0 1.0
O B:HOH3550 2.3 36.4 1.0
O B:HOH3547 2.3 24.6 1.0
OD2 B:ASP254 3.9 23.2 1.0
O B:HOH3225 4.0 34.7 1.0
ND2 B:ASN250 4.0 20.7 1.0
OD1 B:ASP254 4.0 26.2 1.0
O B:HOH3031 4.3 39.1 1.0
CG B:ASP254 4.4 24.1 1.0

Magnesium binding site 3 out of 5 in 3m2v

Go back to Magnesium Binding Sites List in 3m2v
Magnesium binding site 3 out of 5 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 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:30.2
occ:0.60
 O B:HOH4122 2.0 21.1 0.6
O B:HOH811 2.0 24.4 1.0
OD1 B:ASP271 2.0 23.2 1.0
O B:HOH3076 2.0 32.4 1.0
O B:HOH1206 2.3 32.2 1.0
CG B:ASP271 2.9 16.7 1.0
OD2 B:ASP271 3.2 23.2 1.0
OE2 B:GLU274 4.2 31.0 0.6
CB B:ASP271 4.3 18.1 1.0
O B:HOH973 4.4 38.7 1.0
O B:SER267 4.5 15.4 1.0
OE1 B:GLU274 4.6 23.6 0.4
N B:ASP271 4.6 17.9 1.0
CA B:ASP271 4.7 16.1 1.0

Magnesium binding site 4 out of 5 in 3m2v

Go back to Magnesium Binding Sites List in 3m2v
Magnesium binding site 4 out of 5 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 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
C:Mg250

b:32.6
occ:1.00
 O C:HOH3557 1.9 27.5 1.0
O C:HOH3558 1.9 30.0 1.0
O C:HOH3556 2.1 31.4 1.0
OE2 C:GLU30 2.1 27.7 1.0
O C:HOH3555 2.1 24.7 1.0
O C:HOH1095 2.3 34.1 1.0
CD C:GLU30 3.0 22.6 1.0
OE1 C:GLU30 3.2 26.7 1.0
O C:HOH722 4.1 25.6 1.0
NZ C:LYS135 4.1 38.9 1.0
O C:HOH3795 4.2 46.6 1.0
O C:HOH1542 4.4 36.0 1.0
O C:ILE31 4.4 27.2 1.0
CG C:GLU30 4.4 22.2 1.0
OE2 C:GLU139 4.4 25.9 1.0
NZ C:LYS27 4.4 20.5 1.0
O C:HOH2304 4.5 37.3 1.0
O C:HOH1319 4.7 26.3 1.0

Magnesium binding site 5 out of 5 in 3m2v

Go back to Magnesium Binding Sites List in 3m2v
Magnesium binding site 5 out of 5 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
F:Mg250

b:28.0
occ:1.00
 O F:HOH3554 2.0 24.4 1.0
OE2 F:GLU30 2.0 22.9 1.0
O F:HOH3552 2.1 25.6 1.0
O F:HOH3551 2.1 31.1 1.0
O F:HOH3553 2.2 22.4 1.0
O F:HOH1294 2.2 29.4 1.0
CD F:GLU30 3.1 21.9 1.0
OE1 F:GLU30 3.5 21.3 1.0
O F:ILE31 3.9 26.0 1.0
NZ F:LYS135 3.9 40.1 1.0
O F:HOH752 4.1 26.5 1.0
O F:HOH1096 4.2 37.1 1.0
O F:HOH715 4.2 36.9 1.0
OE2 F:GLU139 4.3 28.6 1.0
CG F:GLU30 4.4 21.6 1.0
CE F:LYS135 4.6 38.0 1.0
NZ F:LYS27 4.7 25.4 1.0
C F:ILE31 4.9 25.7 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: Mon Aug 11 00:27:51 2025

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