Atomistry » Magnesium » PDB 3m1v-3mfh » 3m2r
Atomistry »
  Magnesium »
    PDB 3m1v-3mfh »
      3m2r »

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

Go back to Magnesium Binding Sites List in 3m2r
Magnesium binding site 1 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 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

Go back to Magnesium Binding Sites List in 3m2r
Magnesium binding site 2 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 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

Go back to Magnesium Binding Sites List in 3m2r
Magnesium binding site 3 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 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

Go back to Magnesium Binding Sites List in 3m2r
Magnesium binding site 4 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 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

Go back to Magnesium Binding Sites List in 3m2r
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: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

Go back to Magnesium Binding Sites List in 3m2r
Magnesium binding site 6 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 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

Go back to Magnesium Binding Sites List in 3m2r
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: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

Go back to Magnesium Binding Sites List in 3m2r
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: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

Go back to Magnesium Binding Sites List in 3m2r
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:15.8
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy