Atomistry » Magnesium » PDB 3pip-3px4 » 3pot
Atomistry »
  Magnesium »
    PDB 3pip-3px4 »
      3pot »

Magnesium in PDB 3pot: Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

Enzymatic activity of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

All present enzymatic activity of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis:
2.8.4.1;

Protein crystallography data

The structure of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 3pot was solved by P.E.Cedervall, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.886, 118.165, 122.388, 90.00, 91.94, 90.00
R / Rfree (%) 13.2 / 15.6

Other elements in 3pot:

The structure of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Potassium (K) 1 atom
Iodine (I) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis (pdb code 3pot). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 3pot:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 1 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg551

b:13.6
occ:1.00
 O A:HOH850 2.0 13.7 1.0
O D:HOH899 2.0 16.5 1.0
O A:HOH3425 2.1 16.2 1.0
O D:HOH3524 4.0 23.6 1.0
O D:HOH3187 4.1 24.1 1.0
O D:HOH857 4.2 14.0 1.0
O A:HOH724 4.3 14.3 1.0
OE2 A:GLU134 4.3 13.2 1.0
OE1 A:GLU134 4.4 12.8 1.0
CG D:PRO54 4.6 10.0 1.0
CD A:GLU134 4.8 11.8 1.0

Magnesium binding site 2 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 2 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg552

b:8.6
occ:0.30
 O A:HOH600 1.9 8.5 0.3
O A:HOH2090 2.0 22.1 1.0
O A:HOH725 2.1 13.2 1.0
O A:HOH1508 2.1 11.3 0.3
O A:HOH1212 2.1 11.8 0.3
O A:HOH1856 2.1 10.7 0.3
O A:HOH1508 2.7 10.4 0.3
O A:HOH1212 3.6 9.4 0.3
NZ A:LYS531 3.8 21.6 1.0
O A:HOH1481 4.0 11.7 0.3
O A:HOH1510 4.0 22.9 1.0
O A:HOH600 4.1 13.1 0.7
MG A:MG553 4.1 8.3 0.3
OE2 A:GLU528 4.1 9.1 1.0
OE1 A:GLU528 4.3 14.7 1.0
O A:VAL519 4.5 9.6 1.0
CD A:GLU528 4.7 9.6 1.0
CE A:LYS531 4.9 17.7 1.0
O A:HOH1159 5.0 22.2 1.0
CD A:LYS531 5.0 14.4 1.0

Magnesium binding site 3 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 3 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg553

b:8.3
occ:0.30
 O A:HOH1508 2.0 10.4 0.3
O A:HOH1159 2.0 22.2 1.0
O A:HOH1481 2.1 11.7 0.3
O A:HOH1212 2.1 9.4 0.3
O A:HOH1456 2.1 14.7 0.3
O A:HOH1968 2.2 10.5 0.3
O A:HOH1212 2.3 11.8 0.3
O A:HOH1508 3.7 11.3 0.3
MG A:MG552 4.1 8.6 0.3
O A:HOH732 4.2 14.9 1.0
O A:HOH2187 4.4 42.0 1.0
O A:HOH942 4.4 25.4 1.0
OD2 A:ASP521 4.5 12.4 1.0
O A:HOH725 4.5 13.2 1.0
O A:ASP516 4.5 10.4 1.0
O A:HOH1856 4.6 10.7 0.3
CB A:ASP521 4.6 8.2 1.0
CG A:ASP521 4.7 8.4 1.0
OD1 A:ASP516 4.8 22.0 1.0
CB A:ASP516 4.9 12.5 1.0

Magnesium binding site 4 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 4 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg554

b:16.8
occ:1.00
 O A:HOH3450 2.0 21.8 1.0
O A:HOH1037 2.1 19.0 1.0
O A:HOH1115 2.1 16.4 1.0
O A:HOH3449 2.2 22.0 1.0
O A:HOH1919 4.0 33.5 1.0
CD A:PRO178 4.1 12.5 1.0
O A:ASP174 4.3 15.3 1.0
O A:HOH1844 4.4 23.8 1.0
O A:GLU175 4.4 17.6 1.0
O A:HOH1963 4.6 40.0 1.0
O A:ILE176 4.6 13.6 1.0
O A:HOH1349 4.7 28.7 1.0
CG A:PRO178 4.8 17.9 1.0

Magnesium binding site 5 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 5 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg444

b:19.6
occ:1.00
 O B:HOH1103 2.0 17.9 1.0
O B:HOH1305 2.0 19.1 1.0
O B:HOH3453 2.0 33.3 1.0
O B:HOH3452 2.1 34.4 1.0
O B:HOH2344 2.1 34.6 1.0
O B:HOH1163 4.0 27.0 1.0
ND2 B:ASN250 4.1 14.5 1.0
OD2 B:ASP254 4.1 12.9 1.0
OD1 B:ASP254 4.1 13.5 1.0
CG B:ASP254 4.5 11.7 1.0

Magnesium binding site 6 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 6 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg445

b:9.9
occ:0.30
 OD1 B:ASP271 2.0 15.1 1.0
O B:HOH2168 2.1 12.8 0.3
O B:HOH1911 2.1 25.2 1.0
O B:HOH670 2.1 23.3 0.6
O B:HOH1040 2.1 18.6 1.0
O B:HOH976 2.2 31.6 1.0
O B:HOH670 2.9 16.2 0.4
CG B:ASP271 3.0 13.1 1.0
OD2 B:ASP271 3.4 13.3 1.0
OE2 B:GLU274 4.1 38.1 1.0
O B:HOH1272 4.3 25.1 1.0
CB B:ASP271 4.3 11.1 1.0
OE1 B:GLU274 4.4 37.2 1.0
O B:SER267 4.5 9.9 1.0
CA B:ASP271 4.6 10.6 1.0
N B:ASP271 4.6 9.9 1.0
CD B:GLU274 4.6 34.0 1.0

Magnesium binding site 7 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 7 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg250

b:13.1
occ:1.00
 O C:HOH3417 2.0 15.9 1.0
O C:HOH726 2.1 15.7 1.0
O C:HOH3419 2.1 13.9 1.0
OE2 C:GLU30 2.1 12.9 1.0
O C:HOH3418 2.1 16.7 1.0
O C:HOH3420 2.1 16.0 1.0
CD C:GLU30 3.1 11.8 1.0
OE1 C:GLU30 3.4 12.7 1.0
NZ C:LYS135 4.0 22.4 1.0
O C:HOH745 4.0 16.1 1.0
O C:HOH1428 4.1 25.0 1.0
O C:ILE31 4.1 12.6 1.0
O C:HOH1445 4.2 29.2 1.0
OE2 C:GLU139 4.2 13.5 1.0
O C:HOH3558 4.4 26.4 1.0
O C:HOH742 4.4 18.6 1.0
CG C:GLU30 4.4 10.9 1.0
NZ C:LYS27 4.5 14.2 1.0
CE C:LYS135 4.9 21.0 1.0

Magnesium binding site 8 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 8 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg251

b:11.8
occ:0.30
 O A:HOH3614 2.0 31.6 1.0
O C:HOH1328 2.1 23.0 1.0
O C:HOH1849 2.3 12.0 0.3
O A:HOH1660 4.0 30.9 1.0
O C:HOH1333 4.0 19.9 1.0
O C:HOH540 4.4 18.0 1.0
NE C:ARG225 4.6 14.8 1.0
OD1 C:ASP226 4.7 14.8 1.0
CD C:ARG225 4.7 13.9 1.0
CZ C:ARG225 5.0 14.1 1.0

Magnesium binding site 9 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 9 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg551

b:17.2
occ:1.00
 O D:HOH3430 2.0 17.7 1.0
O D:HOH1211 2.0 24.3 1.0
O D:HOH1613 2.1 23.3 1.0
O D:HOH3429 2.1 21.5 1.0
O D:HOH3428 2.1 29.8 1.0
O D:HOH664 4.1 13.5 1.0
OD1 D:ASP516 4.3 18.5 1.0
OD2 D:ASP521 4.4 12.3 1.0
O D:ASP516 4.5 9.6 1.0
O D:HOH1095 4.6 16.8 1.0
CB D:ASP521 4.6 7.9 1.0
CG D:ASP521 4.7 9.6 1.0
CB D:ASP516 4.7 12.0 1.0
CG D:ASP516 4.9 16.0 1.0

Magnesium binding site 10 out of 12 in 3pot

Go back to Magnesium Binding Sites List in 3pot
Magnesium binding site 10 out of 12 in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg444

b:18.1
occ:1.00
 O E:HOH3439 2.0 21.4 1.0
O E:HOH1993 2.0 22.0 1.0
O E:HOH3440 2.1 23.7 1.0
O E:HOH2253 2.2 27.1 1.0
O F:HOH1083 4.0 30.5 1.0
O E:HOH2747 4.1 32.3 1.0
OE1 E:GLU287 4.1 22.2 1.0
O E:HOH759 4.1 18.7 1.0
O E:HOH3587 4.2 32.1 1.0
O E:HOH1769 4.2 31.4 1.0
O E:HOH2567 4.3 35.1 1.0
O E:HOH3574 4.4 29.3 1.0
CD E:GLU287 4.6 22.4 1.0
NZ E:LYS292 4.6 25.3 1.0
OE2 E:GLU287 4.7 22.8 1.0

Reference:

P.E.Cedervall, M.Dey, X.Li, R.Sarangi, B.Hedman, S.W.Ragsdale, C.M.Wilmot. Structural Analysis of A Ni-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis. J.Am.Chem.Soc. V. 133 5626 2011.
ISSN: ISSN 0002-7863
PubMed: 21438550
DOI: 10.1021/JA110492P
Page generated: Thu Aug 15 09:41:08 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