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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 08:40:37 2020

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