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Magnesium in PDB 7suc: Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase

Enzymatic activity of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase

All present enzymatic activity of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase:
2.8.4.1;

Protein crystallography data

The structure of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase, PDB code: 7suc was solved by C.J.Ohmer, M.Dasgupta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.25 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.082, 119.777, 123.21, 90, 91.73, 90
R / Rfree (%) 15.2 / 18.6

Other elements in 7suc:

The structure of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase (pdb code 7suc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase, PDB code: 7suc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7suc

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Magnesium binding site 1 out of 7 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:59.0
occ:1.00
 O A:HOH890 2.9 45.4 1.0
O A:HOH740 3.0 34.3 1.0
OXT A:ACT605 3.8 37.1 0.5
H1 A:ACT605 4.0 37.2 0.5
O A:VAL519 4.2 23.2 1.0
C A:ACT605 4.3 29.9 0.5
HZ3 A:LYS531 4.4 52.0 1.0
CH3 A:ACT605 4.5 31.0 0.5
H2 A:ACT605 4.6 37.2 0.5
HZ1 A:LYS531 5.0 52.0 1.0

Magnesium binding site 2 out of 7 in 7suc

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Magnesium binding site 2 out of 7 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:63.2
occ:1.00
 HE2 B:TYR11 3.5 47.9 1.0
HD22 B:ASN250 3.7 47.7 1.0
O B:GLY15 4.0 42.0 1.0
ND2 B:ASN250 4.1 39.8 1.0
HD21 B:ASN250 4.1 47.7 1.0
HH B:TYR11 4.2 48.9 1.0
CE2 B:TYR11 4.3 39.9 1.0
OH B:TYR11 4.9 40.7 1.0
HD2 B:TYR11 5.0 50.4 1.0

Magnesium binding site 3 out of 7 in 7suc

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Magnesium binding site 3 out of 7 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:56.6
occ:1.00
 HZ1 C:LYS135 2.0 68.7 1.0
OE2 C:GLU30 2.0 40.0 1.0
O C:HOH410 2.1 45.4 1.0
HZ3 C:LYS135 2.2 68.7 1.0
O C:HOH429 2.4 49.6 1.0
NZ C:LYS135 2.5 57.2 1.0
HZ2 C:LYS135 2.9 68.7 1.0
CD C:GLU30 3.1 38.8 1.0
OE1 C:GLU30 3.5 36.4 1.0
HE2 C:LYS135 3.7 60.9 1.0
CE C:LYS135 3.7 50.8 1.0
HZ1 C:LYS27 3.8 49.2 1.0
OE2 C:GLU139 4.0 34.2 1.0
O C:HOH447 4.1 38.8 1.0
O C:ILE31 4.1 43.7 1.0
HE3 C:LYS135 4.3 60.9 1.0
HZ3 C:LYS27 4.4 49.2 1.0
NZ C:LYS27 4.4 41.0 1.0
CG C:GLU30 4.4 34.3 1.0
HG3 C:GLU30 4.4 41.1 1.0
HZ2 C:LYS27 4.5 49.2 1.0
HA C:SER32 4.5 47.0 1.0
HD2 C:LYS135 4.5 49.0 1.0
CD C:LYS135 4.8 40.9 1.0
HG2 C:GLU30 4.8 41.1 1.0
H C:ILE31 4.9 46.1 1.0

Magnesium binding site 4 out of 7 in 7suc

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Magnesium binding site 4 out of 7 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg601

b:55.8
occ:1.00
 OE2 a:GLU376 3.1 46.1 1.0
HH22 c:ARG225 3.2 39.1 0.5
HH21 c:ARG225 3.3 40.9 0.5
NH2 c:ARG225 3.4 32.6 0.5
HH21 c:ARG225 3.6 39.1 0.5
HH22 c:ARG225 3.6 40.9 0.5
NH2 c:ARG225 3.7 34.0 0.5
CD a:GLU376 3.9 37.4 1.0
CZ c:ARG225 4.0 31.9 0.5
OE1 a:GLU376 4.0 37.5 1.0
HH12 c:ARG225 4.2 39.8 0.5
NH1 c:ARG225 4.3 33.2 0.5
O a:HOH730 4.6 32.4 1.0
NE c:ARG225 4.7 33.1 0.5
CZ c:ARG225 4.7 31.8 0.5
HE c:ARG225 4.8 39.8 0.5
HH11 c:ARG225 5.0 39.8 0.5

Magnesium binding site 5 out of 7 in 7suc

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Magnesium binding site 5 out of 7 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg602

b:61.4
occ:1.00
 HB2 a:ASP521 4.6 25.9 1.0
O a:ASP516 4.9 24.1 1.0
OD2 a:ASP521 5.0 29.1 1.0

Magnesium binding site 6 out of 7 in 7suc

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Magnesium binding site 6 out of 7 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg501

b:66.6
occ:1.00
 HZ1 b:LYS292 3.1 85.9 1.0
HZ2 b:LYS292 3.9 85.9 1.0
NZ b:LYS292 3.9 71.5 1.0
OE1 b:GLU287 4.3 60.9 1.0
HZ3 b:LYS292 4.3 85.9 1.0
HE3 b:LYS292 4.8 86.8 1.0
CE b:LYS292 4.9 72.3 1.0
OE2 b:GLU287 4.9 65.3 1.0

Magnesium binding site 7 out of 7 in 7suc

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Magnesium binding site 7 out of 7 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Mg301

b:52.3
occ:1.00
 OE2 c:GLU30 2.1 40.5 1.0
HZ2 c:LYS135 2.2 66.2 1.0
O c:HOH469 2.3 52.0 1.0
O c:HOH459 2.4 45.4 1.0
O c:HOH466 2.5 44.3 1.0
HZ1 c:LYS135 3.0 66.2 1.0
NZ c:LYS135 3.0 55.1 1.0
CD c:GLU30 3.2 35.8 1.0
HZ3 c:LYS135 3.6 66.2 1.0
HE3 c:LYS135 3.7 62.8 1.0
OE1 c:GLU30 3.8 37.9 1.0
CE c:LYS135 3.9 52.4 1.0
HZ1 c:LYS27 4.0 51.7 1.0
HE2 c:LYS135 4.2 62.8 1.0
O c:ILE31 4.3 37.6 1.0
HG3 c:GLU30 4.4 42.8 1.0
CG c:GLU30 4.5 35.7 1.0
OE2 c:GLU139 4.5 39.8 1.0
HA c:SER32 4.6 52.2 1.0
NZ c:LYS27 4.7 43.1 1.0
HZ2 c:LYS27 4.7 51.7 1.0
HG2 c:GLU30 4.8 42.8 1.0
HZ3 c:LYS27 4.8 51.7 1.0

Reference:

C.J.Ohmer, M.Dasgupta, A.Patwardhan, I.Bogacz, C.Kaminsky, M.D.Doyle, P.Y.Chen, S.M.Keable, H.Makita, P.S.Simon, R.Massad, T.Fransson, R.Chatterjee, A.Bhowmick, D.W.Paley, N.W.Moriarty, A.S.Brewster, L.B.Gee, R.Alonso-Mori, F.Moss, F.D.Fuller, A.Batyuk, N.K.Sauter, U.Bergmann, C.L.Drennan, V.K.Yachandra, J.Yano, J.F.Kern, S.W.Ragsdale. Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase. J.Inorg.Biochem. V. 230 11768 2022.
ISSN: ISSN 0162-0134
PubMed: 35202981
DOI: 10.1016/J.JINORGBIO.2022.111768
Page generated: Thu Oct 3 08:52:55 2024

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