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Magnesium in PDB 7cav: Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)

Protein crystallography data

The structure of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp), PDB code: 7cav was solved by H.Unno, H.Hemmi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.853, 98.91, 193.853, 90, 90, 90
R / Rfree (%) 19.6 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) (pdb code 7cav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp), PDB code: 7cav:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7cav

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Magnesium binding site 1 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:32.9
occ:1.00
 O2A A:DMA301 2.0 31.0 1.0
O2A A:DMA302 2.1 35.7 1.0
O A:HOH415 2.1 32.5 1.0
OD1 A:ASP18 2.1 29.5 1.0
O3B A:DMA302 2.2 28.1 1.0
O A:HOH413 2.2 34.3 1.0
CG A:ASP18 3.1 27.8 1.0
PB A:DMA302 3.2 31.8 1.0
PA A:DMA302 3.4 33.7 1.0
OD2 A:ASP18 3.4 28.7 1.0
PA A:DMA301 3.4 36.6 1.0
O1B A:DMA302 3.6 32.9 1.0
O3A A:DMA302 3.6 33.4 1.0
O1 A:DMA301 3.8 36.2 1.0
NH2 A:ARG69 3.9 33.0 1.0
O1 A:DMA302 4.0 36.5 1.0
O2B A:DMA301 4.0 37.1 1.0
O A:HOH459 4.1 39.5 1.0
O B:HOH404 4.1 37.2 1.0
NH1 A:ARG22 4.3 30.6 1.0
C2 A:DMA302 4.3 51.5 1.0
O3A A:DMA301 4.3 35.0 1.0
O1A A:DMA301 4.4 37.2 1.0
CB A:ASP18 4.5 27.7 1.0
N A:GLY19 4.5 29.4 1.0
O2B A:DMA302 4.6 29.3 1.0
PB A:DMA301 4.6 37.7 1.0
O A:HOH432 4.6 43.7 1.0
O1A A:DMA302 4.7 37.2 1.0
O1B A:DMA301 4.7 36.8 1.0
C1 A:DMA302 4.7 44.8 1.0
NH2 A:ARG168 4.9 30.3 1.0
NH2 A:ARG21 4.9 36.5 1.0
CA A:ASP18 5.0 28.6 1.0

Magnesium binding site 2 out of 8 in 7cav

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Magnesium binding site 2 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:43.4
occ:1.00
 O5 B:DPO303 2.0 42.6 1.0
O1 B:DPO303 2.1 38.1 1.0
OD1 B:ASP18 2.1 37.6 1.0
O B:HOH411 2.1 40.2 1.0
O6 B:DPO304 2.1 51.6 1.0
CG B:ASP18 3.0 34.4 1.0
P1 B:DPO303 3.1 43.6 1.0
P2 B:DPO303 3.3 48.2 1.0
OD2 B:ASP18 3.3 36.4 1.0
O4 B:DPO303 3.5 43.6 1.0
P2 B:DPO304 3.5 67.5 1.0
O2 B:DPO303 3.6 43.6 1.0
O3 B:DPO304 3.8 52.5 1.0
O6 B:DPO303 3.8 43.3 1.0
O7 B:DPO304 4.0 61.4 1.0
NH2 B:ARG69 4.1 53.7 1.0
O7 B:FQ0302 4.2 66.7 1.0
NH1 B:ARG22 4.2 41.7 1.0
NH2 B:ARG172 4.3 58.1 1.0
O4 B:DPO304 4.4 59.1 1.0
CB B:ASP18 4.4 34.1 1.0
O3 B:DPO303 4.5 41.0 1.0
O2 B:DPO304 4.5 57.6 1.0
O5 B:DPO304 4.5 60.5 1.0
N B:GLY19 4.5 32.5 1.0
P1 B:DPO304 4.5 64.8 1.0
O7 B:DPO303 4.5 47.4 1.0
NH2 B:ARG168 4.7 33.5 1.0
NH2 B:ARG21 4.7 49.8 1.0
CA B:ASP18 4.9 32.2 1.0

Magnesium binding site 3 out of 8 in 7cav

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Magnesium binding site 3 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:45.9
occ:1.00
 O2A C:DMA302 2.0 43.9 1.0
O2B C:DMA302 2.0 52.5 1.0
OD1 C:ASP18 2.1 37.5 1.0
O1A C:DMA301 2.1 57.2 1.0
O C:HOH421 2.1 48.5 1.0
O C:HOH404 2.2 42.0 1.0
CG C:ASP18 3.0 40.4 1.0
PB C:DMA302 3.1 52.5 1.0
PA C:DMA302 3.2 45.8 1.0
OD2 C:ASP18 3.2 40.1 1.0
O3A C:DMA302 3.5 48.8 1.0
PA C:DMA301 3.5 56.7 1.0
O3B C:DMA302 3.5 54.3 1.0
O1 C:DMA302 3.9 49.3 1.0
O1 C:DMA301 3.9 57.6 1.0
O1B C:DMA301 4.0 50.6 1.0
O C:HOH418 4.1 58.3 1.0
O C:HOH405 4.1 53.1 1.0
NH1 C:ARG22 4.1 43.8 1.0
C1 C:DMA302 4.3 53.0 1.0
N C:GLY19 4.4 39.5 1.0
CB C:ASP18 4.4 39.4 1.0
O1B C:DMA302 4.4 51.2 1.0
O3A C:DMA301 4.4 52.8 1.0
O1A C:DMA302 4.5 46.7 1.0
O2A C:DMA301 4.5 49.7 1.0
NH2 C:ARG69 4.6 63.4 1.0
PB C:DMA301 4.7 58.9 1.0
NH2 C:ARG168 4.8 37.2 1.0
NH2 C:ARG21 4.9 50.0 1.0
CA C:ASP18 4.9 38.5 1.0
C4 C:DMA302 5.0 59.8 1.0
O2B C:DMA301 5.0 55.3 1.0

Magnesium binding site 4 out of 8 in 7cav

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Magnesium binding site 4 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:34.3
occ:1.00
 O1A D:DMA302 2.0 34.5 1.0
O1A D:DMA301 2.0 34.4 1.0
OD1 D:ASP18 2.0 30.7 1.0
O D:HOH424 2.1 39.1 1.0
O2B D:DMA301 2.2 34.1 1.0
O D:HOH404 2.2 36.2 1.0
CG D:ASP18 3.0 33.1 1.0
PA D:DMA301 3.2 40.4 1.0
PB D:DMA301 3.2 35.5 1.0
PA D:DMA302 3.3 39.4 1.0
OD2 D:ASP18 3.4 36.0 1.0
O3A D:DMA301 3.5 36.9 1.0
O3B D:DMA301 3.7 33.5 1.0
O1 D:DMA302 3.8 39.9 1.0
O1 D:DMA301 3.8 39.7 1.0
O1B D:DMA302 3.8 43.0 1.0
NH2 D:ARG69 3.9 35.8 1.0
C1 D:DMA301 4.2 44.3 1.0
O C:HOH403 4.2 38.6 1.0
O3A D:DMA302 4.3 40.9 1.0
NH1 D:ARG22 4.3 36.1 1.0
O D:HOH402 4.4 48.4 1.0
CB D:ASP18 4.4 30.8 1.0
O2A D:DMA302 4.4 41.9 1.0
N D:GLY19 4.4 31.8 1.0
O2A D:DMA301 4.5 38.9 1.0
PB D:DMA302 4.6 41.3 1.0
O1B D:DMA301 4.6 34.0 1.0
CA D:ASP18 4.8 31.5 1.0
O2B D:DMA302 4.8 42.8 1.0
NH2 D:ARG168 4.8 33.2 1.0
C5 D:DMA301 4.9 41.0 1.0
NH2 D:ARG21 4.9 39.0 1.0

Magnesium binding site 5 out of 8 in 7cav

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Magnesium binding site 5 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:47.2
occ:1.00
 O2A E:DMA301 2.0 41.8 1.0
O E:HOH403 2.1 38.9 1.0
O3B E:DMA302 2.1 43.7 1.0
OD1 E:ASP18 2.1 39.1 1.0
O2A E:DMA302 2.1 50.0 1.0
O E:HOH422 2.3 42.4 1.0
CG E:ASP18 3.0 40.1 1.0
PB E:DMA302 3.2 48.3 1.0
OD2 E:ASP18 3.3 42.9 1.0
PA E:DMA302 3.3 48.6 1.0
PA E:DMA301 3.4 46.4 1.0
O3A E:DMA302 3.6 49.9 1.0
O1B E:DMA302 3.6 48.0 1.0
O1 E:DMA301 3.8 46.5 1.0
O2B E:DMA301 3.9 45.1 1.0
NH2 E:ARG69 3.9 49.2 1.0
NH1 E:ARG172 4.0 58.1 1.0
O1 E:DMA302 4.1 50.8 1.0
NH1 E:ARG22 4.3 42.9 1.0
O3A E:DMA301 4.3 47.8 1.0
CB E:ASP18 4.4 39.5 1.0
C1 E:DMA302 4.5 53.7 1.0
PB E:DMA301 4.5 49.5 1.0
O1A E:DMA301 4.5 47.2 1.0
N E:GLY19 4.5 45.0 1.0
O2B E:DMA302 4.5 46.5 1.0
O1A E:DMA302 4.5 49.1 1.0
O1B E:DMA301 4.6 43.3 1.0
NH2 E:ARG21 4.8 54.0 1.0
NH2 E:ARG168 4.8 39.1 1.0
CA E:ASP18 4.9 36.7 1.0
C2 E:DMA302 4.9 54.1 1.0

Magnesium binding site 6 out of 8 in 7cav

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Magnesium binding site 6 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:51.8
occ:1.00
 O1 F:DPO303 1.9 49.6 1.0
O5 F:DPO303 2.1 54.1 1.0
O F:HOH406 2.2 43.5 1.0
O3 F:DPO304 2.2 57.8 1.0
OD1 F:ASP18 2.2 42.6 1.0
P1 F:DPO303 3.0 52.5 1.0
CG F:ASP18 3.1 40.9 1.0
P2 F:DPO303 3.2 51.7 1.0
OD2 F:ASP18 3.4 41.1 1.0
O4 F:DPO303 3.4 49.9 1.0
O2 F:DPO303 3.5 49.5 1.0
P1 F:DPO304 3.5 58.6 1.0
O6 F:DPO303 3.8 50.6 1.0
O2 F:DPO304 3.8 55.2 1.0
NH2 F:ARG69 3.9 68.0 1.0
O6 F:DPO304 4.2 78.6 1.0
O7 F:DPO304 4.2 78.1 1.0
O3 F:DPO303 4.3 44.0 1.0
NH1 F:ARG22 4.4 43.7 1.0
O4 F:DPO304 4.4 66.2 1.0
O7 F:FQ0302 4.4 62.5 1.0
O F:HOH432 4.5 51.7 1.0
O7 F:DPO303 4.5 56.0 1.0
NH2 F:ARG21 4.5 52.8 1.0
N F:GLY19 4.5 37.1 1.0
CB F:ASP18 4.5 39.6 1.0
P2 F:DPO304 4.6 75.6 1.0
O1 F:DPO304 4.6 60.7 1.0
NH2 F:ARG168 4.8 34.0 1.0
CZ F:ARG69 5.0 70.3 1.0

Magnesium binding site 7 out of 8 in 7cav

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Magnesium binding site 7 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:45.8
occ:1.00
 O G:HOH410 1.9 41.5 1.0
O3 G:DPO303 2.0 44.8 1.0
O1 G:DPO304 2.1 57.6 1.0
O6 G:DPO303 2.1 50.3 1.0
OD1 G:ASP18 2.2 40.5 1.0
CG G:ASP18 3.0 40.7 1.0
OD2 G:ASP18 3.2 42.9 1.0
P2 G:DPO303 3.3 48.5 1.0
P1 G:DPO303 3.3 50.5 1.0
P1 G:DPO304 3.3 64.2 1.0
O4 G:DPO303 3.6 51.4 1.0
O2 G:DPO304 3.6 55.2 1.0
O7 G:DPO303 3.8 54.5 1.0
O1 G:DPO303 3.9 51.2 1.0
NH2 G:ARG69 4.0 60.8 1.0
NH1 G:ARG22 4.0 44.5 1.0
O7 G:FQ0302 4.1 76.5 1.0
O5 G:DPO304 4.2 71.4 1.0
O3 G:DPO304 4.3 63.2 1.0
O4 G:DPO304 4.4 70.3 1.0
CB G:ASP18 4.4 36.2 1.0
O2 G:DPO303 4.5 50.9 1.0
N G:GLY19 4.5 37.4 1.0
O5 G:DPO303 4.6 48.0 1.0
NH2 G:ARG168 4.6 39.4 1.0
NH2 G:ARG21 4.9 55.7 1.0
P2 G:DPO304 4.9 80.3 1.0
CA G:ASP18 5.0 35.5 1.0

Magnesium binding site 8 out of 8 in 7cav

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Magnesium binding site 8 out of 8 in the Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Versatile Cis-Prenyltransferase MM_0014 From Methanosarcina Mazei (Crystal Type: Co-Fg+Dmapp) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:60.0
occ:1.00
 O H:HOH431 2.0 42.0 1.0
O2 H:DPO303 2.1 49.0 1.0
O5 H:DPO303 2.1 51.4 1.0
O2 G:PO4305 2.1 54.0 1.0
OD1 H:ASP18 2.2 38.6 1.0
O G:HOH418 2.3 48.1 1.0
P1 H:DPO303 3.1 47.5 1.0
CG H:ASP18 3.1 34.1 1.0
O3 H:DPO303 3.3 52.6 1.0
P2 H:DPO303 3.3 51.9 1.0
OD2 H:ASP18 3.3 37.7 1.0
O4 H:DPO303 3.5 52.1 1.0
P G:PO4305 3.5 66.3 1.0
O7 H:DPO303 3.9 47.3 1.0
O1 G:PO4305 4.0 56.4 1.0
O3 G:PO4305 4.2 62.9 1.0
O G:HOH422 4.2 53.8 1.0
NH1 H:ARG22 4.2 41.9 1.0
O1 H:DPO303 4.4 47.0 1.0
O G:LEU217 4.5 39.7 1.0
O6 H:DPO303 4.5 50.7 1.0
CB H:ASP18 4.5 34.4 1.0
N H:GLY19 4.5 36.1 1.0
O7 H:FQ0302 4.6 69.1 1.0
O4 G:PO4305 4.6 65.0 1.0
NH1 H:ARG172 4.6 39.1 1.0
NH2 H:ARG69 4.8 77.1 1.0

Reference:

M.Okada, H.Unno, K.Emi, M.Matsumoto, H.Hemmi. A Versatile Cis-Prenyltransferase From Methanosarcina Mazei Catalyzes Both C- and O-Prenylations. J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Wed Oct 2 13:53:49 2024

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