Magnesium in PDB 6h77: E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl

Protein crystallography data

The structure of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl, PDB code: 6h77 was solved by N.Soudah, P.Padala, F.Hassouna, B.Mashahreh, A.A.Lebedev, M.N.Isupov, E.Cohen-Kfir, R.Wiener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.76 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.110, 105.520, 93.880, 90.00, 102.29, 90.00
R / Rfree (%) 18.4 / 22.1

Other elements in 6h77:

The structure of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl (pdb code 6h77). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl, PDB code: 6h77:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6h77

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Magnesium binding site 1 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:37.0
occ:1.00
 O1B A:ATP401 2.1 26.5 1.0
OD2 A:ASP183 2.1 38.0 1.0
O1A A:ATP401 2.1 36.5 1.0
O A:HOH536 2.1 41.0 1.0
O A:HOH570 2.2 45.3 1.0
O1G A:ATP401 2.2 38.7 1.0
PB A:ATP401 3.0 32.8 1.0
O3B A:ATP401 3.2 30.1 1.0
PG A:ATP401 3.2 37.9 1.0
CG A:ASP183 3.2 34.6 1.0
PA A:ATP401 3.3 33.7 1.0
O3A A:ATP401 3.5 38.5 1.0
CB A:ASP183 3.6 29.2 1.0
O5' A:ATP401 3.6 39.8 1.0
O3G A:ATP401 3.9 38.5 1.0
O A:HOH603 3.9 54.2 1.0
O A:HOH515 4.1 39.7 1.0
OD1 A:ASP183 4.3 31.0 1.0
O2B A:ATP401 4.4 39.0 1.0
O2G A:ATP401 4.4 33.8 1.0
O2A A:ATP401 4.5 40.0 1.0
O A:HOH571 4.8 36.9 1.0
O A:HOH617 4.9 78.0 1.0
O A:HOH593 4.9 67.7 1.0
O A:HOH607 4.9 58.9 1.0
C5' A:ATP401 5.0 41.1 1.0

Magnesium binding site 2 out of 8 in 6h77

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Magnesium binding site 2 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:35.5
occ:1.00
 O A:HOH521 2.1 34.4 1.0
OD2 A:ASP106 2.1 30.6 1.0
O A:HOH506 2.1 27.9 1.0
O A:HOH523 2.2 36.9 1.0
O2B A:ATP401 2.2 39.0 1.0
O A:HOH571 2.2 36.9 1.0
CG A:ASP106 3.2 35.9 1.0
PB A:ATP401 3.3 32.8 1.0
OD1 A:ASP106 3.6 30.1 1.0
O1B A:ATP401 3.6 26.5 1.0
O3G A:ATP401 3.8 38.5 1.0
O A:HOH554 4.0 54.5 1.0
NZ A:LYS127 4.1 32.9 1.0
O3B A:ATP401 4.2 30.1 1.0
O B:HOH505 4.3 61.4 1.0
OD1 A:ASN112 4.4 45.4 1.0
ND2 A:ASN112 4.5 42.8 1.0
O A:LYS107 4.5 34.9 1.0
CB A:ASP106 4.5 31.1 1.0
O3A A:ATP401 4.5 38.5 1.0
CE A:LYS127 4.6 29.8 1.0
PG A:ATP401 4.7 37.9 1.0
CG A:ASN112 4.9 40.1 1.0
CG A:GLU109 5.0 60.0 1.0

Magnesium binding site 3 out of 8 in 6h77

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Magnesium binding site 3 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:38.1
occ:1.00
 OD2 B:ASP183 2.1 40.1 1.0
O2G B:ATP401 2.1 40.0 1.0
O B:HOH532 2.1 40.2 1.0
O1B B:ATP401 2.1 32.9 1.0
O B:HOH580 2.1 38.4 1.0
O2A B:ATP401 2.2 40.8 1.0
PB B:ATP401 3.1 36.1 1.0
CG B:ASP183 3.2 37.0 1.0
PG B:ATP401 3.2 42.2 1.0
O3B B:ATP401 3.3 34.6 1.0
PA B:ATP401 3.4 34.4 1.0
O5' B:ATP401 3.6 43.1 1.0
CB B:ASP183 3.6 29.1 1.0
O3A B:ATP401 3.6 36.2 1.0
O3G B:ATP401 4.0 38.6 1.0
O B:HOH593 4.0 52.3 1.0
O B:HOH537 4.1 53.6 1.0
O B:HOH517 4.2 46.6 1.0
OD1 B:ASP183 4.3 34.8 1.0
O1G B:ATP401 4.5 36.5 1.0
O2B B:ATP401 4.5 35.5 1.0
O1A B:ATP401 4.7 40.6 1.0
O B:HOH564 4.7 56.3 1.0
O B:HOH568 4.8 40.7 1.0
C5' B:ATP401 4.9 34.7 1.0

Magnesium binding site 4 out of 8 in 6h77

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Magnesium binding site 4 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:36.9
occ:1.00
 O B:HOH568 2.1 40.7 1.0
O B:HOH516 2.1 37.0 1.0
OD2 B:ASP106 2.1 36.5 1.0
O B:HOH507 2.1 32.7 1.0
O B:HOH506 2.1 41.2 1.0
O2B B:ATP401 2.1 35.5 1.0
CG B:ASP106 3.1 47.6 1.0
PB B:ATP401 3.4 36.1 1.0
OD1 B:ASP106 3.5 38.4 1.0
OE1 B:GLU109 3.7 55.0 0.5
O1B B:ATP401 3.8 32.9 1.0
O3G B:ATP401 3.9 38.6 1.0
O B:HOH565 4.0 43.5 1.0
CD B:GLU109 4.0 59.0 0.5
OE2 B:GLU109 4.1 56.3 0.5
NZ B:LYS127 4.1 37.7 1.0
O3B B:ATP401 4.2 34.6 1.0
O B:LYS107 4.4 33.1 1.0
OD1 B:ASN112 4.4 41.3 1.0
CB B:ASP106 4.5 33.0 1.0
ND2 B:ASN112 4.5 34.4 1.0
O3A B:ATP401 4.5 36.2 1.0
CE B:LYS127 4.6 34.9 1.0
O B:HOH517 4.7 46.6 1.0
PG B:ATP401 4.8 42.2 1.0
CG B:ASN112 4.9 43.4 1.0
CG B:GLU109 4.9 40.8 0.5
CG B:GLU109 5.0 43.0 0.5

Magnesium binding site 5 out of 8 in 6h77

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Magnesium binding site 5 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:45.1
occ:1.00
 OD2 C:ASP183 2.1 38.0 1.0
O3G C:ATP401 2.1 45.5 1.0
O1A C:ATP401 2.1 37.2 1.0
O2B C:ATP401 2.1 36.4 1.0
O C:HOH560 2.2 51.1 1.0
O C:HOH523 2.2 39.5 1.0
CG C:ASP183 3.2 51.1 1.0
PB C:ATP401 3.2 39.2 1.0
PG C:ATP401 3.3 46.8 1.0
O3B C:ATP401 3.3 29.3 1.0
PA C:ATP401 3.4 38.3 1.0
CB C:ASP183 3.6 36.1 1.0
O3A C:ATP401 3.7 42.1 1.0
O5' C:ATP401 3.7 42.0 1.0
O C:HOH547 4.2 51.2 1.0
O1G C:ATP401 4.2 46.9 1.0
OD1 C:ASP183 4.3 36.7 1.0
O2G C:ATP401 4.4 36.5 1.0
O C:HOH594 4.4 63.4 1.0
O1B C:ATP401 4.5 45.0 1.0
O C:HOH574 4.7 58.6 1.0
O2A C:ATP401 4.7 46.9 1.0
O C:HOH510 4.7 55.0 1.0
NH2 C:ARG115 4.7 72.0 0.4
O C:HOH551 4.9 40.7 1.0

Magnesium binding site 6 out of 8 in 6h77

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Magnesium binding site 6 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:37.3
occ:1.00
 O C:HOH552 2.1 44.5 1.0
OD2 C:ASP106 2.1 35.1 1.0
O1B C:ATP401 2.2 45.0 1.0
O C:HOH507 2.2 34.1 1.0
O C:HOH501 2.2 35.2 1.0
O C:HOH551 2.2 40.7 1.0
CG C:ASP106 3.2 55.8 1.0
PB C:ATP401 3.4 39.2 1.0
OD1 C:ASP106 3.5 35.3 1.0
O2B C:ATP401 3.8 36.4 1.0
O1G C:ATP401 4.0 46.9 1.0
NZ C:LYS127 4.1 38.2 1.0
O3B C:ATP401 4.1 29.3 1.0
O C:LYS107 4.4 38.5 1.0
OD1 C:ASN112 4.4 43.1 1.0
O3A C:ATP401 4.5 42.1 1.0
ND2 C:ASN112 4.5 39.5 1.0
CB C:ASP106 4.5 41.1 1.0
CE C:LYS127 4.6 42.9 1.0
PG C:ATP401 4.8 46.8 1.0
CG C:ASN112 4.9 41.1 1.0
CG C:GLU109 5.0 57.3 1.0

Magnesium binding site 7 out of 8 in 6h77

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Magnesium binding site 7 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:37.2
occ:1.00
 O2B D:ATP401 2.1 28.5 1.0
OD2 D:ASP183 2.1 30.5 1.0
O2G D:ATP401 2.1 39.7 1.0
O D:HOH537 2.1 36.5 1.0
O D:HOH558 2.2 41.9 1.0
O2A D:ATP401 2.2 41.1 1.0
PB D:ATP401 3.0 31.3 1.0
CG D:ASP183 3.2 37.4 1.0
PG D:ATP401 3.2 37.7 1.0
O3B D:ATP401 3.2 31.0 1.0
PA D:ATP401 3.4 35.4 1.0
O3A D:ATP401 3.6 39.9 1.0
CB D:ASP183 3.6 26.3 1.0
O5' D:ATP401 3.8 46.1 1.0
O D:HOH526 3.9 47.8 1.0
O3G D:ATP401 3.9 44.0 1.0
O D:HOH604 4.2 48.4 1.0
OD1 D:ASP183 4.3 30.8 1.0
O1G D:ATP401 4.4 31.8 1.0
O1B D:ATP401 4.4 40.9 1.0
O D:HOH551 4.6 35.7 1.0
O D:HOH554 4.6 48.6 1.0
O1A D:ATP401 4.6 35.8 1.0
O D:HOH530 4.9 53.3 1.0

Magnesium binding site 8 out of 8 in 6h77

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Magnesium binding site 8 out of 8 in the E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E1 Enzyme For Ubiquitin Like Protein Activation in Complex with Ubl within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:34.1
occ:1.00
 OD2 D:ASP106 2.1 35.4 1.0
O D:HOH513 2.1 34.0 1.0
O D:HOH505 2.1 31.4 1.0
O1B D:ATP401 2.1 40.9 1.0
O D:HOH507 2.2 30.6 1.0
O D:HOH551 2.2 35.7 1.0
CG D:ASP106 3.1 38.8 1.0
PB D:ATP401 3.3 31.3 1.0
OD1 D:ASP106 3.5 34.5 1.0
O2B D:ATP401 3.7 28.5 1.0
O3G D:ATP401 3.8 44.0 1.0
NZ D:LYS127 4.1 36.7 1.0
O D:HOH587 4.1 48.8 1.0
O3B D:ATP401 4.2 31.0 1.0
OD1 D:ASN112 4.4 39.5 1.0
ND2 D:ASN112 4.4 43.4 1.0
O D:LYS107 4.4 37.0 1.0
CB D:ASP106 4.4 33.6 1.0
O3A D:ATP401 4.5 39.9 1.0
O D:HOH526 4.5 47.8 1.0
CE D:LYS127 4.6 29.5 1.0
PG D:ATP401 4.7 37.7 1.0
CG D:ASN112 4.9 39.8 1.0
CG D:GLU109 5.0 59.8 1.0

Reference:

N.Soudah, P.Padala, F.Hassouna, M.Kumar, B.Mashahreh, A.A.Lebedev, M.N.Isupov, E.Cohen-Kfir, R.Wiener. An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-Like Protein Activation. J.Mol.Biol. V. 431 463 2019.
ISSN: ESSN 1089-8638
PubMed: 30412706
DOI: 10.1016/J.JMB.2018.10.007
Page generated: Mon Dec 14 22:47:45 2020

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