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Magnesium in PDB 4cw7: Structure of the FAP7-RPS14 Complex in Complex with Atp

Enzymatic activity of Structure of the FAP7-RPS14 Complex in Complex with Atp

All present enzymatic activity of Structure of the FAP7-RPS14 Complex in Complex with Atp:
2.7.4.3;

Protein crystallography data

The structure of Structure of the FAP7-RPS14 Complex in Complex with Atp, PDB code: 4cw7 was solved by J.Loch, M.Blaud, S.Rety, S.Lebaron, P.Deschamps, J.Bareille, J.Jombart, J.Robert-Paganin, L.Delbos, F.Chardon, E.Zhang, C.Charenton, D.Tollervey, N.Leulliot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.448 / 2.46
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.046, 143.079, 83.786, 90.00, 90.00, 90.00
R / Rfree (%) 18.92 / 22.94

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the FAP7-RPS14 Complex in Complex with Atp (pdb code 4cw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of the FAP7-RPS14 Complex in Complex with Atp, PDB code: 4cw7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4cw7

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Magnesium binding site 1 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:33.1
occ:1.00
 O3G A:ATP1001 1.9 38.5 1.0
OG1 A:THR14 2.0 41.5 1.0
O A:HOH2003 2.1 26.5 1.0
O2B A:ATP1001 2.2 37.7 1.0
O A:HOH2005 2.3 33.1 1.0
O A:HOH2004 2.3 29.9 1.0
CB A:THR14 3.0 43.4 1.0
PG A:ATP1001 3.2 58.9 0.4
PB A:ATP1001 3.3 33.3 1.0
O3B A:ATP1001 3.4 49.9 1.0
O2A A:ATP1001 3.9 32.7 1.0
N A:THR14 3.9 38.3 1.0
CA A:THR14 4.0 41.0 1.0
O2G A:ATP1001 4.0 71.7 1.0
CG2 A:THR14 4.1 44.4 1.0
O A:HOH2010 4.1 40.6 1.0
O A:HOH2009 4.2 38.9 1.0
O1G A:ATP1001 4.2 67.3 1.0
OD2 A:ASP71 4.2 48.2 1.0
O3A A:ATP1001 4.3 48.7 1.0
PA A:ATP1001 4.4 33.2 1.0
O1B A:ATP1001 4.4 43.7 1.0
O E:HOH2016 4.4 34.5 1.0
O1A A:ATP1001 4.5 32.5 1.0
OD1 A:ASP71 4.5 49.5 1.0
O A:HOH2012 4.8 38.8 1.0
CG A:ASP71 4.9 38.0 1.0
CB A:LYS13 4.9 32.6 1.0

Magnesium binding site 2 out of 8 in 4cw7

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Magnesium binding site 2 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:84.3
occ:1.00
 O A:HOH2029 2.1 57.1 1.0
OE2 A:GLU166 2.1 71.1 1.0
O A:HOH2026 2.2 54.5 1.0
O A:HOH2030 2.3 48.8 1.0
CD A:GLU166 3.3 71.8 1.0
OD2 A:ASP163 3.5 51.7 1.0
OE1 B:GLU54 3.5 57.3 1.0
OD1 B:ASP51 3.7 82.6 1.0
OE2 B:GLU54 3.9 47.2 1.0
CB A:ASP163 3.9 34.0 1.0
OE1 A:GLU166 4.2 80.5 1.0
CD B:GLU54 4.2 48.3 1.0
CG A:ASP163 4.2 45.5 1.0
CG A:GLU166 4.2 57.0 1.0
CG B:ASP51 4.5 73.3 1.0
O B:HOH2003 4.7 39.9 1.0

Magnesium binding site 3 out of 8 in 4cw7

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Magnesium binding site 3 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:70.5
occ:1.00
 O C:HOH2003 1.9 44.2 1.0
O C:HOH2002 2.1 54.8 1.0
O1B C:ADP1001 2.5 74.5 1.0
OG1 C:THR14 2.6 61.4 1.0
O2B C:ADP1001 3.3 70.4 1.0
PB C:ADP1001 3.5 70.4 1.0
CB C:THR14 3.7 68.3 1.0
O1A C:ADP1001 4.0 72.3 1.0
NH2 C:ARG100 4.2 74.9 1.0
O C:HOH2006 4.5 42.5 1.0
O3A C:ADP1001 4.5 0.7 1.0
N C:THR14 4.5 70.0 1.0
O3B C:ADP1001 4.6 61.0 1.0
OD2 C:ASP71 4.6 74.5 1.0
OD1 C:ASP71 4.7 61.9 1.0
PA C:ADP1001 4.7 70.0 1.0
CA C:THR14 4.7 69.9 1.0
CG2 C:THR14 4.7 67.9 1.0
CE C:LYS13 4.9 57.6 1.0
O C:HOH2001 5.0 42.5 1.0
NZ C:LYS13 5.0 60.5 1.0

Magnesium binding site 4 out of 8 in 4cw7

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Magnesium binding site 4 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:73.6
occ:1.00
 OE1 D:GLU54 2.4 83.1 1.0
OE2 C:GLU166 2.8 69.7 1.0
OD2 D:ASP51 2.9 92.7 1.0
OD2 C:ASP163 3.0 48.5 1.0
O C:HOH2008 3.2 68.7 1.0
CD D:GLU54 3.3 76.4 1.0
OE2 D:GLU54 3.4 76.6 1.0
O C:HOH2009 3.6 53.5 1.0
CB C:ASP163 3.7 44.8 1.0
CG C:ASP163 3.8 48.6 1.0
CD C:GLU166 3.9 68.9 1.0
CG D:ASP51 4.0 86.1 1.0
OD1 D:ASP51 4.5 92.0 1.0
CG C:GLU166 4.5 51.3 1.0
ND2 D:ASN25 4.6 36.8 1.0
CG D:GLU54 4.7 65.8 1.0
OE1 C:GLU166 4.9 78.9 1.0

Magnesium binding site 5 out of 8 in 4cw7

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Magnesium binding site 5 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:33.2
occ:1.00
 O1G E:ATP1001 1.9 29.9 1.0
OG1 E:THR14 2.0 31.1 1.0
O E:HOH2004 2.0 30.4 1.0
O E:HOH2005 2.1 26.9 1.0
O2B E:ATP1001 2.1 37.9 1.0
O E:HOH2006 2.3 29.7 1.0
CB E:THR14 3.0 36.2 1.0
PG E:ATP1001 3.2 43.0 0.6
PB E:ATP1001 3.3 25.6 1.0
O3B E:ATP1001 3.4 47.6 1.0
N E:THR14 3.7 32.0 1.0
CA E:THR14 3.9 35.2 1.0
OD2 E:ASP71 4.0 37.4 1.0
O2A E:ATP1001 4.1 27.8 1.0
O3G E:ATP1001 4.1 47.8 1.0
OD1 E:ASP71 4.1 25.3 1.0
CG2 E:THR14 4.1 30.5 1.0
O2G E:ATP1001 4.3 47.1 1.0
O1B E:ATP1001 4.3 41.9 1.0
O3A E:ATP1001 4.4 31.0 1.0
O E:HOH2009 4.5 23.6 1.0
PA E:ATP1001 4.5 32.2 1.0
CG E:ASP71 4.5 34.3 1.0
O1A E:ATP1001 4.5 30.3 1.0
CB E:LYS13 4.6 24.2 1.0
C E:LYS13 4.7 40.7 1.0
CE E:LYS13 4.9 19.6 1.0

Magnesium binding site 6 out of 8 in 4cw7

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Magnesium binding site 6 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1003

b:79.8
occ:1.00
 O E:HOH2035 2.3 41.3 1.0
OE2 E:GLU166 2.4 63.4 1.0
O E:HOH2031 2.8 57.3 1.0
O E:HOH2032 2.9 50.9 1.0
OE1 F:GLU54 3.3 80.8 1.0
OD1 F:ASP51 3.5 86.1 1.0
CD E:GLU166 3.6 57.6 1.0
OE2 F:GLU54 3.6 69.1 1.0
OD2 E:ASP163 3.7 34.0 1.0
CD F:GLU54 3.9 66.3 1.0
CG E:GLU166 4.2 47.9 1.0
CB E:ASP163 4.3 25.6 1.0
CG E:ASP163 4.4 33.0 1.0
CG F:ASP51 4.5 77.5 1.0
OE1 E:GLU166 4.5 62.6 1.0
OD2 F:ASP51 4.6 94.1 1.0

Magnesium binding site 7 out of 8 in 4cw7

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Magnesium binding site 7 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1002

b:56.3
occ:1.00
 O G:HOH2003 1.9 42.7 1.0
O3B G:ADP1001 2.1 49.7 1.0
O G:HOH2004 2.3 38.5 1.0
O G:HOH2011 2.3 25.3 1.0
OG1 G:THR14 2.5 50.2 1.0
PB G:ADP1001 3.0 48.9 1.0
O1B G:ADP1001 3.0 36.2 1.0
CB G:THR14 3.6 51.3 1.0
N G:THR14 3.9 52.9 1.0
O2B G:ADP1001 3.9 63.9 1.0
OD1 G:ASP71 4.1 59.5 1.0
O G:HOH2007 4.1 43.0 1.0
O G:HOH2002 4.2 33.0 1.0
CE G:LYS13 4.2 52.3 1.0
O1A G:ADP1001 4.2 27.9 1.0
O3A G:ADP1001 4.2 65.0 1.0
OD2 G:ASP71 4.3 57.3 1.0
CA G:THR14 4.3 50.6 1.0
CB G:LYS13 4.3 49.0 1.0
NZ G:LYS13 4.3 43.7 1.0
PA G:ADP1001 4.6 43.4 1.0
CG G:ASP71 4.6 54.7 1.0
NH2 G:ARG100 4.7 55.1 1.0
O2A G:ADP1001 4.8 47.0 1.0
C G:LYS13 4.8 54.0 1.0
CG2 G:THR14 4.8 42.2 1.0
CA G:LYS13 4.9 52.2 1.0

Magnesium binding site 8 out of 8 in 4cw7

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Magnesium binding site 8 out of 8 in the Structure of the FAP7-RPS14 Complex in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the FAP7-RPS14 Complex in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1003

b:64.8
occ:1.00
 O G:HOH2018 2.1 71.5 1.0
OE2 G:GLU166 2.6 64.9 1.0
O G:HOH2020 2.7 70.3 1.0
OE1 H:GLU54 3.3 65.9 1.0
OD2 G:ASP163 3.6 58.8 1.0
OD1 H:ASP51 3.6 88.2 1.0
CD G:GLU166 3.7 57.1 1.0
OE2 H:GLU54 3.8 59.5 1.0
CD H:GLU54 3.9 58.0 1.0
CB G:ASP163 4.1 48.2 1.0
CG G:ASP163 4.3 51.3 1.0
CG H:ASP51 4.4 82.1 1.0
OE1 G:GLU166 4.5 70.5 1.0
CG G:GLU166 4.6 42.3 1.0
O H:HOH2003 4.6 58.5 1.0
O G:HOH2019 4.8 52.7 1.0
OD2 H:ASP51 4.8 87.6 1.0

Reference:

J.Loch, M.Blaud, S.Rety, S.Lebaron, P.Deschamps, J.Bareille, J.Jombart, J.Robert-Paganin, L.Delbos, F.Chardon, E.Zhang, C.Charenton, D.Tollervey, N.Leulliot. Rna Mimicry By the FAP7 Adenylate Kinase in Ribosome Biogenesis Plos Biol. V. 12 01860 2014.
ISSN: ISSN 1544-9173
PubMed: 24823650
DOI: 10.1371/JOURNAL.PBIO.1001860
Page generated: Mon Dec 14 11:42:00 2020

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