Magnesium in PDB 2v55: Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure

All present enzymatic activity of Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure:
2.7.11.1;

The structure of Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure, PDB code: 2v55 was solved by D.Komander, R.Garg, P.T.C.Wan, A.J.Ridley, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.288 / 3.7
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.477, 152.477, 531.274, 90.00, 90.00, 120.00
R / Rfree (%)	23.76 / 26.89

The binding sites of Magnesium atom in the Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure (pdb code 2v55). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure, PDB code: 2v55:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1481 b:0.8 occ:1.00 OD1 A:ASN203 2.9 77.4 1.0 N3B A:ANP1480 3.3 0.1 1.0 O1A A:ANP1480 3.3 0.5 1.0 C5' A:ANP1480 3.3 0.1 1.0 O3G A:ANP1480 3.3 0.7 1.0 O2B A:ANP1480 3.6 0.6 1.0 O3A A:ANP1480 3.7 0.3 1.0 PB A:ANP1480 3.7 0.6 1.0 PA A:ANP1480 3.8 0.7 1.0 O5' A:ANP1480 3.8 0.2 1.0 PG A:ANP1480 3.9 0.4 1.0 CG A:ASN203 3.9 76.8 1.0 OD2 A:ASP216 4.1 0.5 1.0 CE A:LYS200 4.1 65.6 1.0 CB A:ASP202 4.3 0.6 1.0 O A:ASP202 4.3 85.2 1.0 NZ A:LYS200 4.4 69.1 1.0 ND2 A:ASN203 4.4 80.1 1.0 C4' A:ANP1480 4.5 0.7 1.0 C A:ASP202 4.6 86.8 1.0 O3' A:ANP1480 4.7 0.4 1.0 C3' A:ANP1480 4.7 0.2 1.0 CG A:ASP216 4.8 0.3 1.0 CB A:ASP216 4.9 0.1 1.0 O2G A:ANP1480 4.9 0.8 1.0

Magnesium binding site 2 out of 4 in the Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1202 b:50.3 occ:1.00 O2B B:GTP1201 2.4 49.9 1.0 OG1 B:THR37 2.5 48.7 1.0 O2G B:GTP1201 2.6 50.2 1.0 OG1 B:THR55 2.7 49.2 1.0 O B:VAL53 2.9 0.2 1.0 CB B:THR37 3.1 59.9 1.0 N B:THR55 3.2 82.9 1.0 CG2 B:THR55 3.4 49.1 1.0 PB B:GTP1201 3.4 55.8 1.0 CB B:THR55 3.4 71.6 1.0 PG B:GTP1201 3.6 73.4 1.0 O3A B:GTP1201 3.6 0.2 1.0 O1A B:GTP1201 3.6 51.5 1.0 CG2 B:THR37 3.8 63.2 1.0 O3G B:GTP1201 3.8 72.2 1.0 CA B:THR55 3.9 71.8 1.0 O3B B:GTP1201 3.9 93.9 1.0 C B:VAL53 4.0 84.1 1.0 PA B:GTP1201 4.1 69.9 1.0 C B:PRO54 4.2 78.7 1.0 CA B:PRO54 4.3 68.2 1.0 CE1 B:TYR52 4.3 81.4 1.0 CA B:THR37 4.5 57.3 1.0 O2A B:GTP1201 4.5 50.5 1.0 OD2 B:ASP77 4.5 85.6 1.0 N B:THR37 4.6 66.2 1.0 N B:PRO54 4.7 53.2 1.0 CD1 B:TYR52 4.7 85.1 1.0 O1B B:GTP1201 4.7 50.8 1.0 O1G B:GTP1201 4.9 82.2 1.0 N B:VAL53 5.0 74.9 1.0 CZ B:TYR52 5.0 68.0 1.0 C B:THR55 5.0 62.8 1.0

Magnesium binding site 3 out of 4 in the Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1481 b:99.4 occ:1.00 OD1 C:ASN203 2.9 83.1 1.0 O1A C:ANP1480 3.2 0.7 1.0 N3B C:ANP1480 3.2 0.1 1.0 C5' C:ANP1480 3.3 0.2 1.0 O3G C:ANP1480 3.3 0.3 1.0 O2B C:ANP1480 3.6 1.0 1.0 O3A C:ANP1480 3.6 0.7 1.0 PB C:ANP1480 3.7 0.1 1.0 PA C:ANP1480 3.8 0.4 1.0 O5' C:ANP1480 3.8 0.1 1.0 PG C:ANP1480 3.9 0.2 1.0 CG C:ASN203 4.0 80.5 1.0 OD2 C:ASP216 4.0 0.1 1.0 CE C:LYS200 4.1 63.9 1.0 CB C:ASP202 4.3 0.4 1.0 O C:ASP202 4.4 83.7 1.0 NZ C:LYS200 4.4 62.7 1.0 ND2 C:ASN203 4.5 80.1 1.0 C4' C:ANP1480 4.5 0.6 1.0 C C:ASP202 4.6 86.9 1.0 C3' C:ANP1480 4.6 0.6 1.0 O3' C:ANP1480 4.7 0.8 1.0 CG C:ASP216 4.8 0.1 1.0 CB C:ASP216 4.9 0.2 1.0 O2G C:ANP1480 4.9 0.6 1.0

Magnesium binding site 4 out of 4 in the Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1202 b:34.3 occ:1.00 OG1 D:THR55 2.6 31.7 1.0 OG1 D:THR37 2.6 53.4 1.0 O2B D:GTP1201 2.6 30.1 1.0 O2G D:GTP1201 2.7 41.0 1.0 O D:VAL53 2.9 0.4 1.0 CB D:THR37 3.1 65.0 1.0 N D:THR55 3.1 81.2 1.0 CG2 D:THR55 3.3 34.4 1.0 CB D:THR55 3.3 67.8 1.0 PB D:GTP1201 3.5 65.0 1.0 O1A D:GTP1201 3.7 38.2 1.0 O3A D:GTP1201 3.7 1.0 1.0 PG D:GTP1201 3.7 68.4 1.0 CG2 D:THR37 3.7 64.5 1.0 CA D:THR55 3.8 70.5 1.0 O3G D:GTP1201 3.9 73.4 1.0 C D:VAL53 4.0 83.8 1.0 O3B D:GTP1201 4.0 95.7 1.0 C D:PRO54 4.1 77.3 1.0 PA D:GTP1201 4.2 55.6 1.0 CA D:PRO54 4.3 63.4 1.0 CE1 D:TYR52 4.4 83.3 1.0 OD2 D:ASP77 4.4 84.2 1.0 CA D:THR37 4.5 56.7 1.0 O2A D:GTP1201 4.6 38.0 1.0 N D:PRO54 4.6 54.7 1.0 N D:THR37 4.7 66.8 1.0 CD1 D:TYR52 4.7 88.3 1.0 O1B D:GTP1201 4.9 43.8 1.0 C D:THR55 4.9 61.8 1.0 N D:VAL53 5.0 71.7 1.0

D.Komander, R.Garg, P.T.C.Wan, A.J.Ridley, D.Barford. Mechanism of Multi-Site Phosphorylation From A Rock-I:Rhoe Complex Structure. Embo J. V. 27 3175 2008.
ISSN: ISSN 0261-4189
PubMed: 18946488
DOI: 10.1038/EMBOJ.2008.226