Magnesium in PDB 7mpp: Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+

The structure of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+, PDB code: 7mpp was solved by J.D.Lormand, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	126.79 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.929, 126.734, 127.145, 90, 94.28, 90
R / Rfree (%)	15.8 / 18.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ (pdb code 7mpp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+, PDB code: 7mpp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:36.9 occ:1.00 O2P A:5GP301 2.1 35.7 1.0 O A:HOH404 2.1 33.2 1.0 O A:HOH429 2.1 36.9 1.0 OD1 A:ASP25 2.1 32.7 1.0 O A:HOH542 2.2 36.1 1.0 O A:HOH528 2.2 41.5 1.0 CG A:ASP25 3.1 32.7 1.0 P A:5GP301 3.4 38.8 1.0 OD2 A:ASP25 3.4 36.3 1.0 MG A:MG303 3.8 39.8 1.0 O3P A:5GP301 3.9 49.5 1.0 OD1 A:ASP84 4.0 34.3 1.0 O A:THR26 4.0 27.9 1.0 O5' A:5GP301 4.0 39.7 1.0 OD2 A:ASP84 4.0 37.8 1.0 O A:HOH438 4.2 44.4 1.0 C5' A:5GP301 4.2 38.0 1.0 O A:HOH453 4.2 24.5 1.0 O A:HOH504 4.2 29.8 1.0 CG A:ASP84 4.4 29.5 1.0 O A:HIS79 4.4 28.9 1.0 CB A:ASP25 4.5 22.9 1.0 OD2 A:ASP155 4.5 44.7 1.0 N A:THR26 4.6 28.5 1.0 O G:HOH412 4.6 43.2 1.0 O1P A:5GP301 4.6 35.5 1.0 O3' G:5GP301 4.9 51.4 0.9 CA A:ASP25 5.0 24.2 1.0

Magnesium binding site 2 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:39.8 occ:1.00 OD2 A:ASP155 2.1 44.7 1.0 OE2 A:GLU27 2.1 36.0 1.0 OD2 A:ASP25 2.2 36.3 1.0 O2P A:5GP301 2.4 35.7 1.0 O1P A:5GP301 2.7 35.5 1.0 P A:5GP301 2.9 38.8 1.0 CD A:GLU27 3.1 37.1 1.0 CG A:ASP155 3.1 40.2 1.0 CG A:ASP25 3.3 32.7 1.0 OE1 A:GLU27 3.5 34.3 1.0 CB A:ASP155 3.6 29.9 1.0 CE2 A:TYR151 3.7 35.2 1.0 OD1 A:ASP25 3.7 32.7 1.0 MG A:MG302 3.8 36.9 1.0 OH A:TYR151 3.8 35.7 1.0 O A:HOH542 3.8 36.1 1.0 O3P A:5GP301 3.8 49.5 1.0 O A:THR26 3.8 27.9 1.0 NE2 A:GLN42 3.9 27.5 1.0 CZ A:TYR151 4.0 33.6 1.0 OD1 A:ASP155 4.2 32.5 1.0 O5' A:5GP301 4.3 39.7 1.0 CG A:GLU27 4.4 30.0 1.0 O A:HOH429 4.5 36.9 1.0 CB A:ASP25 4.6 22.9 1.0 CD2 A:TYR151 4.6 31.8 1.0 C A:THR26 4.7 30.7 1.0 C5' A:5GP301 4.7 38.0 1.0 O A:HOH438 4.8 44.4 1.0 NZ A:LYS132 4.9 46.3 1.0

Magnesium binding site 3 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:39.2 occ:1.00 O C:HOH407 2.1 30.9 1.0 O3P C:5GP301 2.1 44.6 1.0 O C:HOH421 2.2 33.9 1.0 O C:HOH507 2.2 34.7 1.0 OD1 C:ASP25 2.2 30.8 1.0 O C:HOH518 2.2 43.1 1.0 CG C:ASP25 3.2 34.4 1.0 P C:5GP301 3.4 49.0 1.0 OD2 C:ASP25 3.5 42.3 1.0 MG C:MG303 3.6 44.5 1.0 O5' C:5GP301 3.8 63.9 1.0 O1P C:5GP301 3.9 63.5 1.0 OD1 C:ASP84 4.0 36.4 1.0 O C:THR26 4.0 28.8 1.0 OD2 C:ASP84 4.1 39.7 1.0 O C:HOH529 4.2 39.6 1.0 C5' C:5GP301 4.3 55.4 1.0 O C:HOH451 4.3 29.1 1.0 O C:HOH489 4.3 33.0 1.0 O C:HIS79 4.5 28.2 1.0 CG C:ASP84 4.5 29.7 1.0 OD2 C:ASP155 4.5 43.7 1.0 CB C:ASP25 4.5 27.6 1.0 N C:THR26 4.6 25.6 1.0 O2P C:5GP301 4.6 43.9 1.0 O3' K:5GP301 4.9 68.2 0.9

Magnesium binding site 4 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:44.5 occ:1.00 OD2 C:ASP25 2.1 42.3 1.0 OD2 C:ASP155 2.1 43.7 1.0 O3P C:5GP301 2.2 44.6 1.0 OE2 C:GLU27 2.2 36.1 1.0 O2P C:5GP301 2.7 43.9 1.0 P C:5GP301 2.9 49.0 1.0 CG C:ASP155 3.2 38.7 1.0 CG C:ASP25 3.2 34.4 1.0 CD C:GLU27 3.2 36.7 1.0 OE1 C:GLU27 3.5 35.4 1.0 CB C:ASP155 3.6 35.8 1.0 OD1 C:ASP25 3.6 30.8 1.0 O C:HOH507 3.6 34.7 1.0 MG C:MG302 3.6 39.2 1.0 O5' C:5GP301 3.7 63.9 1.0 OH C:TYR151 3.8 38.2 1.0 O C:THR26 3.8 28.8 1.0 CE2 C:TYR151 3.8 34.4 1.0 NE2 C:GLN42 3.9 29.1 1.0 CZ C:TYR151 4.1 35.1 1.0 O1P C:5GP301 4.2 63.5 1.0 OD1 C:ASP155 4.3 39.4 1.0 O C:HOH421 4.5 33.9 1.0 CG C:GLU27 4.5 27.9 1.0 CB C:ASP25 4.5 27.6 1.0 C C:THR26 4.7 32.9 1.0 CD2 C:TYR151 4.7 39.1 1.0 O C:HOH529 4.8 39.6 1.0

Magnesium binding site 5 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:41.1 occ:1.00 O3P E:5GP301 2.0 42.1 1.0 O E:HOH408 2.1 32.6 1.0 O E:HOH496 2.1 39.4 1.0 O E:HOH415 2.2 39.2 1.0 OD1 E:ASP25 2.2 34.1 1.0 O E:HOH529 2.3 36.9 1.0 CG E:ASP25 3.2 39.1 1.0 P E:5GP301 3.4 46.9 1.0 OD2 E:ASP25 3.5 40.6 1.0 MG E:MG303 3.6 40.4 1.0 O E:HOH538 3.7 61.5 1.0 O2P E:5GP301 3.9 46.8 1.0 O5' E:5GP301 3.9 43.1 1.0 OD1 E:ASP84 3.9 34.0 1.0 O E:THR26 4.0 32.0 1.0 C5' E:5GP301 4.1 46.7 1.0 OD2 E:ASP84 4.2 41.6 1.0 O E:HOH497 4.2 31.0 1.0 O E:HOH471 4.2 42.4 1.0 O E:HOH425 4.4 25.6 1.0 O E:HIS79 4.5 28.8 1.0 CG E:ASP84 4.5 33.2 1.0 O1P E:5GP301 4.5 46.3 1.0 CB E:ASP25 4.5 29.9 1.0 OD2 E:ASP155 4.6 46.9 1.0 N E:THR26 4.6 26.0 1.0 O3' M:5GP301 4.9 64.5 0.8

Magnesium binding site 6 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:40.4 occ:1.00 OD2 E:ASP25 2.1 40.6 1.0 OD2 E:ASP155 2.2 46.9 1.0 OE2 E:GLU27 2.3 38.0 1.0 O3P E:5GP301 2.3 42.1 1.0 O1P E:5GP301 2.8 46.3 1.0 P E:5GP301 3.0 46.9 1.0 CG E:ASP25 3.1 39.1 1.0 CG E:ASP155 3.2 39.2 1.0 CD E:GLU27 3.2 41.0 1.0 OD1 E:ASP25 3.5 34.1 1.0 MG E:MG302 3.6 41.1 1.0 OE1 E:GLU27 3.6 37.1 1.0 CB E:ASP155 3.6 33.9 1.0 O E:HOH529 3.7 36.9 1.0 O E:THR26 3.8 32.0 1.0 CE2 E:TYR151 3.9 41.7 1.0 O2P E:5GP301 3.9 46.8 1.0 OH E:TYR151 3.9 42.9 1.0 NE2 E:GLN42 3.9 29.9 1.0 CZ E:TYR151 4.2 40.4 1.0 O5' E:5GP301 4.3 43.1 1.0 OD1 E:ASP155 4.3 36.2 1.0 O E:HOH408 4.5 32.6 1.0 CB E:ASP25 4.5 29.9 1.0 CG E:GLU27 4.5 31.0 1.0 C5' E:5GP301 4.7 46.7 1.0 C E:THR26 4.7 29.5 1.0 O E:HOH471 4.7 42.4 1.0 NZ E:LYS132 4.7 40.8 1.0 CD2 E:TYR151 4.8 37.3 1.0 O E:HOH496 5.0 39.4 1.0

Magnesium binding site 7 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg303 b:43.6 occ:1.00 O3P G:5GP302 2.0 48.0 1.0 O G:HOH411 2.1 40.2 1.0 OD1 G:ASP25 2.1 38.3 1.0 O G:HOH403 2.1 37.1 1.0 O G:HOH513 2.2 43.5 1.0 O G:HOH495 2.4 49.1 1.0 CG G:ASP25 3.0 39.7 1.0 OD2 G:ASP25 3.2 44.9 1.0 P G:5GP302 3.4 60.8 1.0 MG G:MG304 3.7 47.7 1.0 OD1 G:ASP84 3.8 39.8 1.0 O G:THR26 3.9 37.8 1.0 O1P G:5GP302 4.0 71.8 1.0 O5' G:5GP302 4.0 75.0 1.0 O G:HOH537 4.0 55.6 1.0 OD2 G:ASP84 4.0 45.7 1.0 O G:HOH454 4.2 29.6 1.0 O G:HOH529 4.2 49.9 1.0 O G:HOH498 4.2 34.7 1.0 C5' G:5GP302 4.2 57.0 1.0 CG G:ASP84 4.4 36.4 1.0 CB G:ASP25 4.4 33.0 1.0 N G:THR26 4.4 28.7 1.0 O G:HIS79 4.5 32.5 1.0 O2P G:5GP302 4.6 59.7 1.0 OD2 G:ASP155 4.8 51.6 1.0 CA G:ASP25 4.9 28.8 1.0 C G:THR26 5.0 40.0 1.0

Magnesium binding site 8 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg304 b:47.7 occ:1.00 OE2 G:GLU27 2.1 50.4 1.0 OD2 G:ASP155 2.2 51.6 1.0 OD2 G:ASP25 2.2 44.9 1.0 O3P G:5GP302 2.3 48.0 1.0 O2P G:5GP302 2.6 59.7 1.0 P G:5GP302 2.9 60.8 1.0 CD G:GLU27 3.0 47.3 1.0 CG G:ASP155 3.3 42.5 1.0 CG G:ASP25 3.4 39.7 1.0 OE1 G:GLU27 3.4 44.1 1.0 O5' G:5GP302 3.6 75.0 1.0 MG G:MG303 3.7 43.6 1.0 CB G:ASP155 3.7 41.7 1.0 O G:THR26 3.7 37.8 1.0 NE2 G:GLN42 3.8 32.4 1.0 OD1 G:ASP25 3.9 38.3 1.0 O G:HOH513 3.9 43.5 1.0 OH G:TYR151 4.0 43.4 1.0 CE2 G:TYR151 4.0 37.1 1.0 O1P G:5GP302 4.2 71.8 1.0 CZ G:TYR151 4.2 42.3 1.0 CG G:GLU27 4.3 34.0 1.0 OD1 G:ASP155 4.4 48.0 1.0 CB G:ASP25 4.6 33.0 1.0 O G:HOH411 4.6 40.2 1.0 C G:THR26 4.6 40.0 1.0 O G:HOH529 4.7 49.9 1.0 C5' G:5GP302 4.8 57.0 1.0 CD2 G:TYR151 4.9 35.9 1.0 CD G:GLN42 5.0 43.1 1.0

Magnesium binding site 9 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg302 b:41.0 occ:1.00 O I:HOH423 2.0 35.8 1.0 O1P I:5GP301 2.0 41.4 1.0 O I:HOH415 2.1 38.4 1.0 OD1 I:ASP25 2.2 32.8 1.0 O I:HOH526 2.2 33.3 1.0 O I:HOH468 2.3 40.2 1.0 CG I:ASP25 3.2 36.9 1.0 P I:5GP301 3.4 48.4 1.0 OD2 I:ASP25 3.5 39.1 1.0 MG I:MG303 3.7 44.3 1.0 O2P I:5GP301 3.8 49.2 1.0 O5' I:5GP301 4.0 50.7 1.0 OD1 I:ASP84 4.0 37.8 1.0 O I:THR26 4.1 33.0 1.0 O I:HOH462 4.2 44.1 1.0 O I:HOH480 4.2 33.9 1.0 OD2 I:ASP84 4.2 46.4 1.0 C5' I:5GP301 4.2 50.8 1.0 O I:HOH443 4.3 29.0 1.0 OD2 I:ASP155 4.4 48.4 1.0 O I:HIS79 4.4 29.7 1.0 CB I:ASP25 4.5 29.4 1.0 CG I:ASP84 4.6 37.2 1.0 O3P I:5GP301 4.6 44.1 1.0 N I:THR26 4.6 28.5 1.0 O3' O:5GP301 5.0 72.4 0.8

Magnesium binding site 10 out of 16 in the Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Bartonella Henselae Nrnc Cleaving Pgg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg303 b:44.3 occ:1.00 OD2 I:ASP155 2.2 48.4 1.0 OE2 I:GLU27 2.2 39.4 1.0 OD2 I:ASP25 2.3 39.1 1.0 O1P I:5GP301 2.4 41.4 1.0 O3P I:5GP301 2.7 44.1 1.0 P I:5GP301 2.9 48.4 1.0 CD I:GLU27 3.1 36.0 1.0 CG I:ASP155 3.2 44.8 1.0 CG I:ASP25 3.3 36.9 1.0 OE1 I:GLU27 3.4 36.3 1.0 MG I:MG302 3.7 41.0 1.0 CB I:ASP155 3.7 35.4 1.0 OD1 I:ASP25 3.7 32.8 1.0 CE2 I:TYR151 3.8 33.8 1.0 O I:THR26 3.8 33.0 1.0 OH I:TYR151 3.8 41.4 1.0 O2P I:5GP301 3.8 49.2 1.0 O I:HOH526 4.0 33.3 1.0 NE2 I:GLN42 4.0 34.1 1.0 CZ I:TYR151 4.1 35.7 1.0 O5' I:5GP301 4.3 50.7 1.0 OD1 I:ASP155 4.3 39.7 1.0 CG I:GLU27 4.4 31.4 1.0 O I:HOH423 4.5 35.8 1.0 NZ I:LYS132 4.6 34.4 0.5 C5' I:5GP301 4.6 50.8 1.0 CB I:ASP25 4.7 29.4 1.0 C I:THR26 4.7 32.3 1.0 CD2 I:TYR151 4.7 37.2 1.0 O I:HOH462 4.7 44.1 1.0

J.D.Lormand, H.Sondermann. Structural Characterization of Nrnc Identifies Unifying Features of Dinucleotidases To Be Published.