Magnesium in PDB 7npe: Vibrio Cholerae PARA2-Adp

Protein crystallography data

The structure of Vibrio Cholerae PARA2-Adp, PDB code: 7npe was solved by A.V.Parker, J.R.C.Bergeron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.59 / 3.18
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 199.205, 199.205, 260.066, 90, 90, 120
R / Rfree (%) 26.2 / 30.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Vibrio Cholerae PARA2-Adp (pdb code 7npe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Vibrio Cholerae PARA2-Adp, PDB code: 7npe:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7npe

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Magnesium binding site 1 out of 4 in the Vibrio Cholerae PARA2-Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vibrio Cholerae PARA2-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg451

b:56.9
occ:1.00
O2B A:ADP450 1.9 58.1 1.0
OG A:SER125 1.9 86.7 1.0
O3B A:ADP450 1.9 63.0 1.0
O1A A:ADP450 1.9 67.7 1.0
PB A:ADP450 2.4 62.1 1.0
H A:SER125 2.7 110.8 1.0
HB2 A:SER125 2.7 91.6 1.0
CB A:SER125 2.8 91.6 1.0
PA A:ADP450 2.9 67.2 1.0
O3A A:ADP450 3.0 64.9 1.0
N A:SER125 3.4 110.8 1.0
HB3 A:SER125 3.7 91.6 1.0
O1B A:ADP450 3.7 63.0 1.0
CA A:SER125 3.7 83.8 1.0
O2A A:ADP450 3.8 67.7 1.0
HZ1 A:LYS124 3.8 94.1 1.0
O5' A:ADP450 4.2 68.0 1.0
HB3 A:LYS124 4.2 104.3 1.0
H A:MET126 4.3 91.8 1.0
HA A:SER125 4.4 83.8 1.0
HZ2 A:LYS124 4.4 94.1 1.0
NZ A:LYS124 4.6 94.1 1.0
H A:LYS124 4.6 91.5 1.0
C A:LYS124 4.7 91.2 1.0
HE2 A:LYS124 4.7 78.9 1.0
H A:GLY121 4.7 87.8 1.0
HG2 A:LYS124 4.7 99.0 1.0
C A:SER125 4.7 81.4 1.0
N A:MET126 4.9 91.8 1.0
CB A:LYS124 5.0 104.3 1.0

Magnesium binding site 2 out of 4 in 7npe

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Magnesium binding site 2 out of 4 in the Vibrio Cholerae PARA2-Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vibrio Cholerae PARA2-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg451

b:66.2
occ:1.00
O1B B:ADP450 1.9 67.6 1.0
O3B B:ADP450 1.9 69.1 1.0
O1A B:ADP450 2.0 73.3 1.0
OG B:SER125 2.0 78.4 1.0
PB B:ADP450 2.4 69.2 1.0
HB2 B:SER125 2.6 81.8 1.0
H B:SER125 2.7 86.8 1.0
CB B:SER125 2.8 81.8 1.0
HG B:SER125 2.9 78.4 1.0
PA B:ADP450 3.0 72.9 1.0
O3A B:ADP450 3.1 71.1 1.0
HG2 B:LYS124 3.5 112.0 1.0
N B:SER125 3.5 86.8 1.0
HB3 B:SER125 3.7 81.8 1.0
O2B B:ADP450 3.7 69.1 1.0
O2A B:ADP450 3.8 73.3 1.0
CA B:SER125 3.8 77.3 1.0
O5' B:ADP450 4.2 73.8 1.0
HZ3 B:LYS124 4.2 112.9 1.0
H B:MET126 4.3 85.2 1.0
H B:LYS124 4.3 137.7 1.0
HA B:SER125 4.5 77.3 1.0
HZ2 B:LYS124 4.5 112.9 1.0
H B:GLY121 4.6 103.5 1.0
CG B:LYS124 4.6 112.0 1.0
OD2 B:ASP257 4.6 100.4 1.0
C B:LYS124 4.7 92.6 1.0
N B:LYS124 4.8 137.7 1.0
HG3 B:LYS124 4.8 112.0 1.0
C B:SER125 4.8 76.6 1.0
NZ B:LYS124 4.9 112.9 1.0
HA2 B:GLY259 4.9 94.6 1.0
N B:MET126 4.9 85.2 1.0
H B:GLY123 5.0 120.5 1.0

Magnesium binding site 3 out of 4 in 7npe

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Magnesium binding site 3 out of 4 in the Vibrio Cholerae PARA2-Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Vibrio Cholerae PARA2-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg451

b:63.5
occ:1.00
O3B C:ADP450 1.9 63.1 1.0
O2B C:ADP450 1.9 63.1 1.0
OG C:SER125 2.0 115.8 1.0
PB C:ADP450 2.5 65.5 1.0
HG C:SER125 2.8 115.8 1.0
H C:SER125 2.9 134.4 1.0
HB2 C:SER125 2.9 111.9 1.0
CB C:SER125 3.0 111.9 1.0
O2A C:ADP450 3.5 74.6 1.0
O1B C:ADP450 3.6 66.8 1.0
O3A C:ADP450 3.6 69.9 1.0
N C:SER125 3.7 134.4 1.0
HB3 C:SER125 3.8 111.9 1.0
PA C:ADP450 3.9 73.8 1.0
CA C:SER125 3.9 108.6 1.0
HB3 C:LYS124 4.0 109.5 1.0
HE2 C:LYS124 4.1 77.1 1.0
HG2 C:LYS124 4.2 103.1 1.0
HA2 C:GLY259 4.2 96.5 1.0
O1A C:ADP450 4.2 74.6 1.0
HZ3 C:LYS124 4.2 72.4 1.0
OD2 C:ASP257 4.3 106.1 1.0
HD3 C:PRO260 4.4 110.9 1.0
H C:LYS124 4.4 98.5 1.0
HA C:SER125 4.5 108.6 1.0
H C:GLY121 4.7 100.3 1.0
H C:MET126 4.8 89.4 1.0
C C:LYS124 4.8 113.3 1.0
CB C:LYS124 4.8 109.5 1.0
OD2 C:ASP151 4.9 102.2 1.0
OD1 C:ASP257 4.9 103.8 1.0
NZ C:LYS124 4.9 72.4 1.0
CE C:LYS124 5.0 77.1 1.0
CG C:LYS124 5.0 103.1 1.0

Magnesium binding site 4 out of 4 in 7npe

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Magnesium binding site 4 out of 4 in the Vibrio Cholerae PARA2-Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Vibrio Cholerae PARA2-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg451

b:74.5
occ:1.00
O2B D:ADP450 1.9 73.6 1.0
O1B D:ADP450 2.0 73.6 1.0
O1A D:ADP450 2.0 75.4 1.0
OG D:SER125 2.0 115.3 1.0
PB D:ADP450 2.4 73.8 1.0
HB2 D:SER125 2.4 104.4 1.0
CB D:SER125 2.7 104.4 1.0
H D:SER125 2.7 101.7 1.0
HG D:SER125 2.9 115.3 1.0
PA D:ADP450 3.0 75.3 1.0
O3A D:ADP450 3.1 74.5 1.0
N D:SER125 3.4 101.7 1.0
HG2 D:LYS124 3.5 129.6 1.0
HB3 D:SER125 3.6 104.4 1.0
CA D:SER125 3.6 102.6 1.0
O2A D:ADP450 3.7 75.4 1.0
O3B D:ADP450 3.7 73.6 1.0
HA D:SER125 4.2 102.6 1.0
HZ2 D:LYS124 4.3 145.6 1.0
H D:MET126 4.3 96.8 1.0
O5' D:ADP450 4.3 75.8 1.0
HZ3 D:LYS124 4.3 145.6 1.0
H D:LYS124 4.5 123.9 1.0
C D:LYS124 4.5 98.6 1.0
OD2 D:ASP257 4.6 98.0 1.0
CG D:LYS124 4.6 129.6 1.0
H D:GLY121 4.6 114.4 1.0
C D:SER125 4.7 106.6 1.0
NZ D:LYS124 4.8 145.6 1.0
HA2 D:GLY259 4.9 96.4 1.0
N D:LYS124 4.9 123.9 1.0
HG3 D:LYS124 4.9 129.6 1.0
N D:MET126 5.0 96.8 1.0

Reference:

A.V.Parker, D.Mann, S.B.Tzokov, L.C.Hwang, J.R.C.Bergeron. The Cryo-Em Structure of the Bacterial Type I Segregation Filament Reveals Para S Conformational Plasticity Upon Dna Binding To Be Published.
Page generated: Sat Aug 21 16:46:31 2021

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