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Magnesium in PDB 3ncr: GLNK2 From Archaeoglubus Fulgidus, Adp Complex

Protein crystallography data

The structure of GLNK2 From Archaeoglubus Fulgidus, Adp Complex, PDB code: 3ncr was solved by S.Helfmann, W.Lue, C.Litz, S.L.A.Andrade, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.62 / 1.44
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 123.830, 123.830, 125.459, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20

Other elements in 3ncr:

The structure of GLNK2 From Archaeoglubus Fulgidus, Adp Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the GLNK2 From Archaeoglubus Fulgidus, Adp Complex (pdb code 3ncr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the GLNK2 From Archaeoglubus Fulgidus, Adp Complex, PDB code: 3ncr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3ncr

Go back to Magnesium Binding Sites List in 3ncr
Magnesium binding site 1 out of 3 in the GLNK2 From Archaeoglubus Fulgidus, Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of GLNK2 From Archaeoglubus Fulgidus, Adp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg124

b:49.1
occ:0.50
O B:HOH142 1.7 37.1 1.0
O1B A:ADP120 1.9 30.7 1.0
O1A A:ADP120 1.9 26.8 1.0
O A:HOH176 2.3 32.1 1.0
PB A:ADP120 3.0 28.6 1.0
NZ A:LYS90 3.1 41.9 1.0
PA A:ADP120 3.1 23.9 1.0
O3A A:ADP120 3.2 27.6 1.0
O A:HOH288 3.4 41.1 1.0
O3B A:ADP120 3.6 34.8 1.0
CE A:LYS90 3.9 33.5 1.0
O5' A:ADP120 4.0 22.1 1.0
N A:GLN38 4.0 27.8 1.0
CG A:GLN38 4.1 36.5 1.0
NH1 B:ARG101 4.2 62.4 1.0
O2B A:ADP120 4.2 31.0 1.0
O2A A:ADP120 4.3 20.9 1.0
CA A:GLY37 4.3 23.9 1.0
O B:ACT121 4.3 51.9 1.0
N7 A:ADP120 4.4 19.6 1.0
C8 A:ADP120 4.5 19.0 1.0
C B:ACT121 4.6 51.5 1.0
CB A:GLN38 4.7 30.9 1.0
C A:GLY37 4.7 25.8 1.0
OXT B:ACT121 4.7 51.2 1.0

Magnesium binding site 2 out of 3 in 3ncr

Go back to Magnesium Binding Sites List in 3ncr
Magnesium binding site 2 out of 3 in the GLNK2 From Archaeoglubus Fulgidus, Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of GLNK2 From Archaeoglubus Fulgidus, Adp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg123

b:41.3
occ:0.50
O B:HOH145 1.9 22.6 1.0
O B:HOH171 2.0 23.0 1.0
O1A B:ADP120 2.0 19.1 1.0
O1B B:ADP120 2.0 20.2 1.0
PB B:ADP120 3.2 21.2 1.0
PA B:ADP120 3.2 18.9 1.0
O3A B:ADP120 3.4 20.1 1.0
NZ B:LYS90 3.5 27.6 1.0
O B:HOH202 3.5 30.4 1.0
N B:GLN38 3.9 20.2 1.0
O1 B:PO4122 3.9 23.4 1.0
CH3 C:ACT121 4.0 41.5 1.0
O3B B:ADP120 4.0 23.9 1.0
O5' B:ADP120 4.0 19.1 1.0
O3 B:PO4122 4.0 28.8 1.0
CG B:GLN38 4.1 25.8 1.0
N7 B:ADP120 4.1 16.3 1.0
CA B:GLY37 4.1 17.5 1.0
C8 B:ADP120 4.2 17.8 1.0
O2B B:ADP120 4.4 23.1 1.0
O2A B:ADP120 4.4 19.1 1.0
O2 B:PO4122 4.5 24.2 1.0
P B:PO4122 4.5 25.3 1.0
C C:ACT121 4.5 40.6 1.0
NE2 B:GLN38 4.5 33.3 1.0
C B:GLY37 4.5 19.1 1.0
CB B:GLN38 4.6 25.1 1.0
CD B:GLN38 4.7 32.3 1.0
OXT C:ACT121 4.8 44.5 1.0
CE B:LYS90 4.9 28.5 1.0
CA B:GLN38 4.9 22.5 1.0

Magnesium binding site 3 out of 3 in 3ncr

Go back to Magnesium Binding Sites List in 3ncr
Magnesium binding site 3 out of 3 in the GLNK2 From Archaeoglubus Fulgidus, Adp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of GLNK2 From Archaeoglubus Fulgidus, Adp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg123

b:67.3
occ:0.50
O1A C:ADP120 1.7 27.9 1.0
O A:HOH145 1.9 39.2 1.0
O1B C:ADP120 2.0 31.4 1.0
PA C:ADP120 2.9 25.5 1.0
PB C:ADP120 2.9 29.8 1.0
O C:HOH253 3.0 30.2 1.0
O3A C:ADP120 3.1 28.1 1.0
O A:HOH254 3.1 43.5 1.0
NZ C:LYS90 3.2 40.6 1.0
O3B C:ADP120 3.3 35.7 1.0
NH1 A:ARG101 3.7 61.1 0.0
NH2 A:ARG101 3.8 63.4 0.0
O2A C:ADP120 3.8 25.6 1.0
CE C:LYS90 3.9 32.0 1.0
O5' C:ADP120 4.0 22.1 1.0
O A:HOH345 4.0 53.4 1.0
CZ A:ARG101 4.1 60.2 0.0
O2B C:ADP120 4.2 31.6 1.0
N C:GLN38 4.5 27.7 1.0
OE1 C:GLN38 4.5 60.3 1.0
CA C:GLY37 4.7 24.2 1.0
O C:HOH383 4.7 30.3 1.0
C8 C:ADP120 4.8 20.0 1.0
N7 C:ADP120 4.9 19.6 1.0
CB C:GLN38 5.0 33.2 1.0

Reference:

S.Helfmann, W.Lu, C.Litz, S.L.Andrade. Cooperative Binding of Mgatp and Mgadp in the Trimeric P(II) Protein GLNK2 From Archaeoglobus Fulgidus. J.Mol.Biol. V. 402 165 2010.
ISSN: ISSN 0022-2836
PubMed: 20643148
DOI: 10.1016/J.JMB.2010.07.020
Page generated: Mon Dec 14 08:28:22 2020

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