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Magnesium in PDB 2vn2: Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426, PDB code: 2vn2 was solved by C.-Y.Huang, Y.-W.Chang, W.-T.Chen, Y.-J.Sun, C.-D.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.49 / 2.3
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.514, 124.707, 157.230, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426 (pdb code 2vn2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426, PDB code: 2vn2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vn2

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Magnesium binding site 1 out of 4 in the Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1120

b:35.2
occ:1.00
NE2 A:HIS109 2.2 45.7 1.0
OE1 A:GLN113 2.3 22.7 1.0
ND1 A:HIS24 2.3 30.1 1.0
NE2 A:GLN113 2.3 37.1 1.0
OE1 A:GLN27 2.4 51.7 1.0
NE2 A:GLN27 2.6 53.5 1.0
CD A:GLN27 2.6 50.2 1.0
CD A:GLN113 2.6 34.9 1.0
CE1 A:HIS24 2.8 30.1 1.0
CD2 A:HIS109 3.1 43.5 1.0
CE1 A:HIS109 3.2 44.6 1.0
CG A:HIS24 3.6 27.4 1.0
CG A:GLN27 3.9 45.3 1.0
NE2 A:HIS24 4.1 29.7 1.0
CB A:GLN27 4.2 40.0 1.0
CB A:HIS24 4.3 26.2 1.0
CG A:GLN113 4.3 33.3 1.0
CG A:HIS109 4.3 41.2 1.0
ND1 A:HIS109 4.3 44.0 1.0
CD2 A:HIS24 4.5 27.0 1.0
O A:GLY23 4.8 28.6 1.0
CA A:HIS24 4.9 25.6 1.0

Magnesium binding site 2 out of 4 in 2vn2

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Magnesium binding site 2 out of 4 in the Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1120

b:21.8
occ:1.00
NE2 B:GLN113 2.2 58.9 1.0
OE1 B:GLN113 2.3 59.5 1.0
CD B:GLN113 2.3 57.3 1.0
OE1 B:GLN27 2.4 26.0 1.0
NE2 B:HIS24 2.6 33.4 1.0
CD2 B:HIS24 2.7 30.7 1.0
NE2 B:HIS109 2.8 40.7 1.0
O B:HOH2039 3.0 39.1 1.0
CD2 B:HIS109 3.3 39.6 1.0
CG B:GLN113 3.5 53.7 1.0
CD B:GLN27 3.7 36.5 1.0
CB B:GLN113 3.7 49.2 1.0
CE1 B:HIS109 3.8 39.4 1.0
CE1 B:HIS24 3.9 33.2 1.0
CG B:HIS24 4.0 30.0 1.0
NE2 B:GLN27 4.4 40.7 1.0
CG B:HIS109 4.5 38.4 1.0
ND1 B:HIS24 4.6 32.6 1.0
ND1 B:HIS109 4.7 39.1 1.0
CD2 B:LEU110 4.7 29.3 1.0
O B:HIS109 4.9 35.9 1.0

Magnesium binding site 3 out of 4 in 2vn2

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Magnesium binding site 3 out of 4 in the Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1120

b:18.4
occ:1.00
NE2 C:HIS109 2.2 36.0 1.0
OE1 C:GLN27 2.3 55.7 1.0
OE1 C:GLN113 2.3 35.2 1.0
NE2 C:GLN27 2.3 53.9 1.0
ND1 C:HIS24 2.4 29.1 1.0
CD C:GLN27 2.4 50.6 1.0
CD C:GLN113 2.8 41.6 1.0
CE1 C:HIS109 3.0 35.0 1.0
CE1 C:HIS24 3.1 27.5 1.0
NE2 C:GLN113 3.2 43.9 1.0
CD2 C:HIS109 3.3 34.7 1.0
CG C:HIS24 3.5 27.5 1.0
CG C:GLN27 3.7 46.4 1.0
CG C:GLN113 3.9 40.6 1.0
CB C:HIS24 3.9 26.8 1.0
CB C:GLN27 4.1 40.1 1.0
ND1 C:HIS109 4.2 35.1 1.0
NE2 C:HIS24 4.4 27.2 1.0
CG C:HIS109 4.4 34.0 1.0
CD2 C:HIS24 4.6 28.3 1.0
CA C:HIS24 4.6 26.4 1.0
O C:GLY23 4.8 27.2 1.0

Magnesium binding site 4 out of 4 in 2vn2

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Magnesium binding site 4 out of 4 in the Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the N-Terminal Domain of Dnad Protein From Geobacillus Kaustophilus HTA426 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1120

b:23.7
occ:1.00
OE1 D:GLN27 2.1 48.5 1.0
NE2 D:HIS109 2.1 37.6 1.0
NE2 D:GLN27 2.3 45.5 1.0
OE1 D:GLN113 2.3 42.1 1.0
CD D:GLN27 2.4 45.6 1.0
ND1 D:HIS24 2.5 31.9 1.0
CE1 D:HIS109 3.0 37.1 1.0
CD D:GLN113 3.2 45.0 1.0
CE1 D:HIS24 3.2 32.7 1.0
CD2 D:HIS109 3.2 36.0 1.0
NE2 D:GLN113 3.4 44.4 1.0
CG D:GLN27 3.6 42.5 1.0
CG D:HIS24 3.6 30.2 1.0
CB D:GLN27 3.9 37.9 1.0
CB D:HIS24 4.1 26.7 1.0
ND1 D:HIS109 4.2 36.4 1.0
CG D:HIS109 4.3 35.0 1.0
NE2 D:HIS24 4.4 32.9 1.0
CA D:HIS24 4.6 26.1 1.0
CG D:GLN113 4.6 43.3 1.0
CD2 D:HIS24 4.7 30.7 1.0
O D:HIS24 4.9 26.0 1.0
O D:GLY23 4.9 27.0 1.0

Reference:

C.-Y.Huang, Y.-W.Chang, W.-T.Chen. Crystal Structure of the N-Terminal Domain of Geobacillus Kaustophilus HTA426 Dnad Protein. Biochem.Biophys.Res.Commun. V. 375 220 2008.
ISSN: ISSN 0006-291X
PubMed: 18703019
DOI: 10.1016/J.BBRC.2008.07.160
Page generated: Mon Dec 14 07:42:23 2020

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