Magnesium in PDB 5mdn: Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis

Enzymatic activity of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis

All present enzymatic activity of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis:
2.7.7.7;

Protein crystallography data

The structure of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis, PDB code: 5mdn was solved by J.Guo, W.Zhang, A.R.Coker, S.P.Wood, J.B.Cooper, N.Rashid, M.Akhtar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.25 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.190, 100.742, 119.335, 90.00, 94.72, 90.00
R / Rfree (%) 25.2 / 29

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis (pdb code 5mdn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis, PDB code: 5mdn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5mdn

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Magnesium binding site 1 out of 6 in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:35.6
occ:1.00
 OD1 A:ASP7 2.5 58.9 1.0
OD2 A:ASP363 2.8 63.6 1.0
CG A:ASP7 3.3 53.2 1.0
OD2 A:ASP7 3.4 52.4 1.0
CG A:ASP363 3.4 56.6 1.0
OG A:SER269 3.5 44.9 1.0
OD1 A:ASP363 3.5 61.1 1.0
CB A:SER269 4.0 44.5 1.0
O A:ALA8 4.2 56.0 1.0
NE2 A:HIS267 4.3 46.3 1.0
OE1 A:GLN364 4.5 64.2 1.0
CA A:SER269 4.6 45.0 1.0
CB A:ASP363 4.7 52.5 1.0
CB A:ASP7 4.7 51.2 1.0
N A:ALA8 4.9 52.8 1.0

Magnesium binding site 2 out of 6 in 5mdn

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Magnesium binding site 2 out of 6 in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:82.1
occ:1.00
 OD1 A:ASP169 2.7 89.2 1.0
CG A:ASP169 3.6 78.2 1.0
O A:ILE170 3.8 75.3 1.0
OD2 A:ASP236 3.9 70.0 1.0
OD1 A:ASP236 3.9 62.7 1.0
OD2 A:ASP169 4.0 80.5 1.0
O A:TYR230 4.1 54.0 1.0
CG A:ASP236 4.3 61.1 1.0
N A:ILE170 4.4 62.3 1.0
OE2 A:GLU171 4.6 72.4 1.0
CB A:ASP169 4.8 67.9 1.0
C A:ILE170 4.8 66.0 1.0
CA A:ASP169 4.9 63.1 1.0
CG1 A:ILE170 5.0 56.6 1.0

Magnesium binding site 3 out of 6 in 5mdn

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Magnesium binding site 3 out of 6 in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:90.3
occ:1.00
 OE1 A:GLU171 3.7 74.8 1.0
O A:GLY313 4.5 83.8 1.0
CD A:GLU171 4.8 75.8 1.0
O A:VAL172 4.8 79.0 1.0

Magnesium binding site 4 out of 6 in 5mdn

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Magnesium binding site 4 out of 6 in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:44.2
occ:1.00
 OD1 B:ASP7 2.4 58.5 1.0
OD2 B:ASP363 2.7 63.5 1.0
CG B:ASP7 3.0 56.7 1.0
OD2 B:ASP7 3.1 58.2 1.0
CG B:ASP363 3.4 52.6 1.0
OG B:SER269 3.4 52.2 1.0
OD1 B:ASP363 3.6 52.7 1.0
CB B:SER269 4.0 49.1 1.0
O B:ALA8 4.2 63.7 1.0
NE2 B:HIS267 4.4 47.3 1.0
CB B:ASP7 4.5 55.8 1.0
CA B:SER269 4.5 48.7 1.0
CB B:ASP363 4.6 50.2 1.0
NE2 B:GLN364 4.7 56.0 1.0
N B:ALA8 4.9 56.8 1.0
O B:ARG273 4.9 46.4 1.0

Magnesium binding site 5 out of 6 in 5mdn

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Magnesium binding site 5 out of 6 in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:66.0
occ:1.00
 OD1 B:ASP169 3.1 65.2 1.0
OD1 B:ASP236 3.8 52.1 1.0
O B:TYR230 3.8 50.1 1.0
OD2 B:ASP236 3.9 58.8 1.0
O B:ILE170 3.9 66.2 1.0
CG B:ASP169 4.1 61.9 1.0
CG B:ASP236 4.3 53.4 1.0
OD2 B:ASP169 4.4 65.4 1.0
N B:ILE170 4.7 55.6 1.0
OE2 B:GLU171 4.8 61.1 1.0
C B:TYR230 5.0 47.2 1.0

Magnesium binding site 6 out of 6 in 5mdn

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Magnesium binding site 6 out of 6 in the Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:72.6
occ:1.00
 OE1 B:GLU171 3.6 59.1 1.0
O B:VAL172 4.3 63.5 1.0
N B:VAL172 4.5 58.4 1.0
ND2 B:ASN174 4.7 72.9 1.0
O B:GLY313 4.7 63.8 1.0
CD B:GLU171 4.7 62.0 1.0
CG1 B:VAL316 4.8 72.1 1.0

Reference:

J.Guo, W.Zhang, A.R.Coker, S.P.Wood, J.B.Cooper, S.Ahmad, S.Ali, N.Rashid, M.Akhtar. Structure of the Family B Dna Polymerase From the Hyperthermophilic Archaeon Pyrobaculum Calidifontis. Acta Crystallogr D Struct V. 73 420 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28471366
DOI: 10.1107/S2059798317004090
Page generated: Mon Dec 14 20:51:15 2020

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