Atomistry » Magnesium » PDB 5m5l-5mh5 » 5mdn
Atomistry »
  Magnesium »
    PDB 5m5l-5mh5 »
      5mdn »

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

Go back to Magnesium Binding Sites List in 5mdn
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

Go back to Magnesium Binding Sites List in 5mdn
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

Go back to Magnesium Binding Sites List in 5mdn
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

Go back to Magnesium Binding Sites List in 5mdn
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

Go back to Magnesium Binding Sites List in 5mdn
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

Go back to Magnesium Binding Sites List in 5mdn
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: Tue Aug 12 14:57:06 2025

Last articles

Mg in 5WMB
Mg in 5WM8
Mg in 5WNO
Mg in 5WNI
Mg in 5WMT
Mg in 5WM1
Mg in 5WM6
Mg in 5WM4
Mg in 5WKC
Mg in 5WM3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy