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Magnesium in PDB 2gxa: Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp

Protein crystallography data

The structure of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp, PDB code: 2gxa was solved by E.J.Enemark, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.65 / 3.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 100.510, 100.881, 125.023, 92.60, 111.46, 106.01
R / Rfree (%) 23.9 / 29.8

Other elements in 2gxa:

The structure of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp (pdb code 2gxa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp, PDB code: 2gxa:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2gxa

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Magnesium binding site 1 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


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 Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg21

b:25.3
occ:1.00
 O A:HOH578 2.0 25.3 1.0
O B:HOH3 2.0 25.3 1.0
O1B A:ADP1 2.2 31.4 1.0
O3B A:ADP1 2.5 31.4 1.0
O A:HOH579 2.6 25.3 1.0
PB A:ADP1 2.9 31.4 1.0
OG A:SER440 3.0 28.1 1.0
NH2 B:ARG538 3.1 53.4 1.0
OD2 A:ASP479 3.2 67.0 1.0
CB A:SER440 3.8 28.1 1.0
OD2 B:ASP497 3.9 39.2 1.0
O2A A:ADP1 3.9 31.4 1.0
O2B A:ADP1 3.9 31.4 1.0
CL A:CL41 4.0 70.2 1.0
CZ B:ARG538 4.2 53.4 1.0
O3A A:ADP1 4.3 31.4 1.0
CE B:LYS425 4.4 25.3 1.0
NZ B:LYS425 4.4 25.3 1.0
PA A:ADP1 4.4 31.4 1.0
CG A:ASP479 4.4 67.0 1.0
N A:SER440 4.5 38.3 1.0
O1A A:ADP1 4.5 31.4 1.0
NE B:ARG538 4.7 53.4 1.0
CA A:SER440 4.7 38.3 1.0
OD2 A:ASP478 4.7 54.0 1.0
NZ A:LYS439 4.8 42.8 1.0
CG B:ASP497 4.8 39.2 1.0
OD1 A:ASP478 4.9 54.0 1.0
OD1 B:ASP497 5.0 39.2 1.0

Magnesium binding site 2 out of 10 in 2gxa

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Magnesium binding site 2 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


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 Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg22

b:25.3
occ:1.00
 O C:HOH5 2.1 25.3 1.0
O B:HOH4 2.1 27.2 1.0
OG B:SER440 2.4 26.4 1.0
O1B B:ADP2 2.5 55.5 1.0
O3B B:ADP2 2.7 55.5 1.0
O B:HOH6 2.8 67.2 1.0
OD2 B:ASP479 2.9 88.8 1.0
NH2 C:ARG538 3.1 37.9 1.0
PB B:ADP2 3.1 55.5 1.0
CB B:SER440 3.7 26.4 1.0
O2A B:ADP2 3.7 55.5 1.0
OD2 C:ASP497 3.9 35.7 1.0
CL B:CL42 4.0 73.9 1.0
O2B B:ADP2 4.1 55.5 1.0
CG B:ASP479 4.1 88.8 1.0
OD1 B:ASP478 4.2 51.8 1.0
CZ C:ARG538 4.3 37.9 1.0
N B:SER440 4.4 56.8 1.0
O3A B:ADP2 4.4 55.5 1.0
PA B:ADP2 4.4 55.5 1.0
OD2 B:ASP478 4.4 51.8 1.0
O1A B:ADP2 4.4 55.5 1.0
NZ C:LYS425 4.5 36.0 1.0
CA B:SER440 4.6 56.8 1.0
CG B:ASP478 4.7 51.8 1.0
CB B:ASP479 4.8 88.8 1.0
NE C:ARG538 4.8 37.9 1.0
OG1 B:THR521 4.8 28.1 1.0
CE C:LYS425 5.0 36.0 1.0
OD1 B:ASP479 5.0 88.8 1.0
CE2 C:TYR499 5.0 45.1 1.0

Magnesium binding site 3 out of 10 in 2gxa

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Magnesium binding site 3 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


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 Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg23

b:25.3
occ:1.00
 O D:HOH9 1.8 66.4 1.0
O C:HOH7 2.3 36.1 1.0
O1B C:ADP3 2.4 70.0 1.0
OG C:SER440 2.5 50.3 1.0
OD2 C:ASP479 2.8 0.4 1.0
O C:HOH8 2.9 42.4 1.0
O3B C:ADP3 3.3 70.0 1.0
PB C:ADP3 3.4 70.0 1.0
NH2 D:ARG538 3.5 56.2 1.0
CB C:SER440 3.6 50.3 1.0
CG C:ASP479 3.9 0.4 1.0
OD2 D:ASP497 3.9 63.7 1.0
O2B C:ADP3 4.2 70.0 1.0
O2A C:ADP3 4.3 70.0 1.0
OD1 C:ASP478 4.3 63.4 1.0
O1A C:ADP3 4.3 70.0 1.0
OD2 C:ASP478 4.4 63.4 1.0
N C:SER440 4.5 64.3 1.0
NZ D:LYS425 4.6 58.6 1.0
CA C:SER440 4.6 64.3 1.0
CE D:LYS425 4.7 58.6 1.0
O3A C:ADP3 4.7 70.0 1.0
PA C:ADP3 4.7 70.0 1.0
CB C:ASP479 4.7 0.4 1.0
CZ D:ARG538 4.7 56.2 1.0
CG C:ASP478 4.7 63.4 1.0
OD1 C:ASP479 4.7 0.4 1.0
OG1 C:THR521 4.8 30.5 1.0
CG D:ASP497 5.0 63.7 1.0

Magnesium binding site 4 out of 10 in 2gxa

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Magnesium binding site 4 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


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 Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg24

b:50.4
occ:1.00
 O1B D:ADP4 2.1 0.8 1.0
OG D:SER440 2.4 0.3 1.0
O3B D:ADP4 3.1 0.8 1.0
PB D:ADP4 3.1 0.8 1.0
OH E:TYR534 3.2 88.1 1.0
OD2 D:ASP479 3.3 0.8 1.0
CB D:SER440 3.3 0.3 1.0
O1A D:ADP4 3.9 0.8 1.0
O2B D:ADP4 4.0 0.8 1.0
OD2 E:ASP497 4.1 0.1 1.0
OD2 D:ASP478 4.1 0.0 1.0
CE2 E:TYR499 4.2 72.3 1.0
O2A D:ADP4 4.2 0.8 1.0
O3A D:ADP4 4.4 0.8 1.0
PA D:ADP4 4.4 0.8 1.0
CD2 E:TYR499 4.4 72.3 1.0
CG D:ASP479 4.5 0.8 1.0
CZ E:TYR534 4.5 88.1 1.0
CA D:SER440 4.6 87.0 1.0
OD1 D:ASP478 4.6 0.0 1.0
N D:SER440 4.7 87.0 1.0
CG E:ASP497 4.7 0.1 1.0
CG D:ASP478 4.8 0.0 1.0
ND2 E:ASN494 4.9 0.3 1.0

Magnesium binding site 5 out of 10 in 2gxa

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Magnesium binding site 5 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg25

b:30.1
occ:1.00
 OG E:SER440 2.1 96.1 1.0
O3B E:ADP5 2.9 77.6 1.0
O1B E:ADP5 3.0 77.6 1.0
CB E:SER440 3.2 96.1 1.0
OD2 E:ASP479 3.3 1.0 1.0
PB E:ADP5 3.5 77.6 1.0
O2A E:ADP5 4.1 77.6 1.0
OD2 E:ASP478 4.3 77.3 1.0
OH F:TYR534 4.4 60.4 1.0
N E:SER440 4.4 65.4 1.0
OD1 E:ASP478 4.4 77.3 1.0
CA E:SER440 4.4 65.4 1.0
CG E:ASP479 4.4 1.0 1.0
O2B E:ADP5 4.5 77.6 1.0
O1A E:ADP5 4.6 77.6 1.0
CG E:ASP478 4.7 77.3 1.0
PA E:ADP5 4.7 77.6 1.0
CE2 F:TYR499 4.8 79.3 1.0
O3A E:ADP5 4.8 77.6 1.0

Magnesium binding site 6 out of 10 in 2gxa

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Magnesium binding site 6 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg27

b:33.5
occ:1.00
 O G:HOH12 2.1 25.3 1.0
O1B G:ADP7 2.3 58.7 1.0
O3B G:ADP7 2.3 58.7 1.0
O G:HOH10 2.4 25.3 1.0
O G:HOH11 2.6 44.3 1.0
PB G:ADP7 2.8 58.7 1.0
OG G:SER440 2.8 25.3 1.0
OD2 G:ASP479 3.2 0.6 1.0
O2A G:ADP7 3.5 58.7 1.0
NH2 H:ARG538 3.5 70.6 1.0
O2B G:ADP7 3.8 58.7 1.0
CB G:SER440 3.9 25.3 1.0
O3A G:ADP7 4.1 58.7 1.0
PA G:ADP7 4.2 58.7 1.0
O1A G:ADP7 4.2 58.7 1.0
OD2 H:ASP497 4.4 73.8 1.0
N G:SER440 4.4 66.2 1.0
CG G:ASP479 4.4 0.6 1.0
NZ H:LYS425 4.5 51.3 1.0
NZ G:LYS439 4.7 42.9 1.0
CZ H:ARG538 4.7 70.6 1.0
CA G:SER440 4.8 66.2 1.0
OD2 G:ASP478 4.8 39.6 1.0
CE H:LYS425 4.9 51.3 1.0
OD1 G:ASP478 4.9 39.6 1.0

Magnesium binding site 7 out of 10 in 2gxa

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Magnesium binding site 7 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg28

b:25.3
occ:1.00
 O I:HOH15 2.3 74.2 1.0
OG H:SER440 2.4 92.0 1.0
O1B H:ADP8 2.5 70.0 1.0
O H:HOH14 2.6 0.4 1.0
OD2 H:ASP479 2.7 0.4 1.0
O H:HOH13 2.7 27.9 1.0
O3B H:ADP8 3.2 70.0 1.0
PB H:ADP8 3.4 70.0 1.0
CL H:CL48 3.4 80.2 1.0
NH2 I:ARG538 3.5 49.7 1.0
CB H:SER440 3.6 92.0 1.0
CG H:ASP479 3.8 0.4 1.0
O2B H:ADP8 4.1 70.0 1.0
O2A H:ADP8 4.3 70.0 1.0
OD2 I:ASP497 4.3 0.9 1.0
N H:SER440 4.4 86.8 1.0
O1A H:ADP8 4.5 70.0 1.0
OD2 H:ASP478 4.6 53.6 1.0
CB H:ASP479 4.6 0.4 1.0
CA H:SER440 4.6 86.8 1.0
OD1 H:ASP478 4.6 53.6 1.0
OD1 H:ASP479 4.6 0.4 1.0
NZ I:LYS425 4.7 56.3 1.0
CZ I:ARG538 4.7 49.7 1.0
O3A H:ADP8 4.7 70.0 1.0
CE I:LYS425 4.8 56.3 1.0
PA H:ADP8 4.8 70.0 1.0
NZ H:LYS439 4.8 60.7 1.0
CG H:ASP478 4.9 53.6 1.0

Magnesium binding site 8 out of 10 in 2gxa

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Magnesium binding site 8 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg29

b:55.7
occ:1.00
 OG I:SER440 2.0 71.1 1.0
O1B J:ADP9 2.7 89.9 1.0
OD2 I:ASP479 2.9 0.7 1.0
CB I:SER440 3.3 71.1 1.0
O3B J:ADP9 3.4 89.9 1.0
PB J:ADP9 3.5 89.9 1.0
O2B J:ADP9 3.9 89.9 1.0
CG I:ASP479 4.0 0.7 1.0
OD1 I:ASP478 4.0 0.1 1.0
N I:SER440 4.0 72.9 1.0
CA I:SER440 4.2 72.9 1.0
OG1 I:THR521 4.2 50.6 1.0
OD2 I:ASP478 4.3 0.1 1.0
CG I:ASP478 4.5 0.1 1.0
OH J:TYR534 4.5 93.2 1.0
CB I:ASP479 4.6 0.7 1.0
CB I:THR521 4.6 50.6 1.0
OD1 I:ASP479 4.8 0.7 1.0
NZ I:LYS439 4.9 89.7 1.0
CB I:LYS439 4.9 89.7 1.0
N I:ASP479 4.9 91.1 1.0
O3A J:ADP9 5.0 89.9 1.0

Magnesium binding site 9 out of 10 in 2gxa

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Magnesium binding site 9 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg30

b:36.2
occ:1.00
 OG J:SER440 2.4 57.2 1.0
O3B K:ADP10 2.9 67.9 1.0
O1B K:ADP10 2.9 67.9 1.0
CB J:SER440 3.3 57.2 1.0
OD2 J:ASP479 3.3 0.7 1.0
PB K:ADP10 3.5 67.9 1.0
OH K:TYR534 3.8 49.3 1.0
OD2 K:ASP497 4.0 65.1 1.0
O2A K:ADP10 4.2 67.9 1.0
OD2 J:ASP478 4.3 0.5 1.0
O2B K:ADP10 4.4 67.9 1.0
CG K:ASP497 4.5 65.1 1.0
CG J:ASP479 4.6 0.7 1.0
CA J:SER440 4.6 89.1 1.0
N J:SER440 4.6 89.1 1.0
O1A K:ADP10 4.6 67.9 1.0
OD1 J:ASP478 4.7 0.5 1.0
CE2 K:TYR499 4.7 64.8 1.0
O3A K:ADP10 4.8 67.9 1.0
PA K:ADP10 4.8 67.9 1.0
CG J:ASP478 4.9 0.5 1.0
CD2 K:TYR499 4.9 64.8 1.0
OD1 K:ASP497 4.9 65.1 1.0
CZ K:TYR534 5.0 49.3 1.0

Magnesium binding site 10 out of 10 in 2gxa

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Magnesium binding site 10 out of 10 in the Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Papillomavirus E1 Hexameric Helicase with Ssdna and Mgadp within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg31

b:51.7
occ:1.00
 OG K:SER440 2.0 82.7 1.0
O2A L:ADP11 2.2 84.2 1.0
O3B L:ADP11 2.6 84.2 1.0
O1A L:ADP11 2.8 84.2 1.0
CB K:SER440 3.1 82.7 1.0
PA L:ADP11 3.1 84.2 1.0
OD2 K:ASP479 3.2 0.4 1.0
O1B L:ADP11 3.6 84.2 1.0
PB L:ADP11 3.6 84.2 1.0
O3A L:ADP11 3.8 84.2 1.0
NH1 L:ARG493 4.0 95.5 1.0
C5' L:ADP11 4.0 0.9 1.0
OD2 K:ASP478 4.1 82.0 1.0
O5' L:ADP11 4.1 0.9 1.0
OD1 K:ASP478 4.2 82.0 1.0
CA K:SER440 4.3 76.0 1.0
N K:SER440 4.3 76.0 1.0
CG K:ASP479 4.4 0.4 1.0
CG K:ASP478 4.6 82.0 1.0
CB K:ASP479 5.0 0.4 1.0

Reference:

E.J.Enemark, L.Joshua-Tor. Mechanism of Dna Translocation in A Replicative Hexameric Helicase. Nature V. 442 270 2006.
ISSN: ISSN 0028-0836
PubMed: 16855583
DOI: 10.1038/NATURE04943
Page generated: Tue Aug 13 23:37:23 2024

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