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Magnesium in PDB 4ki8: Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State

Protein crystallography data

The structure of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State, PDB code: 4ki8 was solved by X.Fei, D.Yang, N.Laronde-Leblanc, G.H.Lorimer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.17 / 2.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 235.222, 141.655, 156.693, 90.00, 113.84, 90.00
R / Rfree (%) 16.6 / 20.3

Other elements in 4ki8:

The structure of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State also contains other interesting chemical elements:

Potassium (K) 9 atoms
Calcium (Ca) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State (pdb code 4ki8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State, PDB code: 4ki8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4ki8

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Magnesium binding site 1 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:33.9
occ:1.00
 O A:HOH716 2.0 44.5 1.0
O A:HOH710 2.1 32.8 1.0
O A:HOH750 2.1 48.5 1.0
O3B A:ADP601 2.2 49.5 1.0
OD1 A:ASP87 2.2 72.9 1.0
OD2 A:ASP87 2.3 63.8 1.0
O2A A:ADP601 2.4 39.7 1.0
CG A:ASP87 2.6 66.5 1.0
PB A:ADP601 3.3 57.0 1.0
O1B A:ADP601 3.4 58.3 1.0
PA A:ADP601 3.7 51.8 1.0
O3A A:ADP601 3.9 75.2 1.0
O A:HOH711 4.0 43.6 1.0
CB A:ASP87 4.1 56.7 1.0
C5' A:ADP601 4.2 56.1 1.0
O A:HOH749 4.4 68.6 1.0
O A:HOH770 4.4 61.2 1.0
O5' A:ADP601 4.4 55.7 1.0
N A:GLY88 4.5 43.8 1.0
O2B A:ADP601 4.6 59.9 1.0
O A:HOH745 4.6 57.9 1.0
O A:SER151 4.7 85.2 1.0
CA A:SER151 4.8 64.3 1.0
CA A:ASP87 4.9 39.9 1.0
O1A A:ADP601 4.9 60.9 1.0

Magnesium binding site 2 out of 7 in 4ki8

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Magnesium binding site 2 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:29.0
occ:1.00
 O B:HOH757 2.0 44.0 1.0
O B:HOH753 2.1 43.7 1.0
OD2 B:ASP87 2.2 46.4 1.0
O2B B:ADP601 2.2 52.9 1.0
OD1 B:ASP87 2.2 74.1 1.0
O2A B:ADP601 2.5 30.3 1.0
CG B:ASP87 2.5 48.6 1.0
O B:HOH758 2.8 51.2 1.0
PB B:ADP601 3.4 45.9 1.0
O3B B:ADP601 3.5 45.1 1.0
O B:HOH711 3.6 57.9 1.0
PA B:ADP601 3.8 43.0 1.0
O B:HOH761 3.9 63.4 1.0
O3A B:ADP601 4.0 0.6 1.0
CB B:ASP87 4.1 32.3 1.0
C5' B:ADP601 4.2 46.0 1.0
O5' B:ADP601 4.5 46.3 1.0
O B:HOH766 4.6 47.2 0.8
O1B B:ADP601 4.6 47.7 1.0
N B:GLY88 4.6 28.5 1.0
O B:HOH717 4.7 49.1 1.0
O B:HOH799 4.9 38.5 0.6
O B:SER151 4.9 89.9 1.0
CA B:ASP87 4.9 27.7 1.0
CA B:SER151 4.9 57.8 1.0

Magnesium binding site 3 out of 7 in 4ki8

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Magnesium binding site 3 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:34.9
occ:1.00
 O C:HOH781 2.1 92.1 1.0
O C:HOH749 2.1 72.8 1.0
O C:HOH741 2.1 60.3 1.0
O2B C:ADP601 2.1 57.8 1.0
O C:HOH736 2.2 66.1 1.0
OD2 C:ASP87 2.2 52.5 1.0
OD1 C:ASP87 2.3 67.7 1.0
O1A C:ADP601 2.4 43.7 1.0
CG C:ASP87 2.6 58.0 1.0
PB C:ADP601 3.4 58.6 1.0
O C:HOH743 3.7 57.0 0.9
PA C:ADP601 3.7 48.9 1.0
O3B C:ADP601 3.7 57.8 1.0
O3A C:ADP601 4.0 66.1 1.0
CB C:ASP87 4.1 49.2 1.0
C5' C:ADP601 4.2 64.2 1.0
O5' C:ADP601 4.5 64.6 1.0
O C:HOH737 4.5 62.2 1.0
N C:GLY88 4.6 43.3 1.0
O C:HOH721 4.7 42.8 0.6
O1B C:ADP601 4.7 49.3 1.0
O C:HOH752 4.8 56.6 0.8
O C:SER151 4.9 77.5 1.0
OD1 C:ASN153 4.9 88.3 1.0
O C:HOH750 4.9 51.0 1.0
CA C:SER151 4.9 55.1 1.0
CA C:ASP87 5.0 51.4 1.0

Magnesium binding site 4 out of 7 in 4ki8

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Magnesium binding site 4 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:30.2
occ:1.00
 O D:HOH709 2.1 42.6 1.0
O D:HOH756 2.1 73.6 1.0
O D:HOH738 2.1 61.0 1.0
OD2 D:ASP87 2.1 60.6 1.0
OD1 D:ASP87 2.3 52.8 1.0
O2B D:ADP601 2.4 50.7 1.0
CG D:ASP87 2.5 53.4 1.0
O2A D:ADP601 2.6 36.1 1.0
PB D:ADP601 3.6 59.5 1.0
O3B D:ADP601 3.9 59.1 1.0
O D:HOH757 3.9 51.7 1.0
PA D:ADP601 3.9 54.7 1.0
CB D:ASP87 4.1 38.7 1.0
O3A D:ADP601 4.3 80.7 1.0
O D:ILE150 4.4 79.3 1.0
C5' D:ADP601 4.4 57.2 1.0
O D:HOH765 4.5 69.8 1.0
O D:HOH737 4.5 63.0 1.0
O D:HOH768 4.7 66.3 1.0
N D:GLY88 4.7 38.5 1.0
CA D:SER151 4.7 61.6 1.0
O D:HOH751 4.7 48.8 0.9
O D:SER151 4.7 83.0 1.0
O5' D:ADP601 4.8 42.2 1.0
O1B D:ADP601 4.9 52.6 1.0
C D:SER151 4.9 78.5 1.0
CB D:ASN153 4.9 0.6 1.0
CA D:ASP87 4.9 37.4 1.0

Magnesium binding site 5 out of 7 in 4ki8

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Magnesium binding site 5 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:38.1
occ:1.00
 OD1 E:ASP87 2.0 83.8 1.0
O E:HOH731 2.1 83.3 1.0
O E:HOH738 2.1 70.2 1.0
O E:HOH737 2.1 93.4 1.0
O1B E:ADP601 2.1 79.1 1.0
O2A E:ADP601 2.3 64.2 1.0
CG E:ASP87 2.6 74.1 1.0
OD2 E:ASP87 3.0 85.6 1.0
O E:HOH747 3.3 80.6 1.0
PB E:ADP601 3.5 67.2 1.0
PA E:ADP601 3.7 57.8 1.0
CB E:ASP87 3.7 59.2 1.0
O3A E:ADP601 4.0 0.6 1.0
O2B E:ADP601 4.0 72.6 1.0
C5' E:ADP601 4.3 70.5 1.0
O5' E:ADP601 4.5 68.8 1.0
CA E:ASP87 4.5 60.4 1.0
O E:SER151 4.5 81.5 1.0
O3B E:ADP601 4.6 57.3 1.0
N E:GLY88 4.7 53.1 1.0
CA E:SER151 4.8 72.6 1.0
O1A E:ADP601 4.9 60.0 1.0

Magnesium binding site 6 out of 7 in 4ki8

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Magnesium binding site 6 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:28.2
occ:1.00
 O F:HOH706 2.0 49.3 0.9
O F:HOH723 2.1 55.6 1.0
O2B F:ADP601 2.1 41.6 1.0
O F:HOH707 2.1 66.9 1.0
OD2 F:ASP87 2.2 58.2 1.0
OD1 F:ASP87 2.3 57.7 1.0
O2A F:ADP601 2.3 38.1 1.0
CG F:ASP87 2.6 50.9 1.0
PB F:ADP601 3.2 55.0 1.0
PA F:ADP601 3.5 51.5 1.0
O3B F:ADP601 3.5 64.9 1.0
O3A F:ADP601 3.7 74.4 1.0
OD1 F:ASN153 3.8 0.7 1.0
O5' F:ADP601 4.0 74.4 1.0
O F:HOH754 4.0 51.1 1.0
C5' F:ADP601 4.0 60.5 1.0
CB F:ASP87 4.1 49.4 1.0
O F:HOH744 4.3 55.6 1.0
O F:SER151 4.5 71.3 1.0
O F:HOH760 4.5 61.0 0.9
O1B F:ADP601 4.5 51.6 1.0
N F:GLY88 4.6 38.8 1.0
O F:HOH737 4.7 37.3 0.7
O F:ILE150 4.8 52.2 1.0
O F:HOH765 4.9 72.2 0.9
O1A F:ADP601 4.9 51.6 1.0
O F:HOH721 4.9 64.0 1.0
CA F:SER151 4.9 56.8 1.0
CG F:ASN153 4.9 0.6 1.0
CA F:ASP87 5.0 41.5 1.0

Magnesium binding site 7 out of 7 in 4ki8

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Magnesium binding site 7 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:25.8
occ:1.00
 O G:HOH733 2.1 54.2 1.0
O G:HOH729 2.1 46.6 1.0
O G:HOH706 2.1 41.3 1.0
OD2 G:ASP87 2.2 52.5 1.0
OD1 G:ASP87 2.2 47.0 1.0
O2B G:ADP601 2.3 45.0 1.0
O2A G:ADP601 2.4 42.2 1.0
CG G:ASP87 2.5 47.9 1.0
PB G:ADP601 3.5 50.6 1.0
O3B G:ADP601 3.7 56.6 1.0
PA G:ADP601 3.7 47.5 1.0
O G:HOH779 3.9 71.5 1.0
O G:HOH712 3.9 63.5 1.0
CB G:ASP87 4.1 32.4 1.0
O3A G:ADP601 4.1 94.7 1.0
C5' G:ADP601 4.2 59.0 1.0
O G:HOH773 4.3 79.7 1.0
O G:HOH710 4.4 44.4 0.9
O5' G:ADP601 4.5 60.0 1.0
O G:HOH743 4.5 79.2 1.0
N G:GLY88 4.6 43.5 1.0
O G:ILE150 4.6 69.3 1.0
O G:SER151 4.7 76.2 1.0
O1B G:ADP601 4.8 46.7 1.0
O G:HOH784 4.9 70.8 0.9
CA G:ASP87 4.9 35.1 1.0
CA G:SER151 4.9 67.8 1.0
O1A G:ADP601 5.0 64.1 1.0

Reference:

X.Fei, D.Yang, N.Laronde-Leblanc, G.H.Lorimer. Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State at 2.7 A Resolution. Proc.Natl.Acad.Sci.Usa V. 110 E2958 2013.
ISSN: ISSN 0027-8424
PubMed: 23861496
DOI: 10.1073/PNAS.1311996110
Page generated: Mon Dec 14 19:03:03 2020

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